A chromosome-level genome assembly of the jade perch (Scortum barcoo)

Abstract

Endemic to Australia, jade perch (Scortum barcoo) is a highly profitable freshwater bass species. It has extraordinarily high levels of omega-3 polyunsaturated fatty acids (PUFAs), which detailed genes involved in are largely unclear. Meanwhile, there were four chromosome-level bass species have been previous sequenced, while the bass ancestor genome karyotypes have not been estimated. Therefore, we sequenced, assembled and annotated a genome of jade perch to characterize the detailed genes for biosynthesis of omega-3 PUFAs and to deduce the bass ancestor genome karyotypes. We constructed a chromosome-level genome assembly with 24 pairs of chromosomes, 657.7 Mb in total length, and the contig and the scaffold N50 of 4.8 Mb and 28.6 Mb respectively. We also identified repetitive elements (accounting for 19.7% of the genome assembly) and predicted 26,905 protein-coding genes. Meanwhile, we performed genome-wide localization and characterization of several important genes encoding some key enzymes in the biosynthesis pathway of PUFAs. These genes may contribute to the high concentration of omega-3 in jade perch. Moreover, we conducted a series of comparative genomic analyses among four representative bass species at a chromosome level, resulting in a series of sequences of a deductive bass ancestor genome.

In Silico Chromosome Mapping of the Male-Specific/Linked Loci in the Jade Perch (Scortum barcoo) Suggests Chromosome 19 as the Putative Y Sex Chromosome

“…All three approaches rely on reliable sequencing data, and reads of repetitive regions cannot be aligned. Therefore, it is not possible to infer whether these structures were important in the recruitment of amh duplicates for sex determination in jade perch, or the possibility of pseudogenes [27,102]. The most likely explanation is that we observed a remnant of amh gene in MLR2, which collectively suggests that the putative sex chromosome of jade perch may be chromosome 19.…”

“…The male-specific/linked loci identified in our previous study, which included twenty jade perch individuals (ten males and ten females) [12] were aligned to the chromosomelevel assembly of jade perch (accession: GCA_023238725.1) using NCBI-BLASTn using default parameters [27]. The loci that passed the 100% filtering criterion with all males were designated as male-specific loci, whereas those passing in 70%-90% of all males were considered male-linked loci.…”

“…Multiple karyotypes in male-linked regions of jade perch were compared to identify linkage homology with whole-genome sequences of other teleosts, namely, European seabass, Asian seabass, Chinese seabass, American black bass, Nile tilapia, zebrafish, three-spined stickleback, medaka, Japanese pufferfish, green-spotted pufferfish, Southern platyfish, and Siam fighting fish, while green anole, Indian cobra, and chicken were used as the outgroup by simulation of the Ensembl database and Genomicus and linkage homology portals [27,52,53]. Genes are represented by small black dots, leading to diagonal lines inside chromosomes, with the order being similar to the reference, and line breaks representing rearrangements.…”

“…Recently, a chromosome-level genome assembly with 24 pairs of jade perch chromosomes (accession: GCA_023238725.1) facilitated the comparison of genomic structures among teleosts at the molecular level and revealed extensive linkage homology with frequent chromosomal rearrangements in teleosts [27]. Here, we used the reference baseline genome data of the jade perch to generate a chromosome map of male-specific/linked loci from our previous study using In silico mapping of the jade perch genome.…”

Chromosome-level genome assembly of the glass catfish (<i>Kryptopterus vitreolus</i>) reveals molecular clues to its transparent phenotype

“…Reconstruction of ancestral chromosomes was based on 13 pairs of potential ancestral chromosomes (Chra~m) that were predicted as the original chromosome karyotype of ancestral teleost from previous studies (Bian et al, 2016;Kasahara et al, 2007;Lu et al, 2022). Protein sets of 10 representative catfish species with diverse chromosome numbers (Supplementary Table S12) were collected for reconstruction of ancestral chromosomes.…”