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

doi:10.1016/j.btre.2021.e00607

Cited by 14 publications

(9 citation statements)

References 74 publications

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“…A similar phenomenon of double copies of members of the SoxE subfamily has also been seen in other teleost, such as the large yellow croaker and spinyhead croaker [33,34]. However, Cyprinus carpio has more SoxE (including CySox8a, CySox8b, CySox8c, CySox8d, CySox9a, CySox9b, CySox9c, CySox9d, CySox10a, and CySox10b) compared with S. maximus and other aforementioned fsh, implying that C. carpio underwent additional genome duplication events during evolution (4R-WGD events) [14].…”

Section: Resultssupporting

confidence: 63%

Molecular Characterization, Phylogeny, and Expression Profiles of SoxE Subfamily in Scophthalmus maximus

Ji,

Guo,

Shi

et al. 2024

Journal of Applied Ichthyology

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SOXE transcription factors, including SOX8, SOX9, and SOX10, regulate several developmental events, such as sex determination, chondrogenesis, and neurogenesis. This study systematically identified six SoxE subfamily genes from the turbot (Scophthalmus maximus) genome and transcriptome, including SmSox8a, SmSox8b, SmSox9a, SmSox9b, SmSox10a, and SmSox10b. The duplicates of three SOXE members revealed that SoxE subfamily genes in the turbot underwent significant expansion. Relatively conserved exon-intron structures and intron insertions were detected using genomic structural analysis. Besides, phylogenetic analysis supported the previous classification of the SoxE subfamily. Results of the expression profile revealed that turbot SoxE subfamily genes may be involved in different activities, such as neurogenesis and gonad development. These findings would assist in the understanding of fish SoxE gene subfamily activities and evolution.

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Section: Resultssupporting

confidence: 63%

Molecular Characterization, Phylogeny, and Expression Profiles of SoxE Subfamily in Scophthalmus maximus

Ji,

Guo,

Shi

et al. 2024

Journal of Applied Ichthyology

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“…As per earlier research, phylogenetic relationships are established between Omicron with other variants based on the distance matrix [ 36 ]. Using the UPGMA algorithm, the mapping of variable strains at different branches was generated per the rules of phylogenetic preparation [ 37 ]. This study established an inference that Omicron shares a monophyletic clade [ 38 ].…”

Section: Discussionmentioning

confidence: 99%

Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages

et al. 2022

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The novel SARS-CoV-2 variant, Omicron (B.1.1.529), is being testified, and the WHO has characterized Omicron as a variant of concern due to its higher transmissibility and very contagious behavior, immunization breakthrough cases. Here, the comparative proteomic study has been conducted on spike-protein, hACE2 of five lineages (α, β, δ, γ and Omicron. The docking was performed on spike protein- hACE-2 protein using HADDOCK, and PRODIGY was used to analyze the binding energy affinity using a reduced Haddock score. Followed by superimposition in different variant-based protein structures and calculated the esteem root mean square deviation (RMSD). This study reveals that Omicron was seen generating a monophyletic clade. Further, as α variant is the principal advanced strain after Wuhan SARS-CoV-2, and that is the reason it was showing the least likeness rate with the Omicron and connoting Omicron has developed of late with the extreme number of mutations. α variant has shown the highest binding affinity with hACE2, followed by β strain, and followed with γ. Omicron showed a penultimate binding relationship, while the δ variant was seen as having the least binding affinity. This proteomic basis in silico analysis of variable spike proteins of variants will impart light on the development of vaccines and the identification of mutations occurring in the upcoming variants.

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“…Members of the gjSOXs family underwent genome-wide screening and were determined based on bioinformatics tools [19]. Briefly, the protein sequence file of G. japonicus was retrieved from the NCBI database (GCF_001447785.1).…”

Section: Analysis Of Conserved Regions Of Gjsox9 and The Gjsox Familymentioning

confidence: 99%

“…Genome data provide valuable resources for identifying genes or gene families via genome-wide identification or characterization [19,20]. BLAST analyses indicated that SOX9 orthologs were present in almost all metazoans [21].…”

Section: Introductionmentioning

confidence: 99%

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

Huang,

Zhao,

et al. 2023

CIMB

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SOX9 plays a crucial role in the male reproductive system, brain, and kidneys. In this study, we firstly analyzed the complete cDNA sequence and expression patterns for SOX9 from Gekko japonicus SOX9 (gjSOX9), carried out bioinformatic analyses of physiochemical properties, structure, and phylogenetic evolution, and compared these with other members of the gjSOX family. The results indicate that gjSOX9 cDNA comprises 1895 bp with a 1482 bp ORF encoding 494aa. gjSOX9 was not only expressed in various adult tissues but also exhibited a special spatiotemporal expression pattern in gonad tissues. gjSOX9 was predicted to be a hydrophilic nucleoprotein with a characteristic HMG-Box harboring a newly identified unique sequence, “YKYQPRRR”, only present in SOXE members. Among the 20 SOX9 orthologs, gjSOX9 shares the closest genetic relationships with Eublepharis macularius SOX9, Sphacrodactylus townsendi SOX9, and Hemicordylus capensis SOX9. gjSOX9 and gjSOX10 possessed identical physicochemical properties and subcellular locations and were tightly clustered with gjSOX8 in the SOXE group. Sixteen gjSOX family members were divided into six groups: SOXB, C, D, E, F, and H with gjSOX8, 9, and 10 in SOXE among 150 SOX homologs. Collectively, the available data in this study not only facilitate a deep exploration of the functions and molecular regulation mechanisms of the gjSOX9 and gjSOX families in G. japonicus but also contribute to basic research regarding the origin and evolution of SOX9 homologs or even sex-determination mode in reptiles.

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

Cited by 14 publications

References 74 publications

Molecular Characterization, Phylogeny, and Expression Profiles of SoxE Subfamily in Scophthalmus maximus

Molecular Characterization, Phylogeny, and Expression Profiles of SoxE Subfamily in Scophthalmus maximus

Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages

gjSOX9 Cloning, Expression, and Comparison with gjSOXs Family Members in Gekko japonicus

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