J Integr Plant Biol. ›› 2014, Vol. 56 ›› Issue (7): 648-662.DOI: 10.1111/jipb.12188

• Molecular Ecology and Evolution • Previous Articles     Next Articles

Evolutionary dynamics of leucine-rich repeat receptor-like kinases and related genes in plants: A phylogenomic approach

Tao Shi1†, Hongwen Huang2, Michael J Sanderson1 and Frans E Tax3,4*   

  1. 1Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
    2South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, China
    3Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
    4School of Plant Sciences, University of Arizona, Tucson, AZ, USA
  • Received:2013-12-06 Accepted:2014-02-19 Published:2014-02-24
  • About author:Current address: School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
    *Correspondence: E-mail: fetax@email.arizona.edu

Abstract:

Leucine-rich repeat (LRR) receptor-like kinases (RLKs), evolutionarily related LRR receptor-like proteins (RLPs) and receptor-like cytoplasmic kinases (RLCKs) have important roles in plant signaling, and their gene subfamilies are large with a complicated history of gene duplication and loss. In three pairs of closely related lineages, including Arabidopsis thaliana and A. lyrata (Arabidopsis), Lotus japonicus, and Medicago truncatula (Legumes), Oryza sativa ssp. japonica, and O. sativa ssp. indica (Rice), we find that LRR RLKs comprise the largest group of these LRR-related subfamilies, while the related RLCKs represent the smallest group. In addition, comparison of orthologs indicates a high frequency of reciprocal gene loss of the LRR RLK/LRR RLP/RLCK subfamilies. Furthermore, pairwise comparisons show that reciprocal gene loss is often associated with lineage-specific duplication(s) in the alternative lineage. Last, analysis of genes in A. thaliana involved in development revealed that most are highly conserved orthologs without species-specific duplication in the two Arabidopsis species and originated from older Arabidopsis-specific or rosid-specific duplications. We discuss potential pitfalls related to functional prediction for genes that have undergone frequent turnover (duplications, losses, and domain architecture changes), and conclude that prediction based on phylogenetic relationships will likely outperform that based on sequence similarity alone.
 

Shi T, Huang H, Sanderson MJ, Tax FE (2014) Evolutionary dynamics of leucine‐rich repeat receptor‐like kinases and related genes in plants: A phylogenomic approach. J Integr Plant Biol 56: 648–662. doi: 10.1111/jipb.12188

Key words: Domain architecture evolution, gene duplication and loss, leucine-rich repeat receptor-like kinases, leucine-rich repeat receptor-like proteins, receptor-like cytoplasmic kinases

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