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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Bibliographic Details
Published in:Biotechnology & Biotechnological Equipment
Main Authors: Huan Zhong, Hong Zhang, Zhanyang Tang, Zhongbao Guo, Jinpeng Yan, Jun Xiao, Yongju Luo, Yi Zhou
Format: Article in Journal/Newspaper
Language:English
Published: Taylor & Francis Group 2018
Subjects:
Parachromis managuensis
adaptation
positive selection
transcriptome
Biotechnology
TP248.13-248.65
atlantic cod
Gadus morhua
Online Access:https://doi.org/10.1080/13102818.2018.1519377
https://doaj.org/article/78fa6e7860914fffb3dbc1423af9e5a7
Description
Summary: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.

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