Abstract
To search the evidence of molecular evolution mechanism for aquatic and cave habitat in Andrias davidianus, the evolution analysis was carried out among several species transcriptome data. The transcriptome data of Notophthalmus viridescens, Xenopus tropicalis, Cynops pyrrhogaster, Hynobius chinensis and A. davidianus were obtained from the Genbank and reassembled except Xenopus tropicalis. The BLAST search of transcriptome data obtained 1244 single-copy orthologous genes among five species. A phylogenetic tree showed A. davidianus to have the closest relationship to H. chinensis. Fourteen positively selected genes were detected in A. davidianus and N. vridescens group and fifteen in A. davidianus and H. chinensis group. Five genes were shared in the both groups which involved in the immune system, suggesting that A. davidianus adaptation to an aquatic and cave environment required rapid evolution of the immune system compared to N. viridescens and H. chinensis.
Highlights
Amphibians played an important role as a transitional group linking aquatic to terrestrial in the evolution of vertebrates [1]
Orthologue identification and phylogenetic analysis To identify the phylogenetic relationship among the species, large-scale transcriptome characterizations were carried out for N. viridescens, X. tropicalis, C. pyrrhogaster, H. chinensis, and A. davidianus, and transcriptome data were downloaded and reassembled (Table 1)
The phylogenetic tree showed A. davidianus to have the closest relationship to H. chinensis, with N. viridescens and C. pyrrhogaster clustered on one separate branch (Additional file 1: Figure S1)
Summary
Amphibians played an important role as a transitional group linking aquatic to terrestrial in the evolution of vertebrates [1]. The genome and mitochondrial DNA are traditionally used to estimate divergence time [2]. Transcriptome sequencing has become a viable alternative to provide rapid developing genomic resources in non-model organisms [3, 4]. Comparative transcriptome analysis is used to estimate the non-synonymous substitution (Ka) and synonymous substitution (Ks) rates to calculate the evolutionary rate [5, 6] and to identify genes involved in environmental adaptation. Distribution of synonymous substitutions can be used to calculate the divergent time based on the coding sequence [2, 7]. The Chinese giant salamander Andrias davidianus is a typical urodele, and an important species both as a biological resource and with respect to its value as a living fossil [8]. The species was historically widespread in China, but environmental degradation and human killing have led to its severe decline in the wild.
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