Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing
Parachromis managuensis is a native cichlid fish from Central America that has been recently introduced to Southern China. The present study aimed to identify the adaptive evolution of P. managuensis using transcriptome data and provided genetic information regarding this novel fish in China. We obt...
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ftdoajarticles:oai:doaj.org/article:78fa6e7860914fffb3dbc1423af9e5a7 2023-05-15T15:27:39+02:00 Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing Huan Zhong Hong Zhang Zhanyang Tang Zhongbao Guo Jinpeng Yan Jun Xiao Yongju Luo Yi Zhou 2018-11-01T00:00:00Z https://doi.org/10.1080/13102818.2018.1519377 https://doaj.org/article/78fa6e7860914fffb3dbc1423af9e5a7 EN eng Taylor & Francis Group http://dx.doi.org/10.1080/13102818.2018.1519377 https://doaj.org/toc/1310-2818 https://doaj.org/toc/1314-3530 1310-2818 1314-3530 doi:10.1080/13102818.2018.1519377 https://doaj.org/article/78fa6e7860914fffb3dbc1423af9e5a7 Biotechnology & Biotechnological Equipment, Vol 32, Iss 6, Pp 1431-1439 (2018) Parachromis managuensis adaptation positive selection transcriptome Biotechnology TP248.13-248.65 article 2018 ftdoajarticles https://doi.org/10.1080/13102818.2018.1519377 2022-12-31T03:48:37Z Parachromis managuensis is a native cichlid fish from Central America that has been recently introduced to Southern China. The present study aimed to identify the adaptive evolution of P. managuensis using transcriptome data and provided genetic information regarding this novel fish in China. We obtained the transcriptome sequences from a mixed cDNA library of P. managuensis. A total of 19,419,739 raw reads were obtained from the cDNA library. The de novo assembly generated a total of 102,977 unigenes. The genomic data of Atlantic cod (Gadus morhua) and Nile tilapia (Oreochromis niloticus) were used to identify orthologs by phylogenetic analysis. Based on the phylogeny, we detected 105 positively selected genes in P. managuensis from 6197 orthologous unigenes. The GO annotation revealed that the T-box protein 20 (TBX20) in the category ‘Immune system process’ was positively selected and four positively selected genes were found in the ‘Immune system’ pathway by KEGG analysis. Among them, the genes encoding for phosphoinositide 3-kinase adapter protein 1, ras-related protein Rap-1b, complement factor I and probable ATP-dependent RNA helicase DHX58 were associated with immune adaptation. These findings can provide additional information regarding the natural selection of P. managuensis and can be used as a representative example for future comparative transcriptome and immunological studies. Article in Journal/Newspaper atlantic cod Gadus morhua Directory of Open Access Journals: DOAJ Articles Biotechnology & Biotechnological Equipment 32 6 1431 1439 |
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Parachromis managuensis adaptation positive selection transcriptome Biotechnology TP248.13-248.65 |
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Parachromis managuensis adaptation positive selection transcriptome Biotechnology TP248.13-248.65 Huan Zhong Hong Zhang Zhanyang Tang Zhongbao Guo Jinpeng Yan Jun Xiao Yongju Luo Yi Zhou Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
topic_facet |
Parachromis managuensis adaptation positive selection transcriptome Biotechnology TP248.13-248.65 |
description |
Parachromis managuensis is a native cichlid fish from Central America that has been recently introduced to Southern China. The present study aimed to identify the adaptive evolution of P. managuensis using transcriptome data and provided genetic information regarding this novel fish in China. We obtained the transcriptome sequences from a mixed cDNA library of P. managuensis. A total of 19,419,739 raw reads were obtained from the cDNA library. The de novo assembly generated a total of 102,977 unigenes. The genomic data of Atlantic cod (Gadus morhua) and Nile tilapia (Oreochromis niloticus) were used to identify orthologs by phylogenetic analysis. Based on the phylogeny, we detected 105 positively selected genes in P. managuensis from 6197 orthologous unigenes. The GO annotation revealed that the T-box protein 20 (TBX20) in the category ‘Immune system process’ was positively selected and four positively selected genes were found in the ‘Immune system’ pathway by KEGG analysis. Among them, the genes encoding for phosphoinositide 3-kinase adapter protein 1, ras-related protein Rap-1b, complement factor I and probable ATP-dependent RNA helicase DHX58 were associated with immune adaptation. These findings can provide additional information regarding the natural selection of P. managuensis and can be used as a representative example for future comparative transcriptome and immunological studies. |
format |
Article in Journal/Newspaper |
author |
Huan Zhong Hong Zhang Zhanyang Tang Zhongbao Guo Jinpeng Yan Jun Xiao Yongju Luo Yi Zhou |
author_facet |
Huan Zhong Hong Zhang Zhanyang Tang Zhongbao Guo Jinpeng Yan Jun Xiao Yongju Luo Yi Zhou |
author_sort |
Huan Zhong |
title |
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
title_short |
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
title_full |
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
title_fullStr |
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
title_full_unstemmed |
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing |
title_sort |
evidence for natural selection of immune genes from parachromis managuensis by transcriptome sequencing |
publisher |
Taylor & Francis Group |
publishDate |
2018 |
url |
https://doi.org/10.1080/13102818.2018.1519377 https://doaj.org/article/78fa6e7860914fffb3dbc1423af9e5a7 |
genre |
atlantic cod Gadus morhua |
genre_facet |
atlantic cod Gadus morhua |
op_source |
Biotechnology & Biotechnological Equipment, Vol 32, Iss 6, Pp 1431-1439 (2018) |
op_relation |
http://dx.doi.org/10.1080/13102818.2018.1519377 https://doaj.org/toc/1310-2818 https://doaj.org/toc/1314-3530 1310-2818 1314-3530 doi:10.1080/13102818.2018.1519377 https://doaj.org/article/78fa6e7860914fffb3dbc1423af9e5a7 |
op_doi |
https://doi.org/10.1080/13102818.2018.1519377 |
container_title |
Biotechnology & Biotechnological Equipment |
container_volume |
32 |
container_issue |
6 |
container_start_page |
1431 |
op_container_end_page |
1439 |
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1766358072863752192 |