Abstract
BackgroundTissue 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.ResultsUsing 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.ConclusionsWe 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.
Highlights
Tissue regeneration is widely distributed across the tree of life
We identified genes from B. ramosi that are differentially expressed during limb regeneration, including multiple conserved protein-coding genes, noncoding RNAs, and putative species-specific genes
Large divergences were expected between salamanders species (180 Million years ago (MYA)), the frequencies of the % identity between B. ramosi vs N. viridescens and B. ramosi vs A. mexicanum during the RHB-Blast showing than the major of the matches were > 80% (Additional file 6)
Summary
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. Molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. Studies of relatively few species suggest that salamanders, in general, have a broad capacity to regenerate different tissues and organs, including the heart, brain, jaws, tail and the complex structures of complete limbs [2]. Transcriptional analyses of limb regeneration have been limited to just a few ambystomatid and salamandrid species (Table 1), with the most transcript data generated for A. mexicanum [7, 8] and N. viridescens [9]. Transcriptomic data were recently generated for the Chinese giant salamander (Andrias davidianus; Family Cryptobranchidae) [10] and Chinese salamander Reference Goal Species Tissue Year Technique.
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