Improved genome assembly of Chinese sucker (Myxocyprinus asiaticus) provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei

Abstract

The Chinese sucker, Myxocyprinus asiaticus (M. asiaticus, Catostomidae, Cypriniformes), is the only living species of Catostomidae in Asia. There are more than 75 species of this family in North America. The fossil record of this group dates back to the early Eocene. As the Chinese sucker is located at the base of the Cyprinoidei phylogeny, this species is also important in clarifying the evolutionary relationships within Cyprinoidei. Here, we assembled a high-quality genome of the Chinese sucker, contig N50 (40.26 ​Mb), which is nearly ten times longer than the previous version (4.19 ​Mb). Phylogenetic analysis identified that Chinese sucker together with Cyprinidae groups are paraphyletic with respect to Cobitoidea. The specific whole genome duplication event of the Chinese sucker was estimated to have occurred ∼25.9 million years ago. Analysis of population historical changes indicated a trend of reduction for the Chinese sucker and T. tibetana. Since Dlx genes play a key role in Cypriniformes pharyngeal teeth development, we conducted a genome-wide identification of Dlx genes, and found that these genes were doubled in whole genome duplication events, followed by the loss of specific copies. Transcriptome results showed that the expression levels of these paralogous genes were similar. This genomic resource provides useful information for the protection of Chinese sucker and functional study of Dlx genes.

Keywords

• Chinese sucker
• Catostomidae
• Genome assembly
• Genome duplication
• Dlx gene