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

Abstract

BackgroundLegumes 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.ResultsIn 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.

Genome-Wide Identification and Characterization of NBS-encoding Genes in Raphanus Sativus L. And Their Roles Related to Fusarium Oxysporum Resistance

“…The CNL:TNL gene ratio was approximately 1:4, which is similar to that in A. thaliana, B. oleracea, and B. rapa [17]. This distinct pattern of TNL gene abundance suggests that the TIR domain is more functionally active than the CC domain in Brassicaceae species [37].…”

Non-host Resistance Induced by the Xanthomonas Effector XopQ Is Widespread within the Genus Nicotiana and Functionally Depends on EDS1

“…The number of plant R genes varies strongly in different Solanaceae species, e.g., 2042 NLRs were annotated in pepper (Chiltepin), whereas tomato (Heinz1706) only encodes 478 NLRs (Wei et al, 2016). Furthermore, a high evolution rate of R genes and R gene clusters was shown, e.g., in various Solanaceae plants (Jupe et al, 2012; Quirin et al, 2012; Andolfo et al, 2013), Fabaceae (Zheng et al, 2016), Arabidopsis lyrata (Buckley et al, 2016) and grasses (Yang et al, 2008, 2013; Luo et al, 2012; Zhang et al, 2014). We observed variable plant responses between members of the section Nicotiana and even between closely related members of the species N. tabacum , indicating dynamic acquisition and loss of R genes.…”

Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut

“…Since the majority of the R-genes in study belong to PRRs and others with STK domains (~ 80%), it is difficult to draw a significant conclusion about all R-gene evolution in peanuts. In a study analyzing molecular phylogeny and evolution in legumes, R-genes were observed to undergo purifying selection instead of positive selection [47]. Initial low-frequency of genes introduced by random recombination may be lost (perhaps due lack of disease pressures, artificial selection by domestication, or fitness costs).…”