Dissecting quantitative traits into Mendelian factors is a great challenge in genetics. Apple fruit storability is a complex trait controlled by multi-genes with unequal effects. We previously identified 62 quantitative trait loci (QTLs) associated with apple fruit storability and genomics-assisted prediction (GAP) models were trained using 56 QTL-based markers. Here, three candidate genes, MdNAC83, MdBPM2, and MdRGLG3, were screened from the regions of QTLs with large G’ value and large genetic effects. Both a 216-bp deletion and an SNP934 T/C at the promoter of MdNAC83 were associated with higher MdNAC83 expression but an SNP388 G/A at the coding region significantly reduced the activity to activate the expression of the target genes MdACO1, MdMANA3, and MdXTH28. MdBPM2 and MdRGLG3 participated in the ubiquitination of MdNAC83. SNP657 T/A of MdBPM2 and SNP167 C/G of MdRGLG3 caused a reduction in the activity to ubiquitinate MdNAC83. By the addition of functional markers to the GenoBaits SNP array, the prediction accuracy of the updated GAP models increased to 0.7723/0.6231 and 0.5639/0.5345 for flesh firmness/crispness at harvest and flesh firmness/crispness retainability, respectively. The variation network involving eight simple Mendelian variations in six genes helps to gain insight into the molecular quantitative genetics, to improve breeding strategy, and to provide targets for future genome editing.

Soybean is one of the most economically important crops worldwide and a valuable source of protein for human consumption and animal feed. The use of wild soybean accessions as a source of new alleles for improvement of soybean quality remains challenging owing to linkage drag. Here, using segregating populations derived from a set of wild soybean chromosome segment substitution lines, we fine-mapped quantitative trait loci (QTLs) (qPC-06-1) for seed protein content to a 48.8-Kb interval on chromosome 6. A gene encoding an S-adenosyl- L-methionine-dependent methyltransferase (GmMET) was determined to be the causal gene underlying the qPC-06-1 locus. Three single-nucleotide polymorphism/insertion-deletion markers (SNPs/InDels) in the coding region were found to modulate the methyltransferase activity of different GmMET alleles, thereby influencing seed protein content. Transgenic and multi-omics analyses provided preliminary evidence for the pathways through which GmMET influences seed protein content and exerts pleiotropic effects on seed oil content, oil composition, and related traits. Additional analyses showed that an elite GmMET allele was under selection during soybean domestication and improvement and is now widespread in modern cultivars, particularly in southern China. Our findings thus reveal that a methyltransferase gene affects the protein content of soybean seeds, providing a foundation for the continued development of high-protein soybean cultivars.

The original WGBS and RNA-seq data are available at the China National Center for Bioinformation (https://ngdc.cncb.ac.cn/gsa/) under accession numbers CRA024004 and CRA024005.

Seed weight is a pivotal yield-determining trait in crops, and yet, the genetic and molecular mechanisms underlying its regulation in polyploid species remain underexplored. In a previous study, we identified cqSW.A03-2, a QTL that regulates thousand seed weight (TSW) in rapeseed (Brassica napus). Here, we identify BnaA3.AHK2, encoding a histidine kinase, as the causal gene of cqSW.A03-2. BnaA3.AHK2 enhances TSW through maternal control of seed coat cell expansion without significantly compromising other yield-related traits. Protein sequence divergence between parental haplotypes caused functional differentiation, with only the ZY50 allele showing functional kinase activity and rescuing developmental defects in Arabidopsis cytokinin receptor mutants. Strikingly, BnaA3.AHK2 seems to be a cytokinin-independent operator, contrasting with the canonical cytokinin signaling pathway. Transcriptome and protein interaction analyses reveal a signaling module where BnaA3.AHK2 engages BnaAHP–BnaARR phosphorelay components to regulate downstream targets. Notably, the favorable cqSW.A03-2 haplotype has been historically selected in modern breeding, and its introgression into elite hybrids boosted TSW by 3.6%–9.1%, demonstrating its breeding value. Our findings unveil a non-canonical signaling pathway for seed size regulation, providing a strategic genetic target to break yield trade-offs in polyploid crops.

All raw data generated during the course of this study—provided as a table (Supplemental Data Set) containing the raw data for all result figures—are available to readers for download.

Wild perennial sister species Medicago archiducis-nicolai (rhizomatous/alpine) and M. ruthenica (non-rhizomatous/xeric) constitute vital genetic resources for forage improvement. To decode the genomic basis of their contrasting trait and habitat adaptation, we generated chromosome-scale genome assemblies, resequenced 128 individuals, profiled transcriptomes under cold/heat stress, and functionally validated causal alleles. We demonstrate that structural variations (SVs)—particularly gene duplications—are primary drivers of rhizome formation and alpine/xeric adaptation. Further, pervasive presence–absence SVs (PAVs) in noncoding regulatory regions underpin divergent allele-specific expression governing rhizome development and stress responses. Crucially, these regulatory PAVs induce contrasting expression patterns during trait development and stress adaptation. Our findings reveal a dual mechanism whereby coding and regulatory SVs convergently orchestrate phenotypic innovation and ecological specialization in sister species, offering valuable genomic resources for legume evolution studies and alfalfa breeding.

All raw sequencing data and final chromosome-level genome assemblies for M. archiducis-nicolai and M. ruthenica generated in this study have been deposited in the National Genomics Data Center (NGDC; https://ngdc.cncb.ac.cn/) under BioProject accession number PRJCA040972. In addition, genome assemblies, gene annotations, and TE annotation files are accessible on Figshare: https://figshare.com/s/93c9122fae7352edeaca. All data sets will be released publicly upon acceptance and publication of this manuscript.

