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

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

Resultado de la investigación: Article

8 Citas (Scopus)

Resumen

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 non-existent. 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 28.3. ×. 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, 33.5% 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.

Idioma originalEnglish
Páginas (desde-hasta)105-107
Número de páginas3
PublicaciónMarine Genomics
Volumen18
N.ºPB
DOI
EstadoPublished - 1 dic 2014

Huella dactilar

Eels
eel
Transcriptome
transcriptome
Fishes
RNA Sequence Analysis
Biological Phenomena
genomics
Skeletal Muscle
resource
fish
transcriptomics
biological processes
skeletal muscle
RNA
Muscles
muscle
sequence analysis
Liver
coasts

ASJC Scopus subject areas

  • Aquatic Science
  • Genetics

Citar esto

Aedo, J. E. ; Maldonado, J. ; Estrada, J. M. ; Fuentes, E. N. ; Silva, H. ; Gallardo-Escarate, C. ; Molina, A. ; Valdés, J. A. / Sequencing and de novo assembly of the red cusk-eel (Genypterus chilensis) transcriptome. En: Marine Genomics. 2014 ; Vol. 18, N.º PB. pp. 105-107.
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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 non-existent. 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 28.3. ×. 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, 33.5{\%} 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.",
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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.; Valdés, J. A.

En: Marine Genomics, Vol. 18, N.º PB, 01.12.2014, p. 105-107.

Resultado de la investigación: Article

TY - JOUR

T1 - Sequencing and de novo assembly of the red cusk-eel (Genypterus chilensis) transcriptome

AU - Aedo, J. E.

AU - Maldonado, J.

AU - Estrada, J. M.

AU - Fuentes, E. N.

AU - Silva, H.

AU - Gallardo-Escarate, C.

AU - Molina, A.

AU - Valdés, J. A.

PY - 2014/12/1

Y1 - 2014/12/1

N2 - 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 non-existent. 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 28.3. ×. 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, 33.5% 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.

AB - 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 non-existent. 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 28.3. ×. 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, 33.5% 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.

KW - Liver transcriptome

KW - NGS

KW - Red cusk-eel

KW - Skeletal muscle transcriptome

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