Restrepo-Montoya Daniel, McClean Phillip E, Osorno Juan M
Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND, 58108-6050, USA.
Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
BMC Genomics. 2021 Feb 10;22(1):113. doi: 10.1186/s12864-021-07384-w.
Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses directly involve plasma membrane receptor proteins known as receptor-like kinases and receptor-like proteins. Evaluating the homology relations among RLK and RLP for seven legume species, and exploring their presence among synteny blocks allow an increased understanding of evolutionary relations, physical position, and chromosomal distribution in related species and their shared roles in stress responses.
Typically, a high proportion of RLK and RLP legume proteins belong to orthologous clusters, which is confirmed in this study, where between 66 to 90% of the RLKs and RLPs per legume species were classified in orthologous clusters. One-third of the evaluated syntenic blocks had shared RLK/RLP genes among both legumes and non-legumes. Among the legumes, between 75 and 98% of the RLK/RLP were present in syntenic blocks. The distribution of chromosomal segments between Phaseolus vulgaris and Vigna unguiculata, two species that diverged ~ 8 mya, were highly similar. Among the RLK/RLP synteny clusters, seven experimentally validated resistance RLK/RLP genes were identified in syntenic blocks. The RLK resistant genes FLS2, BIR2, ERECTA, IOS1, and AtSERK1 from Arabidopsis and SLSERK1 from Solanum lycopersicum were present in different pairwise syntenic blocks among the legume species. Meanwhile, only the LYM1- RLP resistant gene from Arabidopsis shared a syntenic blocks with Glycine max.
The orthology analysis of the RLK and RLP suggests a dynamic evolution in the legume family, with between 66 to 85% of RLK and 83 to 88% of RLP belonging to orthologous clusters among the species evaluated. In fact, for the 10-species comparison, a lower number of singleton proteins were reported among RLP compared to RLK, suggesting that RLP positions are more physically conserved compared to RLK. The identification of RLK and RLP genes among the synteny blocks in legumes revealed multiple highly conserved syntenic blocks on multiple chromosomes. Additionally, the analysis suggests that P. vulgaris is an appropriate anchor species for comparative genomics among legumes.
豆科植物因其富含蛋白质的生理特性而成为重要的植物模型。豆科植物的适应性和生产力受到主要生物和非生物胁迫的限制。对这些胁迫的反应直接涉及被称为类受体激酶和类受体蛋白的质膜受体蛋白。评估七种豆科植物中RLK和RLP之间的同源关系，并探索它们在同线基因块中的存在情况，有助于加深对相关物种进化关系、物理位置和染色体分布及其在胁迫反应中共同作用的理解。
通常，豆科植物中很大一部分RLK和RLP蛋白属于直系同源簇，本研究证实了这一点，其中每个豆科植物物种中66%至90%的RLK和RLP被归类到直系同源簇中。三分之一的评估同线基因块在豆科植物和非豆科植物中都有共享的RLK/RLP基因。在豆科植物中，75%至98%的RLK/RLP存在于同线基因块中。菜豆和豇豆这两个大约在800万年前分化的物种之间的染色体片段分布高度相似。在RLK/RLP同线基因簇中，在同线基因块中鉴定出七个经过实验验证的抗性RLK/RLP基因。来自拟南芥的RLK抗性基因FLS2、BIR2、ERECTA、IOS1和AtSERK1以及来自番茄的SLSERK1存在于豆科植物物种不同的成对同线基因块中。同时，只有来自拟南芥的LYM1 - RLP抗性基因与大豆共享一个同线基因块。
RLK和RLP的直系同源分析表明豆科家族存在动态进化，在所评估的物种中，66%至85%的RLK和83%至88%的RLP属于直系同源簇。事实上，在10个物种的比较中，与RLK相比，RLP中报道的单拷贝蛋白数量更少，这表明与RLK相比，RLP的位置在物理上更保守。在豆科植物的同线基因块中鉴定RLK和RLP基因揭示了多条染色体上多个高度保守的同线基因块。此外，分析表明菜豆是豆科植物中进行比较基因组学研究的合适锚定物种。