The highly transformable maize inbred line LH244 represents an attractive model for gene discovery and genome engineering. However, the lack of a high-quality genome assembly has limited its utility in functional genomics research. Here, we present a 2.29 Gb near-complete assembly of the LH244 maize genome, with an overall base accuracy of 99.998%. Except for five gaps associated with super-long thymine–adenine–guanine (TAG) repeat arrays, all the genome sequences were assembled from telomere to telomere (T2T). Comparative analysis revealed high genetic similarity between LH244 and B73, including 80.06% genome-wide synteny and 90.92% of genes nearly identical. The LH244 genome was also compared with the complete Mo17 genome and revealed extensive intraspecific genomic variations. A total of 14 megabase-scale structural variations (SVs) were identified, including a 3.15 Mb insertion, harboring 95 genes, within the 45S rDNA array of LH244 but not in the Mo17 genome. In addition, there were five knob arrays, with an average size of 21.76 Mb and the longest of 38.70 Mb, only existing in the LH244 genome. Despite the substantial variation in knob abundance, knob-6S and knob-8L were highly conserved between LH244 and Mo17, showing strong synteny and sequence identity, as well as consistent insertion patterns of genes and transposable elements (TEs). Overall, our study provides a near-complete reference genome of an important transformable maize germplasm, which will serve as a much-needed resource for functional genomics and genome editing of maize.

The raw sequencing reads for LH244 were deposited in the National Genomics Data Center (NGDC) database under project accession number PRJCA033451. The GenBank accession number of the genome sequences is JBMAMC000000000. The genome assembly and annotation files can also be found in Zenodo (https://doi.org/10.5281/zenodo.17218050) and MaizeGDB (Woodhouse et al., 2021).

Parent-of-origin effects are usually caused by selective expression of maternal or paternal alleles. Although genome-wide studies suggest that imprinted gene expression occurs primarily in the endosperm in plants, detailed studies of allele-specific gene expression and its associations with parent-of-origin phenotypes are scarce. NAC20 and NAC26 (NAC20/26 hereafter), a pair of tightly linked NAC-family transcription factors, redundantly regulate grain filling and albumin accumulation in rice endosperm. Here, we show that NAC20/26 exhibited allele-specific maternal expression, and the floury endosperm phenotype of the nac20/26 double mutant was inherited with a maternal effect. Further studies showed that the imprinted NAC20/26 expression and floury endosperm phenotype with a maternal effect are associated with insertions of two TEs in NAC20/26 of two Japonica rice varieties, but not in two Indica ones examined. The maternal NAC20/26 expression was associated with elevated DNA methylation in their paternal DMRs, and deletions of those TEs by gene editing led to decreased methylation in these DMRs, and biallelic NAC20/26 expression. Geographical analyses showed that Japonica varieties with high-latitude origins examined carried these TEs. These results establish that TE-mediated DNA methylation lead to grain filling with a maternal effect in high-latitude Japonica rice varieties, which may associate with northward expansion of rice during domestication.

Transposable elements (TEs) are abundant and evolutionarily important components of plant genomes, yet the population-scale landscape of TE insertion polymorphisms (TIPs) and their regulatory roles in gene expression and trait variation remain insufficiently understood. In this study, genomic resequencing, RNA-seq, and agronomic trait data from a panel of 381 Brassica napus accessions were integrated to characterize population-level TIP dynamics and assess their impacts on gene regulation, ecotype differentiation, and phenotypic innovation. Using a developed computational pipeline, a robust pan-TE library was constructed based on 28 diverse reference genomes, and 77,603 TIP loci were profiled by mapping resequencing data from 381 accessions. Most TE insertions were found to be dispensable and weakly linked to neighboring SNPs, suggesting that they represent recent or ecotype-specific variants that serve as independent sources of regulatory and adaptive diversity in B. napus. The regulatory roles of TEs were examined through two complementary strategies (direct-effect analyses and TIP-based eQTL mapping), which together revealed that TEs modulate gene expression via both cis- and long-range trans-effects. Notably, TE-mediated trans-regulation, rarely investigated in previous studies, was found to be widespread, with trans-effects predominating and displaying strong tissue specificity, emphasizing the extensive regulatory influence of TEs on the plant transcriptome. Furthermore, selective sweep analyses identified ecotype-specific TIPs associated with adaptive divergence, particularly those contributing to semi-winter type diversification. TIP-based genome-wide association studies (GWAS) revealed 1,102 candidate insertions significantly associated with key agronomic traits, including flowering time, fatty acid composition, and glucosinolate content, some of which were not detected by SNP-based analyses. This study provides the population-scale atlas of TE insertions in B. napus, uncovers their extensive regulatory roles, and demonstrates their contribution to adaptation and trait variation, offering valuable resources for breeding and functional genomics.

The resequencing and RNA-seq data of the B. napus accessions were obtained from our previous studies (Cui et al., 2023; Zhang et al., 2024) and have been deposited under BioProject accession numbers PRJNA1156901, PRJNA1149544, and PRJNA1153365. The 28 reference genome assemblies were downloaded from the BnaOmics database (https://bnaomics.ocri-genomics.net/).

O-Methyltransferases (OMTs) play crucial roles in plant defense, environmental adaptation, and quality formation by catalyzing the biosynthesis of diverse methylated metabolites. Although OMT (COMT and CCoAOMT) genes have been functionally characterized in various plant species, the evolutionary trajectory of the entire OMT gene family and the functional divergence of the CCoAOMT subfamily remain to be systematically elucidated. In this study, we performed pan-genome analysis of the OMT gene family in 61 tomato (Solanum spp.) accessions and conducted phylogenetic analysis across 20 plant species (from algae to angiosperms), identifying 2,882 OMT genes. Phylogenetic reconstruction revealed that all extant plant CCoAOMT genes evolved from a single ancestral lineage (Clade I) originating before the divergence of red and green algae. In tomato, 2,199 OMT genes were classified into 42 orthogroups: nine core, five soft-core, 22 dispensable, and six private orthogroups, with 52.4% classified as dispensable genes. OMT genes in the Solanum genus have predominantly undergone purifying selection. Among all COMT orthogroups, a single tandem duplicate cluster stands out as exclusively conserved. Members of this cluster have evolved a distinct catalytic role, as evidenced by the finding that SlCOMT2c exclusively catalyzes the formation of kaempferide via the 4′-O-methylation of kaempferol. Ion mobility spectrometry showed that SlAOMT, a member of the CCoAOMT-like subfamily, catalyzes the methylation of luteolin to produce two isomeric products identified as diosmetin and chrysoeriol while losing the canonical catalytic function of the CCoAOMT subfamily. In addition, we identified a potential gene regulatory network associated with methylated flavonoid biosynthesis. This study establishes an integrative framework for elucidating OMT evolution and provides analytical tools for identifying genes involved in isomeric methylated flavonoid biosynthesis, paving the way for studying adaptive evolution and specialized metabolic pathways in plants.

