LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.
LRR-RLK family from two Citrus species: genome-wide identification and evolutionary aspects.
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来自两个柑橘属物种的 LRR-RLK 家族：全基因组鉴定和进化方面。
DOI：
10.1186/s12864-016-2930-9
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发表时间：
2016-08-12
期刊：
影响因子：
4.4
通讯作者：
De Souza AA
中科院分区：
文献类型：
--
作者：
Magalhães DM;Scholte LL;Silva NV;Oliveira GC;Zipfel C;Takita MA;De Souza AA
富含亮氨酸的重复受体样激酶（LRR-RLK）是植物RLK中最大的亚家族。大多数LRR-RLKs的功能尚未被发现，一些已经被实验表征的功能已被证明在生长和发育以及防御反应中具有重要作用。虽然RLK亚家族已经在许多植物中进行了研究，但在柑橘属物种中还没有对该基因家族进行全面的研究，柑橘属物种具有很高的经济重要性，并且是新兴病原体的常见靶标。在这项研究中，我们进行了计算机分析，以确定和分类的预测蛋白质组的柑橘克莱门蒂（克莱门汀）和柑橘（甜橙子）LRR-RLK同源。此外，我们使用大规模的系统发育方法来阐明LRR-RLKs的进化关系，并进一步缩小分析LRR-XII组，其中包含几个先前描述的细胞表面免疫受体。我们使用从全基因组获得的所有预测蛋白质序列构建了柑橘和柑橘的整合蛋白质签名数据库。在C. clementina和C. sinensis，分别。最大似然系统发育树估计使用拟南芥LRR-RLK作为模板，他们允许我们将柑橘LRR-RLK分为16组。LRR-XII组显示出显著的扩增，包含在每个柑橘基因组中编码的大约150个旁系同源物。系统发育分析还表明存在两个不同的LRR-XII分支，每个分支主要由RD和非RD激酶组成。我们从C. clementina和C. LRR-XII基因。此外，在旁系同源物中，我们确定了一个子集的78和62个聚类基因可能来自串联重复事件的基因组中的C。clementina和C. sinensis，分别。这项工作提供了柑橘LRR-RLKs的第一个全面的进化分析。LRR-XII在柑橘基因组中的大量扩增表明，它可能在宿主-病原体协同进化的适应性反应中发挥关键作用，与柑橘作物物种的多年生生活史和驯化有关。本文的在线版本（doi：10.1186/s12864-016-2930-9）包含补充材料，可供授权用户使用。
Leucine-rich repeat receptor-like kinases (LRR-RLKs) represent the largest subfamily of plant RLKs. The functions of most LRR-RLKs have remained undiscovered, and a few that have been experimentally characterized have been shown to have important roles in growth and development as well as in defense responses. Although RLK subfamilies have been previously studied in many plants, no comprehensive study has been performed on this gene family in Citrus species, which have high economic importance and are frequent targets for emerging pathogens. In this study, we performed in silico analysis to identify and classify LRR-RLK homologues in the predicted proteomes of Citrus clementina (clementine) and Citrus sinensis (sweet orange). In addition, we used large-scale phylogenetic approaches to elucidate the evolutionary relationships of the LRR-RLKs and further narrowed the analysis to the LRR-XII group, which contains several previously described cell surface immune receptors. We built integrative protein signature databases for Citrus clementina and Citrus sinensis using all predicted protein sequences obtained from whole genomes. A total of 300 and 297 proteins were identified as LRR-RLKs in C. clementina and C. sinensis, respectively. Maximum-likelihood phylogenetic trees were estimated using Arabidopsis LRR-RLK as a template and they allowed us to classify Citrus LRR-RLKs into 16 groups. The LRR-XII group showed a remarkable expansion, containing approximately 150 paralogs encoded in each Citrus genome. Phylogenetic analysis also demonstrated the existence of two distinct LRR-XII clades, each one constituted mainly by RD and non-RD kinases. We identified 68 orthologous pairs from the C. clementina and C. sinensis LRR-XII genes. In addition, among the paralogs, we identified a subset of 78 and 62 clustered genes probably derived from tandem duplication events in the genomes of C. clementina and C. sinensis, respectively. This work provided the first comprehensive evolutionary analysis of the LRR-RLKs in Citrus. A large expansion of LRR-XII in Citrus genomes suggests that it might play a key role in adaptive responses in host-pathogen co-evolution, related to the perennial life cycle and domestication of the citrus crop species. The online version of this article (doi:10.1186/s12864-016-2930-9) contains supplementary material, which is available to authorized users.