De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean

Javier Hernández-Fernández; Andrés Pinzón; Leonardo Mariño-Ramírez

doi:10.1016/j.gdata.2017.06.005

De novo transcriptome assembly of loggerhead sea turtle nesting of the Colombian Caribbean

Genom Data. 2017 Jun 8:13:18-20. doi: 10.1016/j.gdata.2017.06.005. eCollection 2017 Sep.

Authors

Javier Hernández-Fernández^{1

2}, Andrés Pinzón³, Leonardo Mariño-Ramírez⁴

Affiliations

¹ Genetics, Molecular Biology and Bioinformatics Lab, Department of Natural and Environmental Sciences, Universidad Jorge Tadeo Lozano, Cra. 4 N° 22-61 modulo 7 Piso 6, Bogotá D. C., Colombia.
² Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
³ Bioinformatics and Systems Biology Group, National University of Colombia, Bogotá, Colombia.
⁴ NCBI, NLM, NIH Computational Biology Branch, Building 38A, Room 6S614M 8600 Rockville Pike, MSC 6075 Bethesda, MD 20894-6075, United States.

Abstract

Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads. Trinity pipeline was used to perform a de-novo assembly, we were able to identify 64,930 transcripts for female loggerhead turtle transcriptome with an N50 of 1131 bp. The obtained transcriptome data will be useful for further studies of the physiology, biochemistry and evolution in this species.

Keywords: Caretta caretta turtle; Illumina; N50; RNAseq; Trinity.

Abstract

Grants and funding