Dataset Information

Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice.

ABSTRACT: Low molecular weight metabolites are important plant hormones and signaling molecules, and play an important part among the processes of plant development. Their activities may also be affected by the chemical modifications of methylation performed by SABATH. In this study, a total of 24 and 21 SABATH genes in Arabidopsis and rice, respectively, were identified and taken a comprehensive study. Phylogenetic analysis showed that AtSABATH and OsSABATH genes could be classified into 4 major groups and 6 subgroups. Gene expansion analysis showed that the main expansion mechanism of SABATH gene family in Arabidopsis and rice was tandem duplication and segmental duplication. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of 12 pairs paralogous of AtSABATH and OsSABATH genes indicated that the SABATH gene family in Arabidopsis and rice had gone through purifying selection. Positive selection analysis with site models and branch-site models revealed that AtSABATH and OsSABATH genes had undergone selective pressure for adaptive evolution. Motif analysis showed that certain motifs only existed in specific subgroups or species, which indicated that the SABATH proteins of Arabidopsis and rice appear divergence in different species and subgroups. Functional divergence analysis also suggested that the AtSABATH and OsSABATH subgroup genes had functional differences, and the positive selection sites which contributed to functional divergence among subgroups were detected. These results provide insights into functional conservation and diversification of SABATH gene family, and are useful information for further elucidating SABATH gene family functions.

SUBMITTER: Wang B

PROVIDER: S-EPMC6610438 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice.

Wang Bin B Li Min M Yuan Yijun Y Liu Shaofang S

Evolutionary bioinformatics online 20190703

Low molecular weight metabolites are important plant hormones and signaling molecules, and play an important part among the processes of plant development. Their activities may also be affected by the chemical modifications of methylation performed by SABATH. In this study, a total of 24 and 21 SABATH genes in Arabidopsis and rice, respectively, were identified and taken a comprehensive study. Phylogenetic analysis showed that AtSABATH and OsSABATH genes could be classified ...[more]

PMID: 31320793

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Project description:BackgroundThe Na(+)/Ca(2+) Exchanger (NCX) protein family is a member of the Cation/Ca(2+) exchanger superfamily and its members play important roles in cellular Ca(2+) homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na(+)/Ca(2+) exchangers in plants and their role in various physiological and developmental processes. In the present study, we have identified all the NCX proteins encoded in the genomes of rice and Arabidopsis and studied their phylogeny, domain architecture and expression profiles across different tissues, at various developmental stages and under stress conditions.ResultsThrough whole genome investigation, we identified twenty-two NCX proteins encoded by fifteen genes in rice and sixteen NCX proteins encoded by thirteen genes in Arabidopsis. Based on phylogenetic reconstruction, these could be classified into five clades, members of most of which were found to possess distinct domain architecture. Expression profiling of the identified NCX genes using publicly available MPSS and microarray data showed differential expression patterns under abiotic stresses, and at various development stages. In rice, OsNCX1, OsNCX8, OsNCX9 and OsNCX15 were found to be highly expressed in all the plant parts and various developmental stages. qRT-PCR based expression analysis revealed that OsNCX3, OsNCX10 and OsNCX15 were highly induced by salt and dehydration stress. Besides, expression profiling showed differential regulation of rice NCX genes in response to calcium and EGTA. Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.ConclusionsTogether, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development. Findings of the present investigation should serve as a starting point for future studies aiming functional characterization of plant NCX family proteins.

Project description:BACKGROUND:Reception of and response to exogenous and endogenous osmotic changes is important to sustain plant growth and development, as well as reproductive formation. Hyperosmolality-gated calcium-permeable channels (OSCA) were first characterised as an osmosensor in Arabidopsis and are involved in the perception of extracellular changes to trigger hyperosmolality-induced [Ca(2+)]i increases (OICI). To explore the potential biological functions of OSCAs in rice, we performed a bioinformatics and expression analysis of the OsOSCA gene family. RESULTS:A total of 11 OsOSCA genes were identified from the genome database of Oryza sativa L. Japonica. Based on their sequence composition and phylogenetic relationship, the OsOSCA family was classified into four clades. Gene and protein structure analysis indicated that the 11 OsOSCAs shared similar structures with their homologs in Oryza sativa L. ssp. Indica, Oryza glaberrima, and Oryza brachyantha. Multiple sequence alignment analysis revealed a conserved DUF221 domain in these members, in which the first three TMs were conserved, while the others were not. The expression profiles of OsOSCA genes were analysed at different stages of vegetative growth, reproductive development, and under osmotic-associated abiotic stresses. We found that four and six OsOSCA genes showed a clear correlation between the expression profile and osmotic changes during caryopsis development and seed imbibition, respectively. Orchestrated transcription of three OsOSCAs was strongly associated with the circadian clock. Moreover, osmotic-related abiotic stress differentially induced the expression of 10 genes. CONCLUSION:The entire OSCA family is characterised by the presence of a conserved DUF221 domain, which functions as an osmotic-sensing calcium channel. The phylogenetic tree of OSCA genes showed that two subspecies of cultivated rice, Oryza sativa L. ssp. Japonica and Oryza sativa L. ssp. Indica, are more closely related than wild rice Oryza glaberrima, while Oryza brachyantha was less closely related. OsOSCA expression is organ- and tissue-specific and regulated by different osmotic-related abiotic stresses in rice. These findings will facilitate further research in this gene family and provide potential target genes for generation of genetically modified osmotic-stress-resistant plants.

Dataset Information

Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice.

Publications

Genome-Wide Comprehensive Analysis of the SABATH Gene Family in <i>Arabidopsis</i> and Rice.

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