Rhododendron, a globally important group of alpine flowering plants, provides an exceptional system for investigating ecological adaptation and stress resistance owing to its high-altitude specialization. Using 18 Rhododendron species, a graph-based pangenome was constructed that captures 72,089 nonredundant structural variants. The findings support the integration of subgenus Azaleastrum into subgenus Tsutsusi, with their comparatively smaller genome sizes likely resulting from the contraction of multiple gene families during lineage differentiation. Gene families specific to high-altitude Rhododendron species were significantly enriched in pathways associated with stress resistance. High-altitude-specific long terminal repeat retrotransposons operate through similar regulatory mechanisms, predominantly influencing stress-responsive genes and promoting adaptive evolution. Through an integrated analysis of population genetics (389 re-sequenced samples with a mean coverage of 50.2×), transcriptomics, and real-time quantitative polymerase chain reaction, conserved genes and gene families linked to alpine adaptation in Rhododendron were identified. These include genes implicated in cold-stress responses and ultraviolet (UV) tolerance, such as CML18, CPK1, DREB1E, LPAT2, GPC1, and UVR8. Structural variant profiles within several of these genes offer insights into divergent adaptive mechanisms between high- and low-altitude Rhododendron species. The rapid induction of cold-sensing genes and CBF/DREB1-centered cold-stress signaling pathways indicates an evolutionary adaptation of alpine Rhododendron species to low-temperature habitats. Furthermore, transgenic analyses indicate that cold-resistance genes, such as GPC1 derived from high-altitude Rhododendron, markedly improve cold tolerance in Arabidopsis thaliana and tobacco. Collectively, this study advances insights into high-altitude adaptation in ornamental plants and underscores the value of super-pangenome resources for evolutionary and functional genomics research.

All data supporting the findings of this study are available in the main text and supplementary information. The whole-genome raw sequencing data, transcriptome raw sequencing data, and genome assemblies generated in this study have been deposited at the Genome Sequence Archive and the Genome Warehouse of the National Genomics Data Center (NGDC), China National Center for Bioinformation, Chinese Academy of Sciences, under BioProject ID PRJCA021036. The corresponding accession numbers are CRA013427, CRA013492, CRA041670, GWHEQCY00000000, GWHEQCZ00000000, GWHEQDA00000000, GWHEQDB00000000, GWHEQDC00000000, GWHEQDD00000000, and GWHEQDE00000000. These data sets are publicly accessible on the NGDC platform at https://ngdc.cncb.ac.cn.

The publication of several high-quality genomes has contributed greatly to clarifying the evolution of citrus. However, due to their complex genetic backgrounds, the origins and evolution of many citrus species remain unclear. We assembled de novo the 294-Mbp chromosome-level genome of a more than 200-year-old primitive papeda (DYC002). Comparison between the two sets of homologous chromosomes of the haplotype-resolved genome revealed 1.2% intragenomic variations, including 1.75 million SNPs, 149,471 insertions and 154,215 deletions. Using this genome as a reference, we resequenced and performed population and phylogenetic analyses of 378 representative citrus accessions. Our study confirmed that the primary origin center of core Citrus species is in South China, particularly in the Himalaya–Hengduan Mountains. Papeda species are an ancient Citrus type compared with C. ichangensis. We found that the evolution of the Citrus genus followed two radiations through two routes (to East China and Southeast Asia) along river systems. Evidence for the origin and evolution of some individual citrus species was provided. Papeda probably played an important role in the origins of Australian finger lime, citrons, Honghe papeda and pummelos; Ichang papeda originated from Yuanjiang city of Yunnan Province, China, and C. mangshanensis has a close relationship with kumquat and Ichang papeda. Moreover, the Hunan and Guangdong Provinces of China are predicted to be the origin center of mandarin, sweet orange and sour orange. Additionally, our study revealed that fruit bitterness was significantly selected against during citrus domestication. Taken together, this study provides new insight into the origin and evolution of citrus species and may serve as a valuable genomic resource for citrus breeding and improvement.

Sex chromosomes have evolved independently in numerous lineages across the Tree of Life, in both diploid-dominant species, including many animals and plants, and the less studied haploid-dominant plants and algae. Strict genetic sex determination ensures that individuals reproduce by outcrossing. However, species with separate sexes (termed dioecy in diploid plants, and dioicy in haploid plants) may sometimes evolve different sex systems, and become monoicous, with the ability to self-fertilize. Here, we studied dioicy-monoicy transitions in the ancient liverwort haploid-dominant plant lineage, using three telomere-to-telomere gapless chromosome-scale reference genome assemblies from the Ricciaceae group of Marchantiales. Ancestral liverworts are believed to have been dioicous, with U and V chromosomes (chromosome 9) determining femaleness and maleness, respectively. We confirm the finding that monoicy in Ricciocarpos natans evolved from a dioicous ancestor, and most ancestrally U chromosomal genes have been retained on autosomes in this species. We also describe evidence suggesting the possible re-evolution of dioicy in the genus Riccia, with probable de novo establishment of a sex chromosome from an autosome (chromosome 5), and further translocations of genes from the new sex chromosome to autosomes. Our results also indicated that micro-chromosomes are consistent genomic features, and may have evolved independently from sex chromosomes in Ricciocarpos and Riccia lineages.

