Journal Article

Whole-genome sequencing of Sinocyclocheilus maitianheensis reveals phylogenetic evolution and immunological variances in various Sinocyclocheilus fishes

Li, R., Wang, X., Bian, C., Gao, Z., Zhang, Y., Jiang, W., Wang, M., You, X., Cheng, L., Pan, X., Yang, J. and Shi, Q.

Record Number:
5515
Year:
2021
Journal:
Frontiers in Genetics
Pages:
1-9
Volume:
12:736500
Abstract:
An adult Sinocyclocheilus maitianheensis, a surface-dwelling golden-line barbel fish, was collected from Maitian river (Kunming City, Yunnan Province, China) for whole-genome sequencing, assembly, and annotation. We obtained a genome assembly of 1.7 Gb with a scaffoldN50 of 1.4Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding geneswere annotated. Based on a comparative phylogenetic analysis of five Sinocyclocheilus species and other five representative vertebrates with published genome sequences, we found that S. maitianheensis is close to Sinocyclocheilus anophthalmus (a cave-restricted species with similar locality).Moreover, the assembled genomes of S. maitianheensis and other four Sinocyclocheilus counterparts were used for a fourfold degenerative third-codon transversion (4dTv) analysis. The recent whole-genome duplication (WGD) event was therefore estimated to occur about 18.1 million years ago. Our results also revealed a decreased tendency of copy number in many important genes related to immunity and apoptosis in cave-restricted Sinocyclocheilus species. In summary, we report the first genome assembly of S.maitianheensis,which provides a valuable genetic resource for comparative studies on cavefish biology, species protection, and practical aquaculture of this potentially economical fish. Keywords: Sinocyclocheilus maitianheensis, whole genome sequencing, assembly, annotation, phylogeny, immunity, cave adaptation
Times Cited:
4
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