Song Wei, Li Lingzhi, Huang Hongliang, Jiang Keji, Zhang Fengying, Wang Luming, Zhao Ming, Ma Lingbo
Key Laboratory of East China Sea and Oceanic Fishery Resources Exploitation, Ministry of Agriculture, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai, China.
J Fish Biol. 2019 Feb;94(2):251-260. doi: 10.1111/jfb.13882. Epub 2019 Jan 13.
Here, we explored the liver, heart and muscle tissue transcriptome of the haemoglobinless Antarctic fish Chionodraco hamatus using the Illumina paired-end RNA sequencing. A total of 114,028 unigenes with a mean length of 794.24 bp was produced. Annotation of these unigenes showed that 29.16% and 35.52% of them had hits in the nucleotide (Nt) and protein (Nr) databases, respectively. In addition, 29.10% and 35.28% unigenes were annotated in the SwissProt and TrEMBL databases while 23.27% and 21.08% of unigenes were annotated in the conserved domain (CCD) and protein family (PFAM) databases, respectively. The results of eukaryotic orthologous groups (KOG) classification analysis showed that around 21.36% of unigenes could be mapped. Differential gene expression analysis indicated that 16,331, 16,291 and 13,262 differentially expressed genes (DEG) could be screened between muscle and heart, muscle and liver and heart and liver, respectively. A significant enrichment analysis of these DEGs revealed their implication in important biological processes, molecular functions, cellular components and diverse pathways. Furthermore, a total of 24,455 simple sequence repeats (SSR) were detected from the generated tissue transcriptome. The transcriptome data produced in this study will constitute an important resource for improving our knowledge of C. hamatus functional genomics and will facilitate future studies regarding this species.
在此，我们利用Illumina双末端RNA测序技术，对无血红蛋白的南极鱼类哈氏冰杜父鱼的肝脏、心脏和肌肉组织转录组进行了探究。共产生了114,028个单基因，平均长度为794.24 bp。对这些单基因的注释表明，其中分别有29.16%和35.52%在核苷酸（Nt）数据库和蛋白质（Nr）数据库中有匹配项。此外，分别有29.10%和35.28%的单基因在SwissProt和TrEMBL数据库中得到注释，而分别有23.27%和21.08%的单基因在保守结构域（CCD）数据库和蛋白质家族（PFAM）数据库中得到注释。真核直系同源组（KOG）分类分析结果表明，约21.36%的单基因可以被定位。差异基因表达分析表明，在肌肉与心脏、肌肉与肝脏以及心脏与肝脏之间，分别可以筛选出16,331个、16,291个和13,262个差异表达基因（DEG）。对这些DEG的显著富集分析揭示了它们在重要生物学过程、分子功能、细胞成分和多种途径中的作用。此外，从生成的组织转录组中总共检测到24,455个简单序列重复（SSR）。本研究产生的转录组数据将成为增进我们对哈氏冰杜父鱼功能基因组学了解的重要资源，并将促进关于该物种的未来研究。
