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

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 f...

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Autores principales:	Javier Hernández-Fernández, Andrés Mauricio Pinzón Velasco, Ellie Anne López Barrera, María Del Pilar Rodríguez Becerra, José Luis Villanueva-Cañas, M. Mar Alba, Leonardo Mariño Ramírez
Formato:	article
Lenguaje:	EN
Publicado:	PeerJ Inc. 2021
Materias:	Caretta caretta Transcriptome Peroxiredoxin Thioredoxin KEGG pathway Blood Medicine R
Acceso en línea:	https://doaj.org/article/29b5c2671f16400491e50619a2920616
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spelling	oai:doaj.org-article:29b5c2671f16400491e50619a29206162021-11-20T15:05:11ZDe novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins10.7717/peerj.123952167-8359https://doaj.org/article/29b5c2671f16400491e50619a29206162021-11-01T00:00:00Zhttps://peerj.com/articles/12395.pdfhttps://peerj.com/articles/12395/https://doaj.org/toc/2167-8359The 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.Javier Hernández-FernándezAndrés Mauricio Pinzón VelascoEllie Anne López BarreraMaría Del Pilar Rodríguez BecerraJosé Luis Villanueva-CañasM. Mar AlbaLeonardo Mariño RamírezPeerJ Inc.articleCaretta carettaTranscriptomePeroxiredoxinThioredoxinKEGG pathwayBloodMedicineRENPeerJ, Vol 9, p e12395 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Caretta caretta Transcriptome Peroxiredoxin Thioredoxin KEGG pathway Blood Medicine R
spellingShingle	Caretta caretta Transcriptome Peroxiredoxin Thioredoxin KEGG pathway Blood Medicine R Javier Hernández-Fernández Andrés Mauricio Pinzón Velasco Ellie Anne López Barrera María Del Pilar Rodríguez Becerra José Luis Villanueva-Cañas M. Mar Alba Leonardo Mariño Ramírez De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
description	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.
format	article
author	Javier Hernández-Fernández Andrés Mauricio Pinzón Velasco Ellie Anne López Barrera María Del Pilar Rodríguez Becerra José Luis Villanueva-Cañas M. Mar Alba Leonardo Mariño Ramírez
author_facet	Javier Hernández-Fernández Andrés Mauricio Pinzón Velasco Ellie Anne López Barrera María Del Pilar Rodríguez Becerra José Luis Villanueva-Cañas M. Mar Alba Leonardo Mariño Ramírez
author_sort	Javier Hernández-Fernández
title	De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
title_short	De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
title_full	De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
title_fullStr	De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
title_full_unstemmed	De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
title_sort	de novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins
publisher	PeerJ Inc.
publishDate	2021
url	https://doaj.org/article/29b5c2671f16400491e50619a2920616
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De novo assembly and functional annotation of blood transcriptome of loggerhead turtle, and in silico characterization of peroxiredoxins and thioredoxins

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