Abstract
The mandarin fish, Siniperca chuatsi, is an economically important perciform species with widespread aquaculture practices in China. Its special feeding habit, acceptance of only live prey fishes, contributes to its delicious meat. However, little is currently known about related genetic mechanisms. Here, we performed whole-genome sequencing and assembled a 758.78 Mb genome assembly of the mandarin fish, with the scaffold and contig N50 values reaching 2.64 Mb and 46.11 Kb, respectively. Approximately 92.8% of the scaffolds were ordered onto 24 chromosomes (Chrs) with the assistance of a previously established genetic linkage map. The chromosome-level genome contained 19,904 protein-coding genes, of which 19,059 (95.75%) genes were functionally annotated. The special feeding behavior of mandarin fish could be attributable to the interaction of a variety of sense organs (such as vision, smell, and endocrine organs). Through comparative genomics analysis, some interesting results were found. For example, olfactory receptor (OR) genes (especially the beta and delta types) underwent a significant expansion, and endocrinology/vision related npy, spexin, and opsin genes presented various functional mutations. These may contribute to the special feeding habit of the mandarin fish by strengthening the olfactory and visual systems. Meanwhile, previously identified sex-related genes and quantitative trait locis (QTLs) were localized on the Chr14 and Chr17, respectively. 155 toxin proteins were predicted from mandarin fish genome. In summary, the high-quality genome assembly of the mandarin fish provides novel insights into the feeding habit of live prey and offers a valuable genetic resource for the quality improvement of this freshwater fish.
Highlights
The mandarin fish, Siniperca chuatsi, belonging to the family Percichthyidae and order Perciformes, has a relatively high market value and widespread aquaculture throughout China (Liang and Cui, 1982; Liu et al, 1998)
Seven libraries including three short-insert (270, 500, and 800 bp) and four long-insert (2, 5, 10, and 20 kb) were constructed to generate a total of 327 Gb raw reads (Supplementary Table 3). These raw data were filtered, and 233 Gb clean data were obtained for subsequent genome assembly
We found that 16,922 orthologous gene families were shared among the eight teleost fishes, and identified 3,510 single-copy orthologs genes that were used to construct a phylogenetic tree (Figure 3)
Summary
The mandarin fish, Siniperca chuatsi, belonging to the family Percichthyidae and order Perciformes, has a relatively high market value and widespread aquaculture throughout China (Liang and Cui, 1982; Liu et al, 1998). It has a special feeding habit, accepting only live prey fishes and refusing dead food items in the wild (Chiang, 1959; Liu et al, 1998). This conclusion did not justify the food smells from other stimuli (such as hydromechanical stimulus)
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