Transcriptome analysis revealed positive selection of immune-related genes in tilapia
Transcriptome analysis revealed positive selection of immune-related genes in tilapia
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转录组分析揭示罗非鱼免疫相关基因的正向选择
DOI：
10.1016/j.fsi.2015.01.022
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发表时间：
2015
影响因子：
4.7
通讯作者：
Yi Zhou
中科院分区：
文献类型：
--
作者：
Jun Xiao;Huan Zhong;Zhen Liu;Fan Yu;Yongju Luo;Xi Gan;Yi Zhou
转录组的高通量测序为检测物种间的进化差异提供了一种新的方法。到目前为止，关于养殖鱼类，特别是罗非鱼免疫基因进化的信息还很少，这有助于了解免疫表型分化的分子基础。因此，在本研究中，我们利用高通量测序技术获得了大量的蓝罗非鱼基因序列，并对尼罗罗非鱼、蓝罗非鱼和斑马鱼的同源基因的多样性进行了分析。从蓝罗非鱼混合组织(包括脑、垂体、鳃、心、肝、脾、肾、肠、肌肉、睾丸和卵巢)的cDNA文库中获得了52,424,506个粗读片段，代表31,404个非特征基因。根据Ks值计算出尼罗罗非鱼和蓝罗非鱼的分化时间为293万年前。罗非鱼和斑马鱼在1.97亿年前都是分开的。此外，通过计算Ka/Ks比值对阳性选择基因进行了鉴定。有几个免疫相关基因被鉴定为阳性选择基因，如Notch2和nFATC3b。考虑到这些基因在免疫调节功能中起着至关重要的作用，罗非鱼的免疫系统基因在环境选择下发生了很大的变化，这表明养殖罗非鱼免疫系统的进化速度很快。
High-throughput sequencing of transcriptome promises a new approach for detecting evolutionary divergence among species. Up to now, the information about evolution of immune genes in cultured fish, especially in tilapias which would aid to understand the molecular basis of immune phenotypic differentiation is still lack. Thus, in the present study, we used high-throughput sequencing to obtain large amount of gene sequences in blue tilapia and characterized the diversity of orthologs among Nile tilapia, blue tilapia and zebrafish. A total of 52,424,506 raw reads, representing 31,404 unigenes were obtained from blue tilapia cDNA library of mixed tissues, including brain, pituitary, gill, heart, liver, spleen, kidney, intestine, muscle, testis and ovary. Based on Ks value, we calculated that the divergence time between Nile tilapia and blue tilapia is 2.93 million years ago. And the tilapias are both apart from zebrafish in 197 million years ago. Furthermore, the positive selected genes were identified by calculating of Ka/Ks ratio. Several immune-related genes were identified as positively selected genes, such as Notch2 and nfatc3b. Considering that these genes play crucial role in immune regulating function, the immune system genes met a great variation under environment selection in tilapias which suggests fast evolution in immune system of cultured tilapias.