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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.
Chen, Wei; Chen, Hongzhou; Liao, Jiahong; Tang, Min; Qin, Haifen; Zhao, Zhenkun; Liu, Xueyan; Wu, Yanfang; Jiang, Lichun; Zhang, Lixia; Fang, Bohao; Feng, Xueyun; Zhang, Baowei; Reid, Kerry; Merilä, Juha.
Afiliación
  • Chen W; School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China. wchen1949@163.com.
  • Chen H; Anhui Shengjin Lake Wetland Ecology National Long-Term Scientific Research Base, Dongzhi, 247230, China. wchen1949@163.com.
  • Liao J; Anhui Province Key Laboratory of Wetland Ecosystem Protection and Restoration, Anhui University, Hefei, 230601, China. wchen1949@163.com.
  • Tang M; School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
  • Qin H; School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
  • Zhao Z; School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
  • Liu X; School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
  • Wu Y; School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
  • Jiang L; School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
  • Zhang L; School of Resources and Environmental Engineering, Anhui University, Hefei, 230601, China.
  • Fang B; School of Life Science and Technology, Mianyang Normal University, Mianyang, 621000, Sichuan, China.
  • Feng X; Department of Ecology, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
  • Zhang B; Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, MA, USA.
  • Reid K; Ecological Genetics Research Unit, Research Programme in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
  • Merilä J; School of Life Sciences, Anhui University, Hefei, 230601, China.
Front Zool ; 20(1): 1, 2023 Jan 06.
Article en En | MEDLINE | ID: mdl-36604706
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Prognostic_studies Idioma: En Revista: Front Zool Año: 2023 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Tipo de estudio: Prognostic_studies Idioma: En Revista: Front Zool Año: 2023 Tipo del documento: Article País de afiliación: China Pais de publicación: Reino Unido