Near‐complete genome assembly and annotation of the yellow drum (Nibea albiflora) provide insights into population and evolutionary characteristics of this species

Abstract

Yellow drum (Nibea albiflora) is an important fish species in capture fishery and aquaculture in East Asia. We herein report the first and near‐complete genome assembly of an ultra‐homologous gynogenic female yellow drum using Illumina short sequencing reads. In summary, a total of 154.2 Gb of raw reads were generated via whole‐genome sequencing and were assembled to 565.3 Mb genome with a contig N50 size of 50.3 kb and scaffold N50 size of 2.2 Mb (BUSCO completeness of 97.7%), accounting for 97.3%–98.6% of the estimated genome size of this fish. We further identified 22,448 genes using combined methods of ab initio prediction, RNAseq annotation, and protein homology searching, of which 21,614 (96.3%) were functionally annotated in NCBI nr, trEMBL, SwissProt, and KOG databases. We also investigated the nucleotide diversity (around 1/390) of aquacultured individuals and found the genetic diversity of the aquacultured population decreased due to inbreeding. Evolutionary analyses illustrated significantly expanded and extracted gene families, such as myosin and sodium: neurotransmitter symporter (SNF), could help explain swimming motility of yellow drum. The presented genome will be an important resource for future studies on population genetics, conservation, understanding of evolutionary history and genetic breeding of the yellow drum and other Nibea species.

Genome of the four-finger threadfin Eleutheronema tetradactylum (Perciforms: Polynemidae)

“…Among TEs, the largest contribution of sequence comes from DNA transposons (4.27–5.31%), followed by LINEs (1.88–1.99%%), and LTR elements (1.01–1.33%) (Table 2 ). These figures are broadly similar to those reported for the yellow drum Nibea albiflora [ 11 ], another perciform fish with a similarly low TE content.…”

“…At the upper end of the spectrum for perciform fish, the pikeperch (Percidae: Sander lucioperca ) has an estimated genome size of 1014 Mb, and an assembly genome size of ~ 900 Mb [ 32 ], and the red sea bream (Sparidae: Pagrus major ) has an estimated genome size of ~ 806 Mb, and an assembly genome size of 829.3 Mb. Meanwhile, at the lower end of the spectrum, the yellow drum (Sciaenidae: Nibea albiflora ) has an estimated genome of 573–581 Mb and an assembly genome size of 596 Mb [ 11 ], and the Chinese sillago (Sillaginidae: Sillago sinica ) has an estimated genome size of ~ 524 Mb, and an assembly genome size of just 534 Mb [ 33 ]. Comparison of various percid fish genomes showed that E. tetradactylum possesses the largest number of protein-coding genes, but the smallest average protein size, which may contribute to its small overall genome size, despite its large number of genes.…”

“…Consequently, the repeat content of the four-finger threadfin conforms to its relatively small genome size of ~ 610 Mb. However, the genome assembly of the yellow drum is even smaller (~ 565 Mb) than the four-finger threadfin genome presented here, but its repeat content is higher at 13.8% [ 11 ]. Thus, it appears that the repeat content of the four-finger threadfin is especially low, both among fish genomes [ 35 ], and compared to other vertebrate genomes more generally.…”

Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)

“…With the decrease in sequencing costs, it is easy to genotype genome-wide SNPs using whole-genome sequencing or genotyping-by-sequencing (GBS) (Rustagi et al 2017). The genome of yellow drum is only approximately 565 Mb (Han et al 2019), which is a great advantage for use with sequencing techniques to obtain a large number of genome-wide SNPs and favors the application of genomic selection to the yellow drum genetic breeding program. Genome-wide association study (GWAS) analysis is an efficient approach for screening trait-related markers or genes (Wang et al 2019; Yu et al 2019).…”

A haplotype-resolved draft genome of the European sardine (Sardina pilchardus)

“…Similar results were obtained in the Supernova input report estimation (Table 1) of mean distance between heterozygous SNPs in the whole genome of 197 bp. This high SNP heterozygosity (1/206), observed solely in the comparison of the phased alleles, is higher than the average nucleotide diversity of the previously reported marine fish of wild populations: 1/390 in yellow drum [43], 1/309 in herring [44], 1/435 in coelacanth [45], 1/500 in cod [46], and 1/700 in stickleback [47].…”