Tissue-based transcriptomics of Chionodraco hamatus: Sequencing, de novo assembly, annotation and marker discovery
文献类型： 外文期刊
作者： Song, Wei 1 ; Li, Lingzhi 1 ; Huang, Hongliang 1 ; Jiang, Keji 1 ; Zhang, Fengying 1 ; Wang, Luming 1 ; Zhao, Ming 2 ; Ma 1 ;
作者机构： 1.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Key Lab East China Sea & Ocean Fishery Resources, Minist Agr, Shanghai 200090, Peoples R China
2.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Key Lab East China Se
关键词： Antarctic fish; differentially expressed genes; endangered species; organ-specific transcriptome
期刊名称：JOURNAL OF FISH BIOLOGY （ 影响因子：2.051； 五年影响因子：2.25 ）
ISSN： 0022-1112
年卷期： 2019 年 94 卷 2 期
页码：
收录情况： SCI
摘要： 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.
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