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Chromosome-level genome assembly of a high-altitude-adapted frog (Rana kukunoris) from the Tibetan plateau provides insight into amphibian genome evolution and adaptation

Authors :
Wei Chen
Hongzhou Chen
Jiahong Liao
Min Tang
Haifen Qin
Zhenkun Zhao
Xueyan Liu
Yanfang Wu
Lichun Jiang
Lixia Zhang
Bohao Fang
Xueyun Feng
Baowei Zhang
Kerry Reid
Juha Merilä
Source :
Frontiers in Zoology, Vol 20, Iss 1, Pp 1-12 (2023)
Publication Year :
2023
Publisher :
BMC, 2023.

Abstract

Abstract Background The high-altitude-adapted frog Rana kukunoris, occurring on the Tibetan plateau, is an excellent model to study life history evolution and adaptation to harsh high-altitude environments. However, genomic resources for this species are still underdeveloped constraining attempts to investigate the underpinnings of adaptation. Results The R. kukunoris genome was assembled to a size of 4.83 Gb and the contig N50 was 1.80 Mb. The 6555 contigs were clustered and ordered into 12 pseudo-chromosomes covering ~ 93.07% of the assembled genome. In total, 32,304 genes were functionally annotated. Synteny analysis between the genomes of R. kukunoris and a low latitude species Rana temporaria showed a high degree of chromosome level synteny with one fusion event between chr11 and chr13 forming pseudo-chromosome 11 in R. kukunoris. Characterization of features of the R. kukunoris genome identified that 61.5% consisted of transposable elements and expansions of gene families related to cell nucleus structure and taste sense were identified. Ninety-five single-copy orthologous genes were identified as being under positive selection and had functions associated with the positive regulation of proteins in the catabolic process and negative regulation of developmental growth. These gene family expansions and positively selected genes indicate regions for further interrogation to understand adaptation to high altitude. Conclusions Here, we reported a high-quality chromosome-level genome assembly of a high-altitude amphibian species using a combination of Illumina, PacBio and Hi-C sequencing technologies. This genome assembly provides a valuable resource for subsequent research on R. kukunoris genomics and amphibian genome evolution in general.

Details

Language :
English
ISSN :
17429994
Volume :
20
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Frontiers in Zoology
Publication Type :
Academic Journal
Accession number :
edsdoj.4bcaf645184838ac800261d5987d12
Document Type :
article
Full Text :
https://doi.org/10.1186/s12983-022-00482-9