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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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2018-11-01
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| Series: | Biotechnology & Biotechnological Equipment |
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| Online Access: | http://dx.doi.org/10.1080/13102818.2018.1519377 |
| _version_ | 1818303480511594496 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-13T05:55:28Z |
| format | Article |
| id | doaj.art-78fa6e7860914fffb3dbc1423af9e5a7 |
| institution | Directory Open Access Journal |
| issn | 1310-2818 1314-3530 |
| language | English |
| last_indexed | 2024-12-13T05:55:28Z |
| publishDate | 2018-11-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Biotechnology & Biotechnological Equipment |
| spelling | doaj.art-78fa6e7860914fffb3dbc1423af9e5a72022-12-21T23:57:26ZengTaylor & Francis GroupBiotechnology & Biotechnological Equipment1310-28181314-35302018-11-013261431143910.1080/13102818.2018.15193771519377Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencingHuan Zhong0Hong Zhang1Zhanyang Tang2Zhongbao Guo3Jinpeng Yan4Jun Xiao5Yongju Luo6Yi Zhou7Guangxi Academy of Fishery SciencesQinzhou UniversityGuangxi Academy of Fishery SciencesGuangxi Academy of Fishery SciencesCentral South UniversityGuangxi Academy of Fishery SciencesGuangxi Academy of Fishery SciencesGuangxi Academy of Fishery SciencesParachromis 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.http://dx.doi.org/10.1080/13102818.2018.1519377Parachromis managuensisadaptationpositive selectiontranscriptome |
| spellingShingle | 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 Biotechnology & Biotechnological Equipment Parachromis managuensis adaptation positive selection transcriptome |
| title | 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_short | 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 |
| topic | Parachromis managuensis adaptation positive selection transcriptome |
| url | http://dx.doi.org/10.1080/13102818.2018.1519377 |
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