Abstract
The Yenyuan stream salamander (Batrachuperus yenyuanensis) has been previously evaluated with regards to phylogeny, population genetics, and hematology, but genomic information is sparse due to the giant genome size of salamanders which contain highly repetitive sequences, thus resulting in the lack of a complete reference genome. This study evaluates the encoding genetic sequences and provides the first transcriptome assembly of Yenyuan stream salamander based on mixed samples from the liver, spermary, muscle and spleen tissues. Using this transcriptome assembly and available encoding sequences from other vertebrates, the gene families, phylogenetic status, and species divergence time were compared or estimated. A total of 13,750 encoding sequences were successfully obtained from the transcriptome assembly of Yenyuan stream salamander, estimated to contain 40.1% of the unigenes represented in tetrapod databases. A total of 88.79% of these genes could be annotated to a biological function by current databases. Through gene family clustering, we found multiple possible isoforms of the Scribble gene—whose function is related to regeneration—based on sequence similarity. Meanwhile, we constructed a robust phylogenetic tree based on 56 single-copy orthologues, which indicates that based on phylogenetic position, the Yenyuan stream salamander presents the closest relationship with the Chinese giant salamander (Andrias davidianus) of the investigated vertebrates. Based on the fossil-calibrated phylogeny, we estimated that the lineage divergence between the ancestral Yenyuan stream salamander and the Chinese giant salamander may have occurred during the Cretaceous period (~78.4 million years ago). In conclusion, this study not only provides a candidate gene that is valuable for exploring the remarkable capacity of regeneration in the future, but also gives an interesting insight into the understanding of Yenyuan stream salamander by this first transcriptome assembly.
Highlights
The Yenyuan stream salamander (Batrachuperus yenyuanensis [1]), belonging to the family Hynobiidae, order Caudata, is an aquatic organism that is endemic to Western China
The tissues were initially placed in a 1.5 mL tube filled with RNAlater (Ambion, Carlsbad, CA, USA)
All salamander handling and experimental procedures performed in this study were approved (January 1, 2015) by the Animal Care and Use Committee of the College of Animal Science and Technology, Henan University of Science and Technology (CAST2015040010)
Summary
The Yenyuan stream salamander (Batrachuperus yenyuanensis [1]), belonging to the family Hynobiidae, order Caudata, is an aquatic organism that is endemic to Western China. Large amounts of high-throughput third-generation sequencing would be expensive for such a large genome size These reasons hinder the completion of whole-genome assembly for salamanders, the corresponding whole protein-encoding sequences present a similar number to other vertebrates. Through RNA-seq, we successfully assembled the first transcriptome of Yenyuan stream salamander We utilized this assembly to compare the inside gene families with other vertebrates, and deduced the phylogenetic position and lineage divergence time between this species and other vertebrates. Using this approach, we attempted to provide an improved recognition of the molecular evolution of Yenyuan stream salamander
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