Abstract
Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.
Highlights
Eupercaria is by far the largest series of percomorphs with more than 6,600 species arranged in 161 families and at least 16 orders
Recent studies proposed that teleost genomes might contain more copies of genes involved in pigment cell development than tetrapod genomes after an ancient fish-specific genome duplication (FSGD), which might contribute to the evolution and diversification of the pigmentation gene repertoire in teleost fish[10]
We sampled muscle tissue from a Mekong tiger perch captured in the Mekong river (Supplementary Fig. S1) and applied single tube long fragment read[12] technology for whole genome sequencing, generating 122.4 Gb stLFR co-barcode raw reads
Summary
Eupercaria is by far the largest series of percomorphs with more than 6,600 species arranged in 161 families and at least 16 orders. Lobotiformes was reported to be more closely related to Tetraodontiformes than to Sciaedidae using molecular and genomic data, which were not whole-genome sequences for most of the species[4]. Mekong tiger perch is currently assigned as ‘Vulnerable (VN)’ on INCN red list due to the rapidly declined population size[11], and is considered as ‘endangered (EN)’ on Thailand Red Data[2]. The genome assembly of Mekong tiger perch provided a valuable genome resource for further fish studies in Lobotiformes, and contributes to the understanding of skin color development as well as demographic history and biological conservation
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