De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins

PeerJ

article

Javier Hernández-Fernández¹  Andrés Mauricio Pinzón Velasco³  Ellie Anne López Barrera⁴  María Del Pilar Rodríguez Becerra¹  José Luis Villanueva-Cañas⁵  M. Mar Alba⁶  Leonardo Mariño Ramírez⁸ 

[1] Department of Natural and Environmental Sciences, Faculty of Science and Engineering, Genetics, Molecular Biology and Bioinformatic Research Group—GENBIMOL, Universidad Jorge Tadeo Lozano;Faculty of Sciences, Department of Biology, Pontificia Universidad Javeriana;Grupo de Bioinformática y Biología de Sistemas, Universidad Nacional de Colombia;Institute of Environmental Studies and Services. IDEASA Research Group—IDEASA, Sergio Arboleda University;Molecular Biology CORE ,(CDB), Hospital Clínic de Barcelona;Evolutionary Genomics Group, Research Program on Biomedical Informatics ,(GRIB), Hospital del Mar Research Institute ,(IMIM), Universitat Pompeu Fabra;Catalan Institution for Research and Advanced Studies;Computational Biology Branch

关键词: Caretta caretta;    Transcriptome;    Peroxiredoxin;    Thioredoxin;    KEGG pathway;    Blood;    RNA-seq;    3D modelling;   

DOI  :  10.7717/peerj.12395

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

The aim of this study was to generate and analyze the atlas of the loggerhead turtle blood transcriptome by RNA-seq, as well as identify and characterize thioredoxin (Tnxs) and peroxiredoxin (Prdxs) antioxidant enzymes of the greatest interest in the control of peroxide levels and other biological functions. The transcriptome of loggerhead turtle was sequenced using the Illumina Hiseq 2000 platform and de novo assembly was performed using the Trinity pipeline. The assembly comprised 515,597 contigs with an N50 of 2,631 bp. Contigs were analyzed with CD-Hit obtaining 374,545 unigenes, of which 165,676 had ORFs encoding putative proteins longer than 100 amino acids. A total of 52,147 (31.5%) of these transcripts had significant homology matches in at least one of the five databases used. From the enrichment of GO terms, 180 proteins with antioxidant activity were identified, among these 28 Prdxs and 50 putative Tnxs. The putative proteins of loggerhead turtles encoded by the genes Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip were predicted and characterized in silico. When comparing Prdxs and Txns of loggerhead turtle with homologous human proteins, they showed 18 (9%), 52 (18%) 94 (43%), 36 (16%), 35 (33%) and 74 (19%) amino acid mutations respectively. However, they showed high conservation in active sites and structural motifs (98%), with few specific modifications. Of these, Prdx1, Prdx3, Prdx5, Prdx6, Txn and Txnip presented 0, 25, 18, three, six and two deleterious changes. This study provides a high quality blood transcriptome and functional annotation of loggerhead sea turtles.

【 授权许可】

CC BY