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De Novo Transcriptome Characterization and Growth-Related Gene Expression Profiling of Diploid and Triploid Bighead Catfish (Clarias macrocephalus Günther, 1864).
- Source :
-
Marine biotechnology (New York, N.Y.) [Mar Biotechnol (NY)] 2017 Feb; Vol. 19 (1), pp. 36-48. Date of Electronic Publication: 2017 Feb 08. - Publication Year :
- 2017
-
Abstract
- To enhance understanding of triploid gene expression, the transcriptome information from bighead catfish (Clarias macrocephalus Günther, 1864) was studied using the paired-end Illumina HiSeq™ 2000 sequencing platform. In total, 68,227,832 raw reads were generated from liver tissues and 53,149 unigenes were assembled, with an average length of 765 bp and N50 length of 1283 bp. Of these unigenes, 33,428 (62.89%) could be annotated according to their homology with matches in the NCBI non-redundant (Nr), NCBI nucleotide (Nt), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Relative expression of liver genes between diploid and triploid bighead catfish revealed more than 90% of the annotated unigenes similarly expressed, regardless of ploidy, whereas 362 upregulated and 83 downregulated with at least a twofold change in triploid relative to diploid. Quantitative real-time PCR of 15 differentially expressed growth-related genes showed consistency between the expression profiles of those genes with the results from RNA-seq analysis. Our results showed that genes in C. macrocephalus liver responded independently to triploidy with the majority showing similar expression levels between diploid and triploid (a dosage compensation phenomenon). The underlying mechanism of the varying gene expression patterns was discussed. Notably, 5 of the top 20 upregulated genes associated with stress response and thus may reflect stress caused by triploidy. The present study adds a substantial contribution to the sequence data available for C. macrocephalus and hence provides valuable resources for further studies. Furthermore, it gives information that may enhance understanding of triploid physiology.
- Subjects :
- Animals
Catfishes growth & development
Contig Mapping
Female
Gene Expression Profiling
Gene Ontology
High-Throughput Nucleotide Sequencing
Male
Molecular Sequence Annotation
Catfishes genetics
Diploidy
Fish Proteins genetics
Gene Expression Regulation, Developmental
Genome
Transcriptome
Triploidy
Subjects
Details
- Language :
- English
- ISSN :
- 1436-2236
- Volume :
- 19
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Marine biotechnology (New York, N.Y.)
- Publication Type :
- Academic Journal
- Accession number :
- 28181037
- Full Text :
- https://doi.org/10.1007/s10126-017-9730-3