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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 scaffold N50 of 1.4 Mb and a contig N50 of 24.7 kb. A total of 39,977 protein-coding genes were 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.

frontiers in genetics

Whole-Genome Sequencing of Sinocyclocheilus maitianheensis Reveals Phylogenetic Evolution and Immunological Variances in Various Sinocyclocheilus Fishes