Genome assemblies of three liverwort species and their annotations are available at Figshare (https://doi.org/10.6084/m9.figshare.23805990). All raw sequencing data used for analysis have been deposited in the China National GeneBank DataBase (CNGBdb) under project CNP0004629. Scripts and pipelines applied for analysis in this work can be found freely at GitHub (https://github.com/abysw/Sexualarticle2023).

The domains rearranged methyltransferases (DRMs) play a critical role in the RNA-directed DNA methylation (RdDM) pathway in plants. However, the effects of inactivating the RdDM pathway on gene expression, transposable element (TE) activity, and phenotype in soybean remain unexplored. Here, we employed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 gene editing to generate a quintuple mutant line in soybean (Gmdrm2a^-/-2b^-/-2c^-/-3a^-/-3b^-/-, designated Gmdrm). Gmdrm exhibited severe developmental abnormalities, including dwarfism and delayed growth, albeit remaining viable and fertile; however, the fully homozygous mutant could be maintained for a limited number of generations (T0-T3). Whole genome bisulfite sequencing revealed a significant reduction in DNA methylation across all cytosine sequence contexts, with an average loss of 10%. The loss of ^mC was biased toward euchromatic regions, which is in contrast to the chromomethylase mutant. Transcriptome profiling identified 1,685 up-regulated genes, including photosynthesis-related genes, accompanied with altered chloroplast ultrastructure. Additionally, a cluster of resistance (R) genes on chromosome 16 was significantly up-regulated, coinciding with their reduced non-CG methylation. We also observed 3,164 differentially expressed TEs (DETs), of which, 2,655 were up-regulated and hypomethylated along their entire length. A substantial reduction in the abundance of 24-nt small interfering RNAs (siRNAs) in the Gmdrm mutant was detected by small RNA sequencing. Of note, the DRM-targeted TEs typically display higher levels of 24-nt siRNA abundance, shorter lengths, and are more AT-rich compared to chromomethylase-targeted TEs, highlighting 24-nt siRNAs as key determinants of DRM-dependent TE regulation. Together, this study documents a critical role of DRM-mediated DNA methylation in regulating gene expression, TE silencing, and normal development in soybean.

The raw WGBS, RNA-seq and sRNA-seq read sequences produced in this study have been submitted to the National Genomics Data Center (https://ngdc.cncb.ac.cn/) and can be accessed under the accession number PRJCA021234.

Diverse heterotic groups have been developed in China over several decades, but their genomic divergences have not been systematically studied after improvement. In this study, we performed Maize6H-60K array of 5,822 maize accessions and whole-genome re-sequencing of 150 inbred lines collected in China. Using multiple population structure analysis methods, we established a genetic boundary used to categorize heterotic groups and germplasm resources. We identified three chloroplast–cytoplasmic types that evolved during adaptation to diverse climatic environments in maize through phylogenetic and haplotype analyses. Comparative analyses revealed obvious genetic differences between heterotic groups and germplasm resources at both the chloroplast and nuclear genome levels, especially in the unique heterotic groups HG1 and HG2, which exhibited distinct regionality and genetic uniqueness. The divergent differentiation of heterotic groups from germplasm resources was driven by differential selection in specific genomic regions. Genome-wide selective sweep analysis identified core selected regions and candidate selected genes associated with traits between heterotic groups, highlighting that stress response- and plant defense-related genes were selected for environmental adaptation across a broad latitudinal range in China. Meanwhile, a genome-wide association study analysis provided evidence that core selected genes served as an important candidate gene pool with a potential role in genetic improvement. Gene exchanges among heterotic groups, which avoided the predominant heterotic patterns as much as possible, occurred to achieve population improvement during modern maize breeding. This study provides insights into the population differentiation and genetic characteristics of heterotic groups, which will facilitate the utilization of germplasm resources, the creation of novel maize germplasm, and the optimization of heterotic patterns during future maize breeding in China.

The re-sequencing data are available at NCBI SRA (PRJNA1142681). Other relevant data are presented within the article and supporting information.

Avena barbata, a wild oat species within the genus Avena, is a widely used model for studying plant ecological adaptation due to its strong environmental adaptability and disease resistance, serving as a valuable genetic resource for oat improvement. Here, we phased the high-quality chromosome-level genome assembly of A. barbata (6.88 Gb, contig N50 = 53.74 Mb) into A (3.57 Gb with 47,687 genes) and B (3.31 Gb with 46,029 genes) subgenomes. Comparative genomics and phylogenomic analyses clarified the evolutionary relationships and trajectories of A, B, C and D subgenomes in Avena. We inferred that the A subgenome donor of A. barbata was Avena hirtula, while the B subgenome donor was probably an extinct diploid species closely related to Avena wiestii. Genome evolution analysis revealed the dynamic transposable element (TE) content and subgenome divergence, as well as extensive structure variations across A, B, C, and D subgenomes in Avena. Population genetic analysis of 211 A. barbata accessions from distinct ecotypes identified several candidate genes related to environmental adaptability and drought resistance. Our study provides a comprehensive genetic resource for exploring the genetic basis underlying the strong environmental adaptability of A. barbata and the molecular identification of important agronomic traits for oat breeding.

For convenient and effective use of this genome resource, the raw sequencing data and genome assembly were deposited in the Chinese National Genomics Data Center database (https://bigd.big.ac.cn/) under the BioProject accession numbers PRJCA027164. Source data are provided in this article and the associated supplementary materials.

