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BMC Genomics. 2016 May 26;17:402. doi: 10.1186/s12864-016-2736-9.

Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family.

Author information

1
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.
2
BGI-Shenzhen, Shenzhen, 518083, China.
3
HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong.
4
Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
5
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.
6
BGI-Shenzhen, Shenzhen, 518083, China. zhaoshancen@genomics.cn.
7
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.

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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.

KEYWORDS:

Coiled-coil (CC) domain; Evolution; Legumes; Leucine-rich repeat (LRR) domain; Nucleotide-binding site (NBS); R-genes; Toll/Interleukin-1 receptor (TIR) domain

PMID:
27229309
PMCID:
PMC4881053
DOI:
10.1186/s12864-016-2736-9
[Indexed for MEDLINE]
Free PMC Article

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