3.7 Genome re-sequencing for SNP calling
The genome re-sequencing of 54 individuals of P. leopardusproduced a total of 2,232,057,448 raw sequencing reads. After quality
filtering, we obtained a total of 668.90 Gb clean data, with an
averagely 12.39 Gb for each fish and a mean sequencing depth of 14.0×
(Supplementary Table S5 ). The clean reads were aligned to the
assembled genome for each individuals, with 99.63 % of the total reads
mapped to the genome. Based on these alignments, we identified a total
of 5,178,453 SNPs after quality filtering. The location and effects of
these SNPs were also annotated, showing that 132,709 and 57,082 were
synonymous and nonsynonymous SNPs, respectively, locating in coding
regions (Table 6 ). These SNPs will provide an important genomic
resource for the genetic studies, such as population structure analysis,
dissection of agronomical traits, identification of selective sweeps,
and for genomic selective breeding for superior strains. In the future
work, we will use these genomic variations and recorded phenotypes of
the corresponding individuals to dissect the genomic associations and to
identify key genes playing important roles in the phenotypic
differences.
Conclusion
Here we provide a chromosomal-scale genome assembly of the P.
leopardus by integration of 10× Genomics, Hi-C and PacBio long read
sequencing technologies. The genome assembly and annotation supplies the
first genome of genus Plectropomus and implement the Epinephelidae
genomes, in addition to E. lanceolatus and E. akaara , thus
supplying important genomic data for whole-genome analysis to elucidate
the population genetics, evolution and to dissect the genetic diversity
underlying their phenotypic traits and adaptions. The genomic
variations, together with their functional annotations, will promote
accurate genetic analysis and accelerate the genomic breeding programs
in aquaculture of the P. leopardus .