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

David Aciole Barbosa1, Bruno C Araújo2, Giovana Souza Branco3

  • 1Center of Biotechnology, University of Mogi das Cruzes, Av. Dr. Cândido X. de Almeida e Souza, 200 - Centro Cívico, Mogi das Cruzes, SP, 08780-911, Brazil.

Marine Biotechnology (New York, N.Y.)
|December 2, 2021
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Summary

This study presents the first de novo transcriptome assembly for cobia (Rachycentron canadum), a valuable aquaculture species. This genomic resource enhances our understanding of cobia

Keywords:
AquacultureCobiaLncRNAMicrosatellitesRachycentron canadumTranscriptome

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Area of Science:

  • Marine Biology
  • Genomics
  • Aquaculture Science

Background:

  • Cobia (Rachycentron canadum) is a globally significant marine aquaculture species.
  • Limited genomic information for cobia hinders research into its physiology, ecology, evolution, and genetics.
  • Addressing this gap is crucial for advancing aquaculture and understanding this species.

Purpose of the Study:

  • To perform the first de novo transcriptome assembly for Rachycentron canadum liver.
  • To expand the available gene sequence data for cobia.
  • To provide a foundation for future research in cobia genetics and aquaculture.

Main Methods:

  • Illumina sequencing of liver transcripts generated over 1.6 billion high-quality reads.
  • De novo assembly yielded 101,789 unigenes and 163,096 isoforms.
  • Functional annotation was performed against six public databases.

Main Results:

  • The assembly produced over 100,000 unigenes, with 77.3% functionally annotated.
  • Identified 701 putative non-coding RNAs (ncRNAs) and 35,414 putative long non-coding RNAs (lncRNAs).
  • Discovered 7,894 microsatellites associated with cobia lncRNAs, with 410 lncRNAs showing homology to other fish species.

Conclusions:

  • This transcriptome assembly significantly enhances the genomic resources for Rachycentron canadum.
  • The identified genes, ncRNAs, lncRNAs, and microsatellites will support future nutrigenomics and breeding programs.
  • This work provides critical data for advancing the aquaculture of this important fish species.