Related Experiment Video
Updated: Feb 1, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
Published on: May 9, 2017
Tissue-based transcriptomics of Chionodraco hamatus: Sequencing, de novo assembly, annotation and marker discovery
Wei Song1, Lingzhi Li1, Hongliang Huang1
1Key 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.
Abstract:
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.
Related Concept Videos
Genome Annotation and Assembly
Drug Discovery: Overview
Cis-regulatory Sequences
Protein Complex Assembly
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Sequences
Sanger Sequencing

