Multi-Tissue Transcriptomes Yield Information on High-Altitude Adaptation and Sex-Determination in Scutiger cf. sikimmensis.

Sylvia Hofmann,Matthias Stöck,Heiner Kuhl,Chitra Bahadur Baniya

doi:10.3390/genes10110873

Abstract

The Himalayas are one of earth’s hotspots of biodiversity. Among its many cryptic and undiscovered organisms, including vertebrates, this complex high-mountain ecosystem is expected to harbour many species with adaptations to life in high altitudes. However, modern evolutionary genomic studies in Himalayan vertebrates are still at the beginning. Moreover, in organisms, like most amphibians with relatively high DNA content, whole genome sequencing remains bioinformatically challenging and no complete nuclear genomes are available for Himalayan amphibians. Here, we present the first well-annotated multi-tissue transcriptome of a Greater Himalayan species, the lazy toad Scutiger cf. sikimmensis (Anura: Megophryidae). Applying Illumina NextSeq 500 RNAseq to six tissues, we obtained 41.32 Gb of sequences, assembled to ~111,000 unigenes, translating into 54362 known genes as annotated in seven functional databases. We tested 19 genes, known to play roles in anuran and reptile adaptation to high elevations, and potentially detected diversifying selection for two (TGS1, SENP5) in Scutiger. Of a list of 37 genes, we also identify 27 candidate genes for sex determination or sexual development, all of which providing the first such data for this non-model megophryid species. These transcriptomes will serve as a valuable resource for further studies on amphibian evolution in the Greater Himalaya as a biodiversity hotspot.

Highlights

The Himalayas are a distinct biogeographic eco-region with high biodiversity and endemism due to great topographic and climatic variation [1] and isolation
The uplift of Tibet and the Himalayas since about 45 million years ago (Mya), with the Greater Himalayas starting to rise presumably the earliest in the post-Eocene, or even more recently (~20–10 Mya; for a review see the supplementary in Hofmann et al [2]) appears to have resulted in a unique assemblage of species evolved under gradual high-altitude adaptation, as already shown for several Tibetan reptiles [3] and anurans [4,5] as well as interspecies comparisons with evidence for parallel evolution [6,7,8]
With respect to high-altitude adaptation in the Greater Himalayas, there is still a considerable knowledge deficiency as there is a general lack of knowledge about the biodiversity of this high-mountain range, causing its relatively large number of cryptic and undiscovered species [9], even among vertebrates

Summary

Introduction

The Himalayas are a distinct biogeographic eco-region with high biodiversity and endemism due to great topographic and climatic variation [1] and isolation. With respect to high-altitude adaptation in the Greater Himalayas, there is still a considerable knowledge deficiency as there is a general lack of knowledge about the biodiversity of this high-mountain range, causing its relatively large number of cryptic and undiscovered species [9], even among vertebrates. Molecular evolutionary studies of truly Greater Himalayan animal species are extremely rare (e.g., [13]) and, genomic data are lacking for most vertebrates (e.g., a PubMed search for “genomic” and “Himalaya” yielded 72 hits, only 18 when including “vertebrates” but zero for “amphibians”). To allow future studies in population genomics and phylogenetics, for example, using sequences capture approaches and to generally close this major data gap for regional amphibians, in the present paper, we have generated a new molecular marker set based on RNAseq for an anuran species from the Greater Himalaya

Methods

Results

Conclusion