Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Mar 14;25(6):3293.
doi: 10.3390/ijms25063293.

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

Siyu Ma  1 , Xiang Zhao  1 , Na Song  1
Affiliations

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

Siyu Ma et al. Int J Mol Sci. .

Abstract

As one of the most abundant groups in marine fish families, Gobiidae fish are important fishery resources in China, and some are also invasive species in certain regions worldwide. However, the phylogenetic relationships of Gobiidae fish remain ambiguous, and the study of their invasion-related genes is still scarce. This study