Chromosome-scale genome assemblies and population re-sequence of the mango tilapia provide insights into the adaptive evolution

Abstract

Mango tilapia (Sarotherodon galilaeus) is a commercially important species valued for its ecological resilience and nutritional profile. To elucidate its genome structure and environmental adaptability, we sequenced a male adult by combined technologies of Illumina sequencing, PacBio sequencing, and high-throughput chromosome conformation capture (Hi-C). A 0.98 Gb chromosome-scale assembly of mango tilapia (GenBank accession No. GCA_046562855.1) were constructed with a contig N50 length of 31.06 Mb, which was fully annotated to predict 31,865 protein-coding and 4448 non-coding genes. The BUSCO assessment of genome and annotation respectively exhibited a 97.97 % and 97.25 % completeness. A reconstructed phylogenetic tree using 2763 one-to-one single-copy genes estimated that mango tilapia diverged from its closest related species Nile tilapia 15.95 million years ago. Comparative analyses across 12 Actinopterygii observed that it underwent the frequent large-scale fragment duplications, resulting in a rapidly expansion of the gene families involved in environmental responses. A genome re-sequencing of three wild populations detected a total of 7,201,267 SNPs among the populations, through which a selection sweep analysis of a population in the north of the Tropic of Cancer against another two populations in the south of that localized 49 candidate genes under the significant selection. The 49 genes were annotated to be mainly involved in cell signaling and environmental responses, of which a homolog encoding DNA (cytosine-5)-methyltransferase 1 (DNMT1), a key enzyme responsible for maintaining DNA methylation in environmental stress responses, carried 13 homozygous substitutions only in the CW population, including a missense substitution in its coding region. These findings suggested a rapid evolution of adaption to the changes in environmental temperature. A fully annotated genome of mango tilapia was supposed to benefit for molecular breeding of tilapias.