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Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)

Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcrip...

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Autores principales: Zafar, Imran, Iftikhar, Rida, Ahmad, Syed Umair, Rather, Mohd Ashraf
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8076717/
https://www.ncbi.nlm.nih.gov/pubmed/33936955
http://dx.doi.org/10.1016/j.btre.2021.e00607
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author Zafar, Imran
Iftikhar, Rida
Ahmad, Syed Umair
Rather, Mohd Ashraf
author_facet Zafar, Imran
Iftikhar, Rida
Ahmad, Syed Umair
Rather, Mohd Ashraf
author_sort Zafar, Imran
collection PubMed
description Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost.
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spelling pubmed-80767172021-04-29 Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio) Zafar, Imran Iftikhar, Rida Ahmad, Syed Umair Rather, Mohd Ashraf Biotechnol Rep (Amst) Research Article Common carp (Cyprinus carpio) is a commercial fish species valuable for nutritious components and plays a vital role in human healthy nutrition. The SOX (SRY-related genes systematically characterized by a high-mobility group HMG-box) encoded important gene regulatory proteins, a family of transcription factors found in a broad range of animal taxa and extensively known for its contribution in multiple developmental processes including contribution in sex determination across phyla. In our current study, we initially accomplished a genome-wide analysis to report the SOX gene family in common carp fish based on available genomic sequences of zebrafish retrieved from gene repository databases, we focused on the global identification of the Sox gene family in Common carp among wide range of vertebrates and teleosts based on bioinformatics tools and techniques and explore the evolutionary relationships. In our results, a total of 27 SOX (high-mobility group HMG-box) domain genes were identified in the C. carp genome. The full length sequences of SOX genes ranging from 3496 (SOX6) to 924bp (SOX17b) which coded with putative proteins series from 307 to 509 amino acids and all gene having exon number expect SOX9 and SOX13. All the SOX proteins contained at least one conserved DNA-binding HMG-box domain and two (SOX7 and SOX18) were found C terminal. The Gene ontology revealed SOX proteins maximum involvement is in metabolic process 49.796 %, average in biological regulation 45.188 %, biosynthetic process (19.992 %), regulation of cellular process 39.68, 45.508 % organic substance metabolic process, multicellular organismal process 23.23 %,developmental process 21.74 %, system development 16.59 %, gene expression 16.05 % and 14.337 % of RNA metabolic process. Chromosomal location and syntanic analysis show all SOX gene are located on different chromosomes and apparently does not fallow the unique pattern. The maximum linkage of chromosome is (2) on Unplaced Scaffold region. Finally, our results provide important genomic suggestion for upcoming studies of biochemical, physiological, and phylogenetic understanding on SOX genes among teleost. Elsevier 2021-03-16 /pmc/articles/PMC8076717/ /pubmed/33936955 http://dx.doi.org/10.1016/j.btre.2021.e00607 Text en © 2021 Published by Elsevier B.V. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Research Article
Zafar, Imran
Iftikhar, Rida
Ahmad, Syed Umair
Rather, Mohd Ashraf
Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title_full Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title_fullStr Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title_full_unstemmed Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title_short Genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (Cyprinus carpio)
title_sort genome wide identification, phylogeny, and synteny analysis of sox gene family in common carp (cyprinus carpio)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8076717/
https://www.ncbi.nlm.nih.gov/pubmed/33936955
http://dx.doi.org/10.1016/j.btre.2021.e00607
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