A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae.
A complex interplay of tandem- and whole-genome duplication drives expansion of the L-type lectin receptor kinase gene family in the brassicaceae.
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DOI：
10.1093/gbe/evv020
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发表时间：
2015-01-28
影响因子：
3.3
通讯作者：
Schranz ME
中科院分区：
文献类型：
--
作者：
Hofberger JA;Nsibo DL;Govers F;Bouwmeester K;Schranz ME
由于下一代测序技术的进步，植物基因家族在系统发育框架中的比较分析大大加快。在这项研究中，我们提供了一个进化分析的L-型凝集素受体激酶和L-型凝集素结构域蛋白（L-型LecRKs和LLP），被认为是在植物免疫的组成部分，在植物科植物和相关的外类群。我们结合联合收割机提供的序列同源性，HMM驱动的蛋白质结构域注释，系统发育分析，和基因同线性的证据，大规模识别的L型LecRK和LLP基因在9个核心真双子叶植物基因组。我们发现，多倍体和本地重复事件（串联重复和基因转座重复）发挥了重要作用，在L型LecRK和LLP基因家族的扩展在菊科。我们还发现基于复制模式的分子进化速率存在显着差异。此外，我们发现LLP与L型LecRKs有着共同的进化起源，并提供了一致的基因家族命名法。最后，我们证明了最大和最多样化的L型LecRK分支是谱系特异性的。我们对这些植物免疫组分的进化分析为支持未来的植物抗性育种提供了一个框架。
The comparative analysis of plant gene families in a phylogenetic framework has greatly accelerated due to advances in next generation sequencing. In this study, we provide an evolutionary analysis of the L-type lectin receptor kinase and L-type lectin domain proteins (L-type LecRKs and LLPs) that are considered as components in plant immunity, in the plant family Brassicaceae and related outgroups. We combine several lines of evidence provided by sequence homology, HMM-driven protein domain annotation, phylogenetic analysis, and gene synteny for large-scale identification of L-type LecRK and LLP genes within nine core-eudicot genomes. We show that both polyploidy and local duplication events (tandem duplication and gene transposition duplication) have played a major role in L-type LecRK and LLP gene family expansion in the Brassicaceae. We also find significant differences in rates of molecular evolution based on the mode of duplication. Additionally, we show that LLPs share a common evolutionary origin with L-type LecRKs and provide a consistent gene family nomenclature. Finally, we demonstrate that the largest and most diverse L-type LecRK clades are lineage-specific. Our evolutionary analyses of these plant immune components provide a framework to support future plant resistance breeding.