The first de novo genome assembly and sex marker identification of Pluang Chomphu fish (Tor tambra) from Southern Thailand

Abstract

The Tor genus belongs to the group of cyprinid fish commonly known as mahseer. Although Tor species are rapidly declining in the wild, and some face extinction, ambiguities in species identification hinder their collection and conservation. We conducted a genome survey of male and female Tor tambra collected in Thailand. The genome sizes of the male and female fish were approximately 1,671 and 1,645 Mb, respectively, with repeat contents of approximately 33%. The heterozygosity ratios of the male and female fish, which were 0.34% and 0.39%, respectively, suggested that the sex of T. tambra is determined by the ZW system. A sex marker was identified in silico and confirmed by PCR amplification. The result indicated that T. tambra has a ZZ/ZW sex determination system. Subsequently, comparative genomic and phylogenetic analyses of T. tambra and other fish in the Cyprinidae family were performed to explore the genetic diversity and evolution of the species. We also assembled the complete mitochondrial genome sequences of the T. tambra collected in Thailand. A phylogenetic tree of different Tor species, constructed based on mitochondrial genome sequences, indicated that T. tambra was closely related to T. tambroides. We believe this is the first genome survey of a species from the Tor genus or Mahseer group. Our results may help identify Tor species, providing a reference for genetic studies of the Tor genus and other mahseer fish.

Keywords

• Tor tambra
• Tor douronensis
• Genome survey
• Genetic marker
• Whole-genome sequencing
• De novo assembly