A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

Claudia M. Arenas Gómez; M. Ryan Woodcock; Jeramiah J. Smith; S. Randal Voss; Jean Paul Delgado

doi:10.1016/j.dib.2020.105256

A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

Claudia M. Arenas Gómez, M. Ryan Woodcock, Jeramiah J. Smith, S. Randal Voss, Jean Paul Delgado

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.

Original language	English
Article number	105256
Journal	Data in Brief
Volume	29
DOIs	https://doi.org/10.1016/j.dib.2020.105256
State	Published - Apr 2020

Bibliographical note

Funding Information:
This work was funded by a research grant from COLCIENCIAS 569 (GRANT 027-2103 ) and CODI (Programa Sostenibilidad) 2013–2014 of the University of Antioquia . A PhD fellowship to the first author, Claudia Arenas was funded by the COLCIENCIAS 567 Grant. We thank the lab of Juan Fernando Alzate from the University of Antioquia for their help in developing our bioinformatic methodological approach. We thank Andrea Gómez and Melisa Hincapie for their help in animal collection and husbandry.

Publisher Copyright:
© 2020 The Authors

Keywords

Bolitoglossa
Plethodontid
Salamanders
Skin
Transcriptomics

ASJC Scopus subject areas

General

Access to Document

10.1016/j.dib.2020.105256

Cite this

@article{218ef46432d6464fa7ab74175d8aed3e,

title = "A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia",

abstract = "The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.",

keywords = "Bolitoglossa, Plethodontid, Salamanders, Skin, Transcriptomics",

author = "{Arenas G{\'o}mez}, {Claudia M.} and Woodcock, {M. Ryan} and Smith, {Jeramiah J.} and Voss, {S. Randal} and Delgado, {Jean Paul}",

note = "Funding Information: This work was funded by a research grant from COLCIENCIAS 569 (GRANT 027-2103 ) and CODI (Programa Sostenibilidad) 2013–2014 of the University of Antioquia . A PhD fellowship to the first author, Claudia Arenas was funded by the COLCIENCIAS 567 Grant. We thank the lab of Juan Fernando Alzate from the University of Antioquia for their help in developing our bioinformatic methodological approach. We thank Andrea G{\'o}mez and Melisa Hincapie for their help in animal collection and husbandry. Publisher Copyright: {\textcopyright} 2020 The Authors",

year = "2020",

month = apr,

doi = "10.1016/j.dib.2020.105256",

language = "English",

volume = "29",

}

TY - JOUR

T1 - A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

AU - Arenas Gómez, Claudia M.

AU - Woodcock, M. Ryan

AU - Smith, Jeramiah J.

AU - Voss, S. Randal

AU - Delgado, Jean Paul

N1 - Funding Information: This work was funded by a research grant from COLCIENCIAS 569 (GRANT 027-2103 ) and CODI (Programa Sostenibilidad) 2013–2014 of the University of Antioquia . A PhD fellowship to the first author, Claudia Arenas was funded by the COLCIENCIAS 567 Grant. We thank the lab of Juan Fernando Alzate from the University of Antioquia for their help in developing our bioinformatic methodological approach. We thank Andrea Gómez and Melisa Hincapie for their help in animal collection and husbandry. Publisher Copyright: © 2020 The Authors

PY - 2020/4

Y1 - 2020/4

N2 - The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.

AB - The amphibian order Caudata, contains several important model species for biological research. However, there is need to generate transcriptome data from representative species of the primary salamander families. Here we describe a de novo reference transcriptome for a terrestrial salamander, Bolitoglossa vallecula (Caudata: Plethodontidae). We employed paired-end (PE) illumina RNA sequencing to assemble a de novo reference transcriptome for B. vallecula. Assembled transcripts were compared against sequences from other vertebrate taxa to identify orthologous genes, and compared to the transcriptome of a close plethodontid relative (Bolitoglossa ramosi) to identify commonly expressed genes in the skin. This dataset should be useful to future comparative studies aimed at understanding important biological process, such as immunity, wound healing, and the production of antimicrobial compounds.

KW - Bolitoglossa

KW - Plethodontid

KW - Salamanders

KW - Skin

KW - Transcriptomics

UR - http://www.scopus.com/inward/record.url?scp=85079602573&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85079602573&partnerID=8YFLogxK

U2 - 10.1016/j.dib.2020.105256

DO - 10.1016/j.dib.2020.105256

M3 - Article

AN - SCOPUS:85079602573

VL - 29

M1 - 105256

ER -

A de novo reference transcriptome for Bolitoglossa vallecula, an Andean mountain salamander in Colombia

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this