Budding speciation is a process wherein a new species arises from a small, isolated population within or at the margin of an ancestral species. Well-documented cases of budding speciation are rare, and the roles of various evolutionary factors in this process remain controversial. Based on whole-genome resequencing data from 272 individuals across 27 populations, we reconstructed the evolutionary history of Rhodiola sect. Trifida and explored the relative contributions of natural selection, genetic drift, and chromosomal rearrangements as drivers of lineage divergence. We found that all samples of R. chrysanthemifolia (including R. alterna and R. sinuata) were clustered into three clades. Rhodiola liciae was sister to all other samples in the section, likely due to post-divergence gene flow and the minimal population structure of the progenitor species, while it shared the same ancestry with R. ch-I in population structure analyses. The two populations of R. sinuata were not monophyletic, instead clustering with geographically proximate populations of R. ch-III. Demographic analyses revealed that R. liciae underwent a contraction in population size following its divergence from R. ch-I approximately 0.34 million years ago (Mya), and has remained stable since around 0.1 Mya. Genomic islands and genotype-environment association analyses suggested that genetic drift and the assorting of ancestral polymorphism may have played a more significant role in the speciation of R. liciae than nature selection or chromosomal rearrangements. We propose that R. liciae diverged from R. chrysanthemifolia through budding speciation, although post-divergence gene flow has obscured its phylogenetic signal. Additionally, we identified two potential parallel budding speciation events in R. sinuata at an earlier stage than R. liciae. Our study highlights budding speciation as a prevalent yet poorly characterized mode of plant speciation, with assorting of ancestral polymorphism as a key stochastic mechanism in the process.

All WGR raw data used in the present study are available from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) under BioProject: PRJNA11134919. The chromosomal level genome assembly and annotation of R. chrysanthemifolia and all raw sequencing data have been deposited under NCBI BioProject PRJNA980948.

The SDS-sedimentation volume (SSV) is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality. However, the molecular mechanisms regulating SSV remain poorly understood. In this study, we performed an analysis of quantitative trait loci (QTLs) for SSV using a recombinant inbred line (RIL) population derived from a cross between TAA10 and XX329, and identified four environmentally stable QTLs located on chromosomes 1D, 2D, 4D, and 6D. Among them, the effects of Qssv.cau-1D and Qssv.cau-6D were likely to be explained by genome variations at the Glu-D1 and Gli-D2 loci. We fine mapped Qssv.cau-2D to the candidate causal gene TaSED, encoding a nucleolar protein. Gene-edited TaSED knockout mutants (tased) had a lower SSV, while TaSED overexpression lines showed a higher SSV. We demonstrated that TaSED interacted with the transcription factor TaSPA to enhance its transcriptional activation activity of glutenin and gliadin, whose expression was downregulated in tased and upregulated in TaSED-OE plants, with corresponding differences in glutenin and gliadin content compared with the wild-type. A molecular marker sedTX was further developed based on a nonsynonymous mutation of the parents in TaSED that could be used to identify haplotypes with high SSV effectively. Our findings elucidate a molecular mechanism governing SSV and reveal valuable variants with promising applications for improving wheat quality.

The RNA-seq data in this study have been deposited into the National Center for Biotechnology Information (NCBI) Sequence Read Archives (SRA) under accession code PRJNA1203177.

Pitaya is an important perennial herbaceous fruit tree. The color of fruit determines pitaya nutritive (and attractive) value, which is considered as an important objective in breeding improvement. In this study, we reported the first telomere-to-telomere (T2T) gap-free genome of “Shuangse No. 1” pitaya (Hylocereus polyrhizus; red peel). Two high-quality genomes for “Dahong” (H. polyrhizus; red peel) and “Honghuaqinglong” (H. stenopterus; stay-green) were further assembled, aiming to explore the genetic diversity of pitaya genomes. In further analysis, we noticed a high proportion of viral contamination in pitaya tissues, which hindered the efficient utilization of transcriptomic data. To address this issue, we analyzed 111 pitaya transcriptome data from different geographic regions to characterize and separate viral components. Then we developed an efficient, novel, and universal transcript purification system for pitaya transcriptomes by applying it to 27 samples from different tissues and species, thereby enhancing the utility for transcriptomic and broader biological research. Combining the purified transcriptomic data with comparative genomic analyses, we identified HuERF72, a transcription factor (TF) that potentially regulates chlorophyll degradation in pitaya. Interaction assays and plant transformation elucidated that HuERF72 acts as a repressive TF by directly binding to the promoter of HuSGR1, a key structural gene in the chlorophyll degradation pathway. This study provides high-quality genomic resources and novel methodologies for molecular investigations in pitaya. Additionally, the proposed regulatory network advances our understanding of the transcriptional regulatory mechanisms underlying chlorophyll degradation, offering valuable insights into the genetic improvement of pitaya.

The genome assembly is accessible with Figshare database (https://doi.org/10.6084/m9.figshare.27906300) and Pitaya Genome and Multiomics Database (PGMD, http://pitayagenomic.com/). Additional research materials will be available on request.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan-mitogenome, pan-plastome, and haplotype-resolved nuclear genomes, all assembled from long-read sequences across 33 wild and domesticated grapevine accessions. Structural variation shaped the mitogenomic variation in gene contents, leading to duplications of three specific genes during grapevine domestication (one cox and two rpl genes). Extensive genomic signals of cytonuclear interactions were detected, including a total of 212–431 nuclear–mitochondrial segments (NUMTs) and 95–205 nuclear–plastid segments (NUPTs). These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes, whereas NUPTs dominated in wild grapes, indicating the evolutionary trajectories of cytonuclear interactions during grape domestication. Through Genome-Wide Association Study (GWAS), we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions. Among these, the PFD1 gene acts as a signaling regulator, modulating specific signaling pathways regulated by the mitochondria. Interestingly, there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions, suggesting NUMT-mediated interactions between the nuclear and mitochondrial genomes. Overall, our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication, offering new insight into the impact of cytonuclear interactions on plant evolution, genetics, and breeding.

