A high-resolution genome of an euryhaline and eurythermal rhinogoby (Rhinogobius similis Gill 1895). Issue 2 (18th November 2021)

• Record Type: Journal Article
• Authors: Hu, Yun; Lu, Liang; Zhou, Tao; Sarker, Kishor Kumar; Huang, Junman; Xia, Jianhong; Li, Chenhong
• Editors: Whitehead, A
• Is Part Of: G3. Volume 12:Issue 2(2022)
• Publication Date: 2021-11-18
• Subjects: Rhinogobius similis -- nanopore sequencing -- Hi-C (high-throughput chromosome conformation capture) -- PSMC (pairwise sequentially Markovian coalescent analysis) -- freshwater goby -- transcriptome; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1093/g3journal/jkab395
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: Rhinogobius similis is distributed in East and Southeast Asia. It is an amphidromous species found mostly in freshwater and sometimes brackish waters. We have obtained a high-resolution assembly of the R. similis genome using nanopore sequencing, high-throughput chromosome conformation capture (Hi-C), and transcriptomic data. The assembled genome was 890.10 Mb in size and 40.15% in GC content. Including 1373 contigs with contig N50 is 1.54 Mb, and scaffold N50 is 41.51 Mb. All of the 1373 contigs were anchored on 22 pairs of chromosomes. The BUSCO evaluation score was 93.02% indicating high quality of genome assembly. The repeat sequences accounted for 34.92% of the whole genome, with retroelements (30.13%), DNA transposons (1.64%), simple repeats (2.34%), and so forth. A total of 31, 089 protein-coding genes were predicted in the genome and functionally annotated using Maker, of those genes, 26, 893 (86.50%) were found in InterProScan5. There were 1910 gene families expanded in R. similis, 1171 gene families contracted and 170 gene families rapidly evolving. We have compared one rapidly change gene family ( PF05970 ) commonly found in four species ( Boleophthalmus pectinirostris, Neogobius melanostomus, Periophthalmus magnuspinnatus, and R. similis ), which was found probably related to the lifespan of those species. During 400–10 Ka, the period of the Guxiang Ice Age, the population of R. similis decreased drastically, and then increased gradually following the last interglacial period. A high-resolution genome of R. similis should be useful to study taxonomy, biogeography, comparative genomics, and adaptive evolution of the most speciose freshwater goby genus, Rhinogobius .