Cargando…
Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant
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 biosyn...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9378745/ https://www.ncbi.nlm.nih.gov/pubmed/35970910 http://dx.doi.org/10.1038/s41598-022-18068-0 |
_version_ | 1784768579966599168 |
---|---|
author | Abdullah-Zawawi, Muhammad-Redha Govender, Nisha Muhammad, Nor Azlan Nor Mohd-Assaad, Norfarhan Zainal, Zamri Mohamed-Hussein, Zeti-Azura |
author_facet | Abdullah-Zawawi, Muhammad-Redha Govender, Nisha Muhammad, Nor Azlan Nor Mohd-Assaad, Norfarhan Zainal, Zamri Mohamed-Hussein, Zeti-Azura |
author_sort | Abdullah-Zawawi, Muhammad-Redha |
collection | PubMed |
description | 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 AtSCC 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 OsSCC genes in rice. The gene synteny analysis showed a total of 477 syntenic gene pairs comprised of 89 AtSCC and 265 OsSCC biosynthetic genes in Arabidopsis and rice, respectively. Phylogenetic tree of the collated (AtSCCs and OsSCCs) 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 OsSCC and AtSCC 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. |
format | Online Article Text |
id | pubmed-9378745 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-93787452022-08-17 Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant Abdullah-Zawawi, Muhammad-Redha Govender, Nisha Muhammad, Nor Azlan Nor Mohd-Assaad, Norfarhan Zainal, Zamri Mohamed-Hussein, Zeti-Azura Sci Rep Article 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 AtSCC 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 OsSCC genes in rice. The gene synteny analysis showed a total of 477 syntenic gene pairs comprised of 89 AtSCC and 265 OsSCC biosynthetic genes in Arabidopsis and rice, respectively. Phylogenetic tree of the collated (AtSCCs and OsSCCs) 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 OsSCC and AtSCC 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. Nature Publishing Group UK 2022-08-15 /pmc/articles/PMC9378745/ /pubmed/35970910 http://dx.doi.org/10.1038/s41598-022-18068-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Abdullah-Zawawi, Muhammad-Redha Govender, Nisha Muhammad, Nor Azlan Nor Mohd-Assaad, Norfarhan Zainal, Zamri Mohamed-Hussein, Zeti-Azura Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title | Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title_full | Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title_fullStr | Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title_full_unstemmed | Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title_short | Genome-wide analysis of sulfur-encoding biosynthetic genes in rice (Oryza sativa L.) with Arabidopsis as the sulfur-dependent model plant |
title_sort | genome-wide analysis of sulfur-encoding biosynthetic genes in rice (oryza sativa l.) with arabidopsis as the sulfur-dependent model plant |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9378745/ https://www.ncbi.nlm.nih.gov/pubmed/35970910 http://dx.doi.org/10.1038/s41598-022-18068-0 |
work_keys_str_mv | AT abdullahzawawimuhammadredha genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant AT govendernisha genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant AT muhammadnorazlannor genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant AT mohdassaadnorfarhan genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant AT zainalzamri genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant AT mohamedhusseinzetiazura genomewideanalysisofsulfurencodingbiosyntheticgenesinriceoryzasativalwitharabidopsisasthesulfurdependentmodelplant |