The PacBio data used for mitogenome and plastid genome assembly, along with the raw WGS data for grape accessions, were downloaded from NCBI. BioProject IDs are provided in Tables S1, S6, respectively. Mitochondrial and plastid genome assemblies and annotations of genome and variation maps were uploaded to Zenodo (https://zenodo.org/record/14489445). Custom scripts and workflows are available in the GitHub repository (https://github.com/zhouyflab/Nuclear_Cytoplasmic_Interactions/).

Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.

All raw sequencing reads have been deposited in the National Center for Biotechnology Information (NCBI) database with the BioProject number PRJNA1178355.

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.

The sequencing data sets of peanut roots and root nodules for this project have been submitted to the National Genomics Data Center, under accession number CRA019413. Sequence information about AhNIN, AhMsrA, AhNSP2, AhNFYA1, AhNFRe, AhNOOT1, AhSYMREM1, AhCNGC15b, AhSUS1, AhNRT1.1, Ahnodulin MtN21, AhERN1, AhMATE1, AhSulfite exporter, Ahsyntaxin and Ahankyrin mentioned in this paper can be found in the peanut database (https://www.peanutbase.org/tools/search/gene.html). The accession numbers are as follows: AhNIN (I65W25), AhMsrA (4A36F8), AhNSP2 (JU87H7), AhSUS1 (4VZ14Z), AhNFYA1 (EWBI0W), AhNFRe (W1BJPM), AhNOOT1(A4KSPL), AhSYMREM1 (XJXR2L), AhNRT1.1 (LZ85EL), Ahnodulin MtN21 (L4R73E), AhERN1 (J0DG7J), AhMATE1 (HSA1AU), AhSulfite exporter (FYY1I0), Ahankyrin (4YMK55), Ahsyntaxin (IINC9K) and AhCNGC15b (19E8GC).

Both biotic and abiotic factors are expected to drive species diversification, yet demonstrating their synergistic effects within a single framework is challenging and has rarely been studied. The recent and rapid radiation of the genus Aspidistra (cast-iron plant) provides an ideal system for examining these processes. Here, we generated restriction site-associated DNA sequencing data for 123 Aspidistra taxa and reconstructed well-resolved phylogenies using both concatenation- and coalescent-based approaches. Using a comprehensive suite of diversification models, we quantified the contributions of multiple biotic and abiotic factors and applied phylogenetic path analysis to detect their synergistic effects. Our phylogenetic analyses recovered two main clades that differ in stem habits. We found that the diversification of Aspidistra has been driven by both abiotic factors (paleotemperature and the East Asian monsoon) and biotic factors (interspecific competition and pollination mutualism). Notably, these drivers operated both independently and synergistically to facilitate the rapid radiation of Aspidistra. Beyond providing a robust phylogeny useful for classifying Aspidistra, we present a statistical framework for better understanding the macroevolutionary processes underlying rapid plant radiations. Our findings underscore the critical importance of integrating multiple biotic and abiotic drivers into a unified analytical framework to comprehensively understand diversification history.

The raw sequence data generated in this study have been deposited at the National Center for Biotechnology Information under BioProject no. PRJNA1166698. The resulting phylogenetic trees and custom scripts for diversification analyses are available at GitHub (https://github.com/YangLH2025/Aspidistra_phylogeny_and_diversification).

Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome-level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine-labelled 1 (EM1) and EM6 in N. fruticans underly its crypto-vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

The genome assembly sequences have been deposited in the Genome Warehouse (GWH, https://bigd.big.ac.cn/gwh) in the National Genomics Data Center (NGDC) under accession number GWHBCKC00000000.1 with BioProject ID PRJCA022416 and BioSample ID SAMC3279992.

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole- genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

All data used in this study are publicly available as described in Materials and Methods. All PacBio sequence data have been deposited in the NCBI Sequence Read Archive under project number PRJNA953920 (genome) and PRJNA1082915 (WGS). Genome assembly is also available from the National Genomics Data Center (NGDC) under project number PRJCA024068. The genome assembly and annotation is also available on the website (https://zenodo.org) under number 10842451.

The ancient crop broomcorn millet (Panicum miliaceum L.) is an indispensable orphan crop in semi-arid regions due to its short life cycle and excellent abiotic stress tolerance. These advantages make it an important alternative crop to increase food security and achieve the goal of zero hunger, particularly in light of the uncertainty of global climate change. However, functional genomic and biotechnological research in broomcorn millet has been hampered due to a lack of genetic tools such as transformation and genome-editing techniques. Here, we successfully performed genome editing of broomcorn millet. We identified an elite variety, Hongmi, that produces embryogenic callus and has high shoot regeneration ability in in vitro culture. We established an Agrobacterium tumefaciens-mediated genetic transformation protocol and a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated genome-editing system for Hongmi. Using these techniques, we produced herbicide-resistant transgenic plants and edited phytoene desaturase (PmPDS), which is involved in chlorophyll biosynthesis. To facilitate the rapid adoption of Hongmi as a model line for broomcorn millet research, we assembled a near-complete genome sequence of Hongmi and comprehensively annotated its genome. Together, our results open the door to improving broomcorn millet using biotechnology.

The whole genome sequence (WGS) reads (SRR27197004), PacBio HiFi reads (SRR17406970), ONT ultra-long reads (SRR21203430 and SRR21203431), Hi-C sequences (SRR17406724), and RNA-seq data (Callus: SRR17406736, SRR17406737, and SRR17406725; Seedling: SRR17406729, SRR17406730, SRR17406731, SRR17406732, and SRR17406733; Young ear: SRR17406726, SRR17406727, and SRR17406728; Mature leaf: SRR17406734, SRR17406735, and SRR17406718; Panicle: SRR17406719, SRR17406720, and SRR17406721) of Hongmi (BioProject accession no. PRJNA792682) have been deposited in the National Center for Biotechnology Information SRA. The genome assembly has been deposited in the National Center for Biotechnology Information Genome (JBBDGV000000000). The genome assembly, gene annotation, and transposable element annotation files are also available at Zenodo (https://doi.org/10.5281/zenodo.10369102). All study data are included in the main article and Supplementary Materials. All broomcorn millet accessions are available at the National Crop Genebank of China. All codes or tools used in this study are described in the methods and available from the corresponding authors. Please contact chenjinfeng@ioz.ac.cn for code access.

Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.

Raw sequencing reads of all tea plant accessions used in this study can be freely accessed from the National Center for Biotechnology Information BioProject database under accession numbers PRJNA646044, PRJNA665594, and PRJNA595851, and the National Genomics Data Center under accession number PRJCA002071. Most remaining data are presented in the tables, figures or supplemental tables/figures of the current report. The pipelines and code used in the current report, including the parameters of tools/software and in-house scripts, are presented in Table S13 and the publicly available GitHub repository (https://github.com/tw7649116/Tea_dispensable_genome).

Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T-like1 (FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1^B, derived from the Oryza indica variety, BF3-104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor (Arf)-GTPase-activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1^B facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.

Dissecting the genetic control of apple fruit harvest date (AFHD) into multiple Mendelian factors poses a significant challenge in modern genetics. Here, a quantitative trait locus (QTL) for AFHD was fine-mapped to the NAC transcription factor (TF) MdNAC18 within the interval defined by the overlap of QTLs Z03.5/Z03.6 and F03.2/F03.3. One direct target of MdNAC18 is the ethylene biosynthesis gene MdACO1. The single nucleotide polymorphisms (SNPs) SNP517 and SNP958 in the MdNAC18 coding sequence modulated activation of MdACO1 by MdNAC18. SNP1229 in the MdACO1 promoter destroyed the MdNAC18 binding site and thus abolished MdNAC18 binding. SNP517 and SNP958 also affected MdNAC18 activation of the TF gene MdARF5; MdARF5 activates the ethylene biosynthesis gene MdACS1. SNP517 and SNP958 in MdNAC18, SNP1229 and SNP769 (linked to InDel62) in MdACO1, and InDel162 in MdACS1 constituted a genetic variation network. The genetic effect of this network on AFHD was estimated as 60.3 d, accounting for 52.6% of the phenotype variation of the training population. The joint effects of these polymorphisms increased the accuracy of a genomics-assisted prediction (GAP) model for AFHD (r = 0.7125). Together, our results suggest that genetic variation in MdNAC18 affects AFHD by modulating ethylene biosynthesis and provide an optimized GAP model for apple breeding.

Transcriptome raw sequencing data are available at the NCBI-SRA database (https://www.ncbi.nlm.nih.gov/sra) under accession number PRJNA1045838.

Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C₃ photosynthesis underwater and C₄ photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high-quality genome for E. vivipara, representing the first chromosome-level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one-to-one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole-genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross-section studies showed its terrestrial culms developed C₄ Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co-expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C₄ pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide - malic enzyme and phosphoenolpyruvate carboxykinase type C₄ photosynthesis in E. vivipara, and hypothesize that the evolution of C₄ photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C₃ and C₄ photosynthesis, offering promising avenues for crop improvement and breeding.

The sequencing data and genome assembly presented in this study are accessible in the Genome Warehouse (GWH) at the National Genomics Data Center (NGDC) under BioProject accession number PRJCA021868. Comprehensive genome sequencing datasets, including PacBio long-reads, Hi–C data, and DNB short reads for both DNA and RNA sequencing, have been deposited in the Genome Sequence Archive (GSA) of NGDC under accession number CRA013818. The assembled genome is available in the GWH of NGDC with accession number GWHEQUP00000000. Annotations regarding repeat sequences, gene structures, and functional predictions are also hosted on the Figshare database (https://doi.org/10.6084/m9.figshare.24902079.v2).

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

The assembly and annotation of the haplotype genome have been submitted to Genome Database for Rosaceae website (https://www.rosaceae.org/Analysis/17650638). The resequencing data for the hybrid progeny population of P. davidiana in the present study have been deposited into the NCBI database with BioProject under accessions PRJNA338218 and PRJNA1120329, respectively. Further, the RNA-seq data of leaves with aphid infestation and different tissues of P. davidiana have been deposited into the NCBI database with BioProject under accessions PRJNA692810 (Wang et al., 2022) and PRJNA753201 (Cao et al., 2022).

Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

Supplementary figures and data cited in this paper (assembled genes, gene alignments, gene trees, species tree, orthology genes) are available from the DRYAD Digital Repository (https://doi.org/10.5061/dryad.4tmpg4ff7). The major custom scripts used to reconstruct the phylogenies have been deposited in GitHub (https://github.com/hhy18/Angiosperm-genome-phylogenies).

Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin- degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self- incompatibility in buckwheat.

The raw sequencing data were deposited in the Chinese National Genomics Data Center database (https://bigd.big.ac.cn/) under the BioProject accession numbers PRJCA009237 (F. esculentum) and PRJCA000402 (F. tataricum), with BioSample accession numbers SAMC754381–SAMC754401. The transcriptome data of Al-treated buckwheat root tips has been deposited in the Chinese National Genomics Data Center database under the accession number CRA009298. The final F. esculentum and F. tataricum genome assemblies were also submitted to the Chinese National Genomics Data Center under accession numbers GWHBJBK00000000 and GWHBJBL00000000, respectively. Source data are provided in this article and the associated supplementary materials.

