Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia
Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytopl...
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ftdoajarticles:oai:doaj.org/article:1b7b1bc919904b0d94da9d5bae4b24fd 2023-05-15T15:32:41+02:00 Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia Gangqiao Kuang Wenjing Tao Shuqing Zheng Xiaoshuang Wang Deshou Wang 2020-02-01T00:00:00Z https://doi.org/10.3390/ijms21041230 https://doaj.org/article/1b7b1bc919904b0d94da9d5bae4b24fd EN eng MDPI AG https://www.mdpi.com/1422-0067/21/4/1230 https://doaj.org/toc/1422-0067 1422-0067 doi:10.3390/ijms21041230 https://doaj.org/article/1b7b1bc919904b0d94da9d5bae4b24fd International Journal of Molecular Sciences, Vol 21, Iss 4, p 1230 (2020) cytoplasmic ribosomal protein gene evolution transcriptome analysis nile tilapia Biology (General) QH301-705.5 Chemistry QD1-999 article 2020 ftdoajarticles https://doi.org/10.3390/ijms21041230 2022-12-31T14:51:34Z Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates. Article in Journal/Newspaper Atlantic salmon Directory of Open Access Journals: DOAJ Articles International Journal of Molecular Sciences 21 4 1230 |
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Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
cytoplasmic ribosomal protein gene evolution transcriptome analysis nile tilapia Biology (General) QH301-705.5 Chemistry QD1-999 |
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cytoplasmic ribosomal protein gene evolution transcriptome analysis nile tilapia Biology (General) QH301-705.5 Chemistry QD1-999 Gangqiao Kuang Wenjing Tao Shuqing Zheng Xiaoshuang Wang Deshou Wang Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
topic_facet |
cytoplasmic ribosomal protein gene evolution transcriptome analysis nile tilapia Biology (General) QH301-705.5 Chemistry QD1-999 |
description |
Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. In the present study, we carried out a comprehensive analysis of RPs in chordates and examined the expression profiles of the complete set of 92 cytoplasmic RP genes in Nile tilapia. The RP genes were randomly distributed throughout the tilapia genome. Phylogenetic and syntenic analyses revealed the existence of duplicated RP genes from 2R (RPL3, RPL7, RPL22 and RPS27) and 3R (RPL5, RPL19, RPL22, RPL41, RPLP2, RPS17, RPS19 and RPS27) in tilapia and even more from 4R in common carp and Atlantic salmon. The RP genes were found to be expressed in all tissues examined, but their expression levels differed among different tissues. Gonadal transcriptome analysis revealed that almost all RP genes were highly expressed, and their expression levels were highly variable between ovaries and testes at different developmental stages in tilapia. No sex- and stage-specific RP genes were found. Eleven RP genes displayed sexually dimorphic expression with nine higher in XY gonad and two higher in XX gonad at all stages examined, which were proved to be phenotypic sex dependent. Quantitative real-time PCR and immunohistochemistry ofRPL5b and RPL24 were performed to validate the transcriptome data. The genomic resources and expression data obtained in this study will contribute to a better understanding of RPs evolution and functions in chordates. |
format |
Article in Journal/Newspaper |
author |
Gangqiao Kuang Wenjing Tao Shuqing Zheng Xiaoshuang Wang Deshou Wang |
author_facet |
Gangqiao Kuang Wenjing Tao Shuqing Zheng Xiaoshuang Wang Deshou Wang |
author_sort |
Gangqiao Kuang |
title |
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
title_short |
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
title_full |
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
title_fullStr |
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
title_full_unstemmed |
Genome-Wide Identification, Evolution and Expression of the Complete Set of Cytoplasmic Ribosomal Protein Genes in Nile Tilapia |
title_sort |
genome-wide identification, evolution and expression of the complete set of cytoplasmic ribosomal protein genes in nile tilapia |
publisher |
MDPI AG |
publishDate |
2020 |
url |
https://doi.org/10.3390/ijms21041230 https://doaj.org/article/1b7b1bc919904b0d94da9d5bae4b24fd |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
International Journal of Molecular Sciences, Vol 21, Iss 4, p 1230 (2020) |
op_relation |
https://www.mdpi.com/1422-0067/21/4/1230 https://doaj.org/toc/1422-0067 1422-0067 doi:10.3390/ijms21041230 https://doaj.org/article/1b7b1bc919904b0d94da9d5bae4b24fd |
op_doi |
https://doi.org/10.3390/ijms21041230 |
container_title |
International Journal of Molecular Sciences |
container_volume |
21 |
container_issue |
4 |
container_start_page |
1230 |
_version_ |
1766363168846643200 |