Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing

Author(s)

Barbosa, David Aciole ^[1] ; Araujo, Bruno C. ^[2] ; Branco, Giovana Souza ^[3] ; Simeone, Alexandre S. ^[1] ; Hilsdorf, Alexandre W. S. ^[1] ; Jabes, Daniela L. ^[1] ; Nunes, Luiz R. ^[4] ; Moreira, Renata G. ^[3] ; Menegidio, Fabiano B. ^[1]

Affiliation

^[1] Univ Mogi das Cruzes, Ctr Biotechnol, Ctr Civ, Av Dr Candido X de Almeida E Souza 200, BR-08780911 Mogi Das Cruzes, SP - Brazil

^[2] Cawthron Inst, Nelson 7010 - New Zealand

^[3] Univ Sao Paulo, Biosci Inst, Dept Physiol, BR-05508090 Sao Paulo - Brazil

^[4] Fed Univ ABC, Ctr Nat & Human Sci, BR-09210580 Santo Andre, SP - Brazil

• Document type: Journal article
• Source: MARINE BIOTECHNOLOGY; DEC 2021.
• Web of Science Citations: 0

Abstract

Cobia (Rachycentron canadum) is a marine teleost species with great productive potential worldwide. However, the genomic information currently available for this species in public databases is limited. Such lack of information hinders gene expression assessments that might bring forward novel insights into the physiology, ecology, evolution, and genetics of this potential aquaculture species. In this study, we report the first de novo transcriptome assembly of R. canadum liver, improving the availability of novel gene sequences for this species. Illumina sequencing of liver transcripts generated 1,761,965,794 raw reads, which were filtered into 1,652,319,304 high-quality reads. De novo assembly resulted in 101,789 unigenes and 163,096 isoforms, with an average length of 950.61 and 1,617.34 nt, respectively. Moreover, we found that 126,013 of these transcripts bear potentially coding sequences, and 125,993 of these elements (77.3%) correspond to functionally annotated genes found in six different databases. We also identified 701 putative ncRNA and 35,414 putative lncRNA. Interestingly, homologues for 410 of these putative lncRNAs have already been observed in previous analyses with Danio rerio, Lates calcarifer, Seriola lalandi dorsalis, Seriola dumerili, or Echeneis naucrates. Finally, we identified 7894 microsatellites related to cobia's putative lncRNAs. Thus, the information derived from the transcriptome assembly described herein will likely assist future nutrigenomics and breeding programs involving this important fish farming species. (AU)

• FAPESP's process: 19/26018-0 - Lipid metabolism of bijupirá, Rachycentron canadum juveniles during the postprandial period and using alternative fatty acid sources
• Grantee: Renata Guimarães Moreira Whitton
• Support Opportunities: Regular Research Grants