Chromosome-Level Genome Assembly of Acanthogobius ommaturus Provides Insights Into Evolution and Lipid Metabolism

Abstract

Acanthogobius ommaturus is a large, fast-growing annual fish widely distributed in coastal and estuarine areas. The adults will die after breeding, and its life cycle is only 1 year. The first chromosome-level genome assembly of A. ommaturus was obtained by PacBio and Hi-C sequencing in this study. The final genome assembly after Hi-C correction was 921.49 Mb, with contig N50 and scaffold N50 values of 15.70 Mb and 40.99 Mb, respectively. The assembled sequences were anchored to 22 chromosomes by using Hi-C data. A total of 18,752 protein-coding genes were predicted, 97.90% of which were successfully annotated. Benchmarking Universal Single-Copy Orthologs (BUSCO) assessment results for genome and gene annotations were 93.6% and 84.6%, respectively. A. ommaturus is phylogenetically closely related to Periophthalmodon magnuspinnatus and Boleophthalmus pectinirostris, diverging approximately 31.9 MYA with the two goby species. The A. ommaturus genome displayed 597 expanded and 3,094 contracted gene families compared with the common ancestor. A total of 1,155 positive selected genes (PSGs) (p < 0.05) were identified. Based on comparative genomic analyses, we obtained several expanded genes such as acsbg2, lrp1, lrp6, and znf638 involved in lipid metabolism. A total of twenty candidate genes were identified under positive selection, which associated with lifespan including ercc6, igf1, polg, and tert. Interspecific collinearity analysis showed a high genomic synteny between A. ommaturus and P. magnuspinnatus. The effective population size of A. ommaturus decreased drastically during 200–100 Ka because of Guxiang ice age and then increased gradually following warm periods. This study provides pivotal genetic resources for in-depth biological and evolutionary studies, and underlies the molecular basis for lipid metabolism.

Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes

“…K-mer analysis revealed the genome sizes of five Gobiidae fish: 978.96 Mb for A. flavimanus , 998.27 Mb for A. stigmothonus , 1601.98 Mb for F. gymnauchen , 812.88 Mb for C. microcephalus , and 808.55 Mb for T. barbatus . The genome size of most Osteichthyes fish ranged from 300 Mb to 1 Gb, generally smaller than that of cartilaginous fish genomes [ 26 , 27 , 28 ]. The reported genome sizes of Gobiidae fish ranged from 679.76 Mb (Periophthalmus magnuspinnatus ) to 1003.74 Mb ( Neogobius melanostomus ).…”

“…The reported genome sizes of Gobiidae fish ranged from 679.76 Mb (Periophthalmus magnuspinnatus ) to 1003.74 Mb ( Neogobius melanostomus ). The genome sizes of two Acanthogobius species were relatively large and comparable to A. ommaturus (921.49 Mb) [ 26 ]. Notably, the genome of F. gymnauchen was large, possibly due to a higher repetitive sequence content.…”