Comprehensive Transcriptome Analysis of Six Catfish Species from an Altitude Gradient Reveals Adaptive Evolution in Tibetan Fishes

Abstract

Glyptosternoid fishes (Siluriformes), one of the three broad fish lineages (the two other are schizothoracines and Triplophysa), have a limited distribution in the rivers in the Tibetan Plateau and peripheral regions. To investigate the genetic mechanisms underlying adaptation to the Tibetan Plateau in several fish species from gradient altitudes, a total of 20,659,183–37,166,756 sequence reads from six species of catfish were generated by Illumina sequencing, resulting in six assemblies. Analysis of the 1,656 orthologs among the six assembled catfish unigene sets provided consistent evidence for genome-wide accelerated evolution in the three glyptosternoid lineages living at high altitudes. A large number of genes refer to functional categories related to hypoxia and energy metabolism exhibited rapid evolution in the glyptosternoid lineages relative to yellowhead catfish living in plains areas. Genes showing signatures of rapid evolution and positive selection in the glyptosternoid lineages were also enriched in functions associated with energy metabolism and hypoxia. Our analyses provide novel insights into highland adaptation in fishes and can serve as a foundation for future studies aiming to identify candidate genes underlying the genetic basis of adaptation in Tibetan fishes.

Genetic Adaptation of Schizothoracine Fish to the Phased Uplifting of the Qinghai–Tibetan Plateau

“…Yang et al 2015). Transcriptome studies on the Tibetan catfish and loach revealed similar results (Wang et al 2015b; Ma et al 2015). In terms of individual genes, genes that encoding hypoxia inducible factor 1α (Guan et al 2014) and erythropoietin (Xu et al 2016) are involved in hypoxic adaptation in high-altitude species.…”

Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms

“…; Ma et al. ), Andean and Himalayan catfish specialists are likely to experience slowed biochemical processes relative to closely related taxa at lowland temperatures (Siddiqui and Cavicchioli ; Fields et al. ; Åqvist ).…”

“…; Ma et al. ). Although little is known of the molecular adaptations these fishes may have evolved in response to the decreased temperatures, the morphological and biogeographical similarities strongly suggest that these lineages have been subject to very similar high altitude related selection pressures.…”

Comprehensive Transcriptome Analysis Provides Evidence of Local Thermal Adaptation in Three Loaches (Genus: Misgurnus)

“…Since the development of next-generation sequencing technology, RNA-seq has been widely used as an efficient and accessible approach to determine the evolutionary histories of non-model organisms when no genome information is available [28,29,30]. Here, we sequenced and assembled the transcriptomes of three closely related Misgurnus species, M. anguillicaudatus , M. bipartitus , and M. mohoity , to identify the genetic mechanisms in their adaptation to the temperature variations in their environments and provide valuable information for further studies to understand the genetic makeup of other fishes in thermal adaptations.…”

“…The orthologous genes were discarded if N × dN or S × dS < 1 or dS > 1, according to the criterion proposed in a previous studies [28,55]. The evolutionary rates in each lineage were compared using the Wilcoxon rank sum test in R ().…”