Using Transcriptomics to Enable a Plethodontid Salamander (Bolitoglossa ramosi) for Limb Regeneration Research

Authors

Claudia M. Arenas Gómez, Universidad de Antioquia, Colombia
Ryan M. Woodcock, University of KentuckyFollow
Jeramiah J. Smith, University of KentuckyFollow
Randal S. Voss, University of KentuckyFollow
Jean Paul Delgado, Universidad de Antioquia, Colombia

Abstract

Background: Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration.

Results: Using paired-end Illumina sequencing technology and Trinity assembly, a total of 433,809 transcripts were recovered and we obtained functional annotation for 142,926 non-redundant transcripts of the B. ramosi de novo reference transcriptome. Among the annotated transcripts, 602 genes were identified as differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor from approximately 180 million years ago.

Conclusions: We identified genes from B. ramosi that are differentially expressed during limb regeneration, including multiple conserved protein-coding genes and possible putative species-specific genes. Comparative analyses reveal a subset of genes that show similar patterns of expression with ambystomatid species, which highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders.

Document Type

Article

Publication Date

9-25-2018

Notes/Citation Information

Published in BMC Genomics, v. 19, 704, p. 1-12.

© The Author(s). 2018

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Digital Object Identifier (DOI)

https://doi.org/10.1186/s12864-018-5076-0

Funding Information

This work was funded by grants from the University of Antioquia (CODI) and COLCIENCIAS (569,027-2013) to JPD and CMAG (COLCIENCIAS 567), the grants allowed the design of the study and collection, analysis, interpretation of data and writing of the manuscript. Grants from the National Institutes of Health (R24OD010435) and Army Research Office (W911NF1410165) supported computational resources, bioinformatics training, data analysis, data interpretation, and manuscript writing efforts of MRW, SRV, and JJS at the University of Kentucky.

Related Content

The raw sequence reads have been deposited in the Sequence Read Archive under the accession number SRP120553. The output from RSEM, EBSeq and assembled transcriptome are deposited in The Gene Expression Omnibus (GEO) under the accession number GSE105232.

Repository Citation

Gómez, Claudia M. Arenas; Woodcock, Ryan M.; Smith, Jeramiah J.; Voss, Randal S.; and Delgado, Jean Paul, "Using Transcriptomics to Enable a Plethodontid Salamander (Bolitoglossa ramosi) for Limb Regeneration Research" (2018). Biology Faculty Publications. 165.
https://uknowledge.uky.edu/biology_facpub/165