Sequencing and de novo assembly of the red cusk-eel (Genypterus chilensis) transcriptome

Aedo, J.E.; Maldonado J.; Estrada, J.M.; Fuentes E.N.; Silva H.; Gallardo-Escarate, C; Molina A.; Valdes J.A.

Abstract

The red cusk-eel (Genypterus chilensis) is an endemic fish species distributed along the coasts of the Eastern South Pacific. Biological studies on this fish are scarce, and genomic information for G. chilensis is practically nonexistent Thus, transcriptome information for this species is an essential resource that will greatly enrich molecular information and benefit future studies of red cusk-eel biology. In this work, we obtained transcriptome information of G. chilensis using the Illumina platform. The RNA sequencing generated 66,307,362 and 59,925,554 paired-end reads from skeletal muscle and liver tissues, respectively. De novo assembly using the CLC Genomic Workbench version 7.0.3 produced 48,480 contigs and created a reference transcriptome with a N50 of 846 bp and average read coverage of 28.3x. By sequence similarity search for known proteins, a total of 21,272 (43.9%) contigs were annotated for their function. Out of these annotated contigs, 335% GO annotation results for biological processes, 32.6% GO annotation results for cellular components and 34.5% GO annotation results for molecular functions. This dataset represents the first transcriptomic resource for the red cusk-eel and for a member of the Ophidiimorpharia taxon. (C) 2014 Elsevier B.V. All rights reserved.

Más información

Título de la Revista: MARINE GENOMICS
Volumen: 18
Asunto: PB
Editorial: ELSEVIER SCIENCE BV
Fecha de publicación: 2014-01-01
Página de inicio: 105
Página final: 107
Idioma: English
DOI/URL:

10.1016/j.margen.2014.08.001

Identificador: 10.1016/j.margen.2014.08.001
Notas: ISI, SCOPUS