Naithani Sushma, Dikeman Daemon, Garg Priyanka, Al-Bader Noor, Jaiswal Pankaj
Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.
PeerJ. 2021 Mar 15;9:e11052. doi: 10.7717/peerj.11052. eCollection 2021.
The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the -locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice () SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.
植物中类受体激酶的S结构域亚家族（SDRLKs）的特征尚不明确。目前，该亚家族的大多数成员是根据来自芸苔属的位点受体激酶来确定基因功能的，该激酶作为自交不亲和性（SI）的雌性决定因子。然而，大多数植物中不存在类似芸苔属的SI机制。因此，自动基因本体论（GO）流程不足以对SDRLK亚家族成员进行功能注释，并导致与SI的GO生物学过程产生错误关联。在此，我们表明手动生物编目有助于纠正和改进基因注释以及与相关生物学过程的关联。利用公开可用的基因组和转录组数据集，我们对水稻（）SDRLK亚家族的扩增、单个基因和蛋白质的结构及其表达进行了详细分析。水稻中由144个成员组成的SDRLK家族包括82个类受体激酶（RLKs）（67个全长，15个截短）、12个类受体蛋白、14个SD激酶、26个类激酶和10个含GnK2结构域的激酶及RLKs。除了9个基因外，所有其他SDRLK家族成员在水稻中都有转录，但它们的组织特异性和应激反应表达谱各不相同。此外，98个基因在生物胁迫下表现出差异表达，98个基因在非生物胁迫条件下表现出差异表达，但共有81个基因相同。我们的分析导致鉴定出可能在植物发育、病原体抗性和非生物胁迫耐受性中起重要作用的候选基因。我们基于基因/蛋白质保守结构特征、基因表达谱和文献综述，为144个SDRLK基因家族成员提出了一种命名法。我们的生物编目方法基于可查找性、可访问性、互操作性和可重用性原则，给出了一个示例，说明对大型基因家族进行手动注释如何能够填补由于实施自动GO预测而存在的知识空白，从而有助于提高公共数据库的质量和内容。