Orchidaceae (with >28,000 orchid species) are one of the two largest plant families, with economically and ecologically important species, and occupy global and diverse niches with primary distribution in rainforests. Among orchids, 70% grow on other plants as epiphytes; epiphytes contribute up to ~50% of the plant diversity in rainforests and provide food and shelter for diverse animals and microbes, thereby contributing to the health of these ecosystems. Orchids account for over two-thirds of vascular epiphytes and provide an excellent model for studying evolution of epiphytism. Extensive phylogenetic studies of Orchidaceae and subgroups have ;been crucial for understanding relationships among many orchid lineages, although some uncertainties remain. For example, in the largest subfamily Epidendroideae with nearly all epiphytic orchids, relationships among some tribes and many subtribes are still controversial, hampering evolutionary analyses of epiphytism. Here we obtained 1,450 low-copy nuclear genes from 610 orchid species, including 431 with newly generated transcriptomes, and used them for the reconstruction of robust Orchidaceae phylogenetic trees with highly supported placements of tribes and subtribes. We also provide generally well-supported phylogenetic placements of 131 genera and 437 species that were not sampled by previous plastid and nuclear phylogenomic studies. Molecular clock analyses estimated the Orchidaceae origin at ~132 million years ago (Ma) and divergences of most subtribes from 52 to 29?Ma. Character reconstruction supports at least 14 parallel origins of epiphytism; one such origin was placed at the most recent common ancestor of ~95% of epiphytic orchids and linked to modern rainforests. Ten occurrences of rapid increase in the diversification rate were detected within Epidendroideae near and after the K-Pg boundary, contributing to ~80% of the Orchidaceae diversity. This study provides a robust and the largest family-wide Orchidaceae nuclear phylogenetic tree thus far and new insights into the evolution of epiphytism in vascular plants.

Establishing how lineages with similar traits are phylogenetically related remains critical for understanding the origin of biodiversity on Earth. Floral traits in plants are widely used to explore phylogenetic relationships and to delineate taxonomic groups. The subtribe Swertiinae (Gentianaceae) comprises more than 350 species with high floral diversity ranging from rotate to tubular corollas and possessing diverse nectaries. Here we performed phylogenetic analysis of 60 species from all 15 genera of the subtribe Swertiinae sensu Ho and Liu, representing the range of floral diversity, using data from the nuclear and plastid genomes. Extensive topological conflicts were present between the nuclear and plastome trees. Three of the 15 genera represented by multiple species are polyphyletic in both trees. Key floral traits including corolla type, absence or presence of lobe scales, nectary type, nectary position, and stigma type are randomly distributed in the nuclear and plastome trees without phylogenetic correlation. We also revealed the likely ancient hybrid origin of one large clade comprising 10 genera with diverse floral traits. These results highlight the complex evolutionary history of this subtribe. The phylogenies constructed here provide a basic framework for further exploring the ecological and genetic mechanisms underlying both species diversification and floral diversity.

All the transcriptomic and whole-genome sequencing data are deposited in Genome Sequence Archive (GSA) of National Genomics Data Center (NGDC) under project PRJCA006737.

The north temperate region was characterized by a warm climate and a rich thermophilic flora before the Eocene, but early diversifications of the temperate biome under global climate change and biome shift remain uncertain. Moreover, it is becoming clear that hybridization/introgression is an important driving force of speciation in plant diversity. Here, we applied analyses from biogeography and phylogenetic networks to account for both introgression and incomplete lineage sorting based on genomic data from the New World Vitis, a charismatic component of the temperate North American flora with known and suspected gene flow among species. Biogeographic inference and fossil evidence suggest that the grapes were widely distributed from North America to Europe during the Paleocene to the Eocene, followed by widespread extinction and survival of relicts in the tropical New World. During the climate warming in the early Miocene, a Vitis ancestor migrated northward from the refugia with subsequent diversification in the North American region. We found strong evidence for widespread incongruence and reticulate evolution among nuclear genes within both recent and ancient lineages of the New World Vitis. Furthermore, the organellar genomes showed strong conflicts with the inferred species tree from the nuclear genomes. Our phylogenomic analyses provided an important assessment of the wide occurrence of reticulate introgression in the New World Vitis, which potentially represents one of the most important mechanisms for the diversification of Vitis species in temperate North America and even the entire temperate Northern Hemisphere. The scenario we report here may be a common model of temperate diversification of flowering plants adapted to the global climate cooling and fluctuation in the Neogene.

The data generated and used in this study are available at the National Center for Biotechnology Information (NCBI) under the accession of BioProject ID PRJNA915194.

Physical contact between genes distant on chromosomes is a potentially important way for genes to coordinate their expressions. To investigate the potential importance of distant contacts, we performed high-throughput chromatin conformation capture (Hi-C) experiments on leaf nuclei isolated from Brassica rapa and Brassica oleracea. We then combined our results with published Hi-C data from Arabidopsis thaliana. We found that distant genes come into physical contact and do so preferentially between the proximal promoter of one gene and the downstream region of another gene. Genes with higher numbers of conserved noncoding sequences (CNSs) nearby were more likely to have contact with distant genes. With more CNSs came higher numbers of transcription factor binding sites and more histone modifications associated with the activity. In addition, for the genes we studied, distant contacting genes with CNSs were more likely to be transcriptionally coordinated. These observations suggest that CNSs may enrich active histone modifications and recruit transcription factors, correlating with distant contacts to ensure coordinated expression. This study advances our knowledge of gene contacts and provides insights into the relationship between CNSs and distant gene contacts in plants.

All sequencing data generated for this study have been submitted to the NCBI Sequence Read Archive under accession number PRJNA865393.

Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.

The genomic data generated and analyzed in this study including the raw sequencing data of Oxford Nanopore, Illumina, Hi-C and RNA-seq, as well as genome assembly have been deposited in China National GeneBank DataBase (CNGBd, https://db.cngb.org/) under accession number CNP0003451. All the custom scripts and specific command lines have been deposited at GitHub (https://github.com/ZhangXu-CAS/Alpine_genome).

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses, based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa, using 65 shared protein-coding plastid genes from 313 accessions (including 280 samples of ca. 226 species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions (including 271 samples of Corydalis) covering all 42 previously recognized sections and five independent “series”. Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include: (i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data; the third, subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus; (ii) among all 42 sections and five “series”, 25 sections and one “series” are resolved as monophyletic in both data sets; (iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes; (iv) we provide a new classification of Corydalis with four subgenera (of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.