Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

Abstract

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 S-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 (Oryza sativa) 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.

The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses

“…The phenotypic analysis indicated that the IRO2 overexpression lines germinated and grew better than the WT, while the IRO2-RNAi lines grew slower than the WT [ 74 ]. The D-mannose-binding lectin family protein/S-Domain receptor-like protein-11 (SDRLP-11) is characterized by Ser/Thr kinase domains and induced by salicylic acid [ 75 , 76 ]. Ubiquitin carboxyl-terminal hydrolase family 1/ubiquitin c-terminal hydrolase 5 (UCH5) is an uncharacterized protein.…”

Genome-Wide Association Study of Submergence Tolerance in Rice (Oryza sativa L.)

“…In the qSUB6-1 region, Os06g0164900 was reported to have S-Domain receptor-like kinase-66 (SDRLK-66) that responds to chilling and submergence. Also, in the qSUB12-1 region, Os12g0130500 was reported to have S-Domain receptor like protein-6 (SDRLP-6) that responds to submergence (Mondal et al 2021;Naithani et al 2021). One of the detected QTLs overlapped with the reported qSUB12.1 for submergence tolerance.…”

Genetic dissection of monosaccharides contents in rice whole grain using genome‐wide association study

“…One of the candidate genes for mannose content was LOC_Os09g02410 , an S ‐domain receptor‐like kinase (SDRLK; Table 1), which is originally found in self‐incompatibility responses in Brassica (Zou et al., 2015). Rice has 144 members of SDRLK with varieties of functions in biotic/abiotic stress responses and development (Chen et al., 2013; Fan et al., 2018; Naithani et al., 2021). Transgenic rice plants carrying anti‐sense for a member of SDRLK ( OsESG1 ) developed into fewer crown roots and shorter shoots at seedling stage compared with wild type (Pan et al., 2020).…”