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Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
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Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
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Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
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Journal Article
Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
2022
Overview
Sulfur is an essential element required for plant growth and development, physiological processes and stress responses. Sulfur-encoding biosynthetic genes are involved in the primary sulfur assimilation pathway, regulating various mechanisms at the gene, cellular and system levels, and in the biosynthesis of sulfur-containing compounds (SCCs). In this study, the SCC-encoding biosynthetic genes in rice were identified using a sulfur-dependent model plant, the
Arabidopsis
. A total of 139
At
SCC from
Arabidopsis
were used as reference sequences in search of putative rice SCCs. At similarity index > 30%, the similarity search against
Arabidopsis
SCC query sequences identified 665 putative
Os
SCC genes in rice. The gene synteny analysis showed a total of 477 syntenic gene pairs comprised of 89
At
SCC and 265
Os
SCC biosynthetic genes in
Arabidopsis
and rice, respectively. Phylogenetic tree of the collated (
At
SCCs and
Os
SCCs) SCC-encoding biosynthetic genes were divided into 11 different clades of various sizes comprised of branches of subclades. In clade 1, nearing equal representation of
Os
SCC and
At
SCC biosynthetic genes imply the most ancestral lineage. A total of 25 candidate
Arabidopsis
SCC homologs were identified in rice. The gene ontology enrichment analysis showed that the rice-
Arabidopsis
SCC homologs were significantly enriched in the following terms at false discovery rate (FDR) < 0.05: (i) biological process; sulfur compound metabolic process and organic acid metabolic processes, (ii) molecular function; oxidoreductase activity, acting on paired donors with incorporation or reduction of molecular oxygen and (iii) KEGG pathway; metabolic pathways and biosynthesis of secondary metabolites. At less than five duplicated blocks of separation, no tandem duplications were observed among the SCC biosynthetic genes distributed in rice chromosomes. The comprehensive rice SCC gene description entailing syntenic events with Arabidopsis, motif distribution and chromosomal mapping of the present findings offer a foundation for rice SCC gene functional studies and advanced strategic rice breeding.
