J Integr Plant Biol. ›› 2022, Vol. 64 ›› Issue (3): 649-670.DOI: 10.1111/jipb.13217

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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo (Dendrocalamus latiflorus Munro)

Yushan Zheng1*, Deming Yang1, Jundong Rong1, Liguang Chen1, Qiang Zhu2, Tianyou He2, Lingyan Chen2, Jing Ye1, Lili Fan1, Yubang Gao3, Hangxiao Zhang3 and Lianfeng Gu3*   

  1. 1 College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
    2 College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
    3 Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China

    *Correspondences: Yushan Zheng (zys1960@163.com); Lianfeng Gu (lfgu@fafu.edu.cn, Dr. Gu is fully responsible for the distribution of the materials associated with this article)
  • Received:2021-11-22 Accepted:2022-01-04 Online:2022-01-06 Published:2022-03-01

Abstract: Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot growth. Both genetic transformation and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing techniques are available for D. latiflorus, enabling reverse genetic approaches. Thus, D. latiflorus has the potential to be a model bamboo species. However, the genome sequence of D. latiflorus has remained unreported due to its polyploidy and large genome size. Here, we sequenced the D. latiflorus genome and assembled it into three allele-aware subgenomes (AABBCC), representing the largest genome of a major bamboo species. We assembled 70 allelic chromosomes (2, 737 Mb) for hexaploid D. latiflorus using both single-molecule sequencing from the Pacific Biosciences (PacBio) Sequel platform and chromosome conformation capture sequencing (Hi-C). Repetitive sequences comprised 52.65% of the D. latiflorus genome. We annotated 135 231 protein-coding genes in the genome based on transcriptomes from eight different tissues. Transcriptome sequencing using RNA-Seq and PacBio single-molecule real-time long-read isoform sequencing revealed highly differential alternative splicing (AS) between non-abortive and abortive shoots, suggesting that AS regulates the abortion rate of bamboo shoots. This high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using D. latiflorus as a model species.

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