Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing
Evidence for natural selection of immune genes from Parachromis managuensis by transcriptome sequencing
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DOI：
10.1080/13102818.2018.1519377
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发表时间：
2018-10
影响因子：
1.4
通讯作者：
H. Zhong;Hong Zhang;Zhanyang Tang;Zhongbao Guo;Jinpeng Yan;Jun Xiao;Yongju Luo;Yi Zhou
中科院分区：
文献类型：
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作者：
H. Zhong;Hong Zhang;Zhanyang Tang;Zhongbao Guo;Jinpeng Yan;Jun Xiao;Yongju Luo;Yi Zhou
摘要 Parachromis managuensis 是一种原产于中美洲的丽鱼科鱼类，最近被引入中国南方。本研究旨在利用转录组数据识别 P. managuensis 的适应性进化，并提供有关中国这种新鱼类的遗传信息。我们从 P. managuensis 的混合 cDNA 文库中获得了转录组序列。从cDNA文库中总共获得了19,419,739个原始读数。从头组装总共生成了 102,977 个 unigene。大西洋鳕鱼 (Gadus morhua) 和尼罗罗非鱼 (Oreochromis niloticus) 的基因组数据用于通过系统发育分析来鉴定直系同源物。基于系统发育，我们从6197个直系同源unigenes中检测到了P. managuensis中的105个正选基因。 GO注释显示，“免疫系统过程”类别中的T-box蛋白20（TBX20）被正选，通过KEGG分析，在“免疫系统”通路中发现了4个正选基因。其中，编码磷酸肌醇3激酶接头蛋白1、ras相关蛋白Rap-1b、补体因子I和可能的ATP依赖性RNA解旋酶DHX58的基因与免疫适应相关。这些发现可以提供有关 P. managuensis 自然选择的更多信息，并可以作为未来比较转录组和免疫学研究的代表性例子。
Abstract 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.