Chromosome‐level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water

Abstract

Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome‐level genome assembly of LMB using PacBio and Hi‐C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium‐transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high‐quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome‐level LMB genome will also be a valuable genomic resource for in‐depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.

Comparative Genomics Studies on the dmrt Gene Family in Fish

“…Fish with various sex-determination systems showed significant differences in their conserved sequences and regulatory elements, suggesting that the dmrt1-dmrt3-dmrt2(2a) gene cluster may be related to the sex-determination systems in fish. In our recent study, it reveals that M. salmoides is a XY/XX system species (Sun et al, 2020). In conserved sequences analysis of fish dmrt1-dmrt3-dmrt2(2a) gene clusters, it had much difference in Regions 1-3 between M. salmoides and C. semilaevis (ZW/ZZ).…”

A Chromosome—Level Genome Assembly of the Spotted Scat (Scatophagus argus)

“…PacBio's single-molecule real-time (SMRT) sequencing technology and the high-throughput chromosome conformation capture (Hi-C) assisted genome assembly technique have been used to obtain chromosome-level genome for many teleost species. A hybrid PacBio/Hi-C method generated high-quality chromosome-level reference genomes for nemachilus tibetan ( Triplophysa tibetana ) and largemouth bass ( Micropterus salmoides ), with a scaffold N50 length of 24.9 Mb and 36.5 Mb, respectively ( Yang et al 2019 ; Sun et al 2021 ). In this study, the first chromosome-level genome assembly of S. argus was generated, using a combination of PacBio sequencing with Hi-C technology.…”

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…REs represented 30.45% of the genome, or a total of 172,911,032 bp. Although the proportion of REs in fish genomes can vary greatly at scales from 10% to 60% (Yuan et al, 2018), the proportion of repeat elements in N. macropterus is on par with the proportion observed in other Centrarchiformes (Largemouth bass ( Micropterus salmoides ): 33.79%, Big-eyed mandarin fish ( Siniperca knerii ): 26.55%) (Lu et al, 2020; Sun et al, 2021) and for Perciformes in general (Yuan et al, 2018). Of the REs known in the databases, interspersed repeats accounted for 27.62% of the genome, including 10.87% of DNA transposons and 6.17% of retro-elements (LINEs, LTR, SINEs, and PLE in that order).…”