title: Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family.
abstract: Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family.
  
  
  
  In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates.
  
  
  
  Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars.
authors.affiliation: Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
authors.forename: Fengya
authors.initials: F
authors.lastname: Zheng
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.|HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong.
authors.forename: Haiyang
authors.initials: H
authors.lastname: Wu
authors.affiliation: Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
authors.forename: Rongzhi
authors.initials: R
authors.lastname: Zhang
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Shiming
authors.initials: S
authors.lastname: Li
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.affiliation: Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
authors.forename: Fuk-Ling
authors.initials: FL
authors.lastname: Wong
authors.affiliation: Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
authors.forename: Genying
authors.initials: G
authors.lastname: Li
authors.affiliation: Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. zhaoshancen@genomics.cn.|BGI-Shenzhen, Shenzhen, 518083, China. zhaoshancen@genomics.cn.
authors.forename: Shancen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. honming@cuhk.edu.hk.
authors.forename: Hon-Ming
authors.initials: HM
authors.lastname: Lam
mesh_terms: D060467:Disease Resistance / Q000235:genetics*; D019143:Evolution, Molecular; D007887:Fabaceae / Q000145:classification* / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D000072417:Protein Domains; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D010940:Plant Proteins
keywords: Coiled-coil (CC) domain; Evolution; Legumes; Leucine-rich repeat (LRR) domain; Nucleotide-binding site (NBS); R-genes; Toll/Interleukin-1 receptor (TIR) domain