Chromosome-level assembly of Gymnocypris eckloni genome
Fayan Wang, Lihan Wang, Dan Liu, Qiang Gao, Miaomiao Nie, Shihai Zhu, Chao Yan, Chaojie Yang, Cunfang Zhang, Rigui Yi, Weilin Ni, Fei Tian, Kai Zhao, Delin Qi
Abstract
Gymnocypris eckloni is widely distributed in isolated lakes and the upper reaches of the Yellow River and play significant roles in the trophic web of freshwater communities. In this study, we generated a chromosome-level genome of G. eckloni using PacBio, Illumina and Hi-C sequencing data. The genome consists of 23 pseudo-chromosomes that contain 918.68 Mb of sequence, with a scaffold N50 length of 43.54 Mb. In total, 23,157 genes were annotated, representing 94.80% of the total predicted protein-coding genes. The phylogenetic analysis showed that G. eckloni was most closely related to C. carpio with an estimated divergence time of ~34.8 million years ago. For G. eckloni, we identified a high-quality genome at the chromosome level. This genome will serve as a valuable genomic resource for future research on the evolution and ecology of the schizothoracine fish in the Qinghai-Tibetan Plateau.