AUTHOR=Pan Yu , Sun Zhicheng , Gao Tianxiang , Zhao Linlin , Song Na 

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

JOURNAL=Frontiers in Marine Science

VOLUME=9

YEAR=2022

URL=https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2022.894821

DOI=10.3389/fmars.2022.894821

ISSN=2296-7745

ABSTRACT=<p><italic>Acanthogobius ommaturus</italic> 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 <italic>A. ommaturus</italic> 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. <italic>A. ommaturus</italic> is phylogenetically closely related to <italic>Periophthalmodon magnuspinnatus</italic> and <italic>Boleophthalmus pectinirostris</italic>, diverging approximately 31.9 MYA with the two goby species. The <italic>A. ommaturus</italic> genome displayed 597 expanded and 3,094 contracted gene families compared with the common ancestor. A total of 1,155 positive selected genes (PSGs) (<italic>p</italic> &lt; 0.05) were identified. Based on comparative genomic analyses, we obtained several expanded genes such as <italic>acsbg2</italic>, <italic>lrp1</italic>, <italic>lrp6</italic>, and <italic>znf638</italic> involved in lipid metabolism. A total of twenty candidate genes were identified under positive selection, which associated with lifespan including <italic>ercc6</italic>, <italic>igf1</italic>, <italic>polg</italic>, and <italic>tert</italic>. Interspecific collinearity analysis showed a high genomic synteny between <italic>A. ommaturus</italic> and <italic>P. magnuspinnatus</italic>. The effective population size of <italic>A. ommaturus</italic> 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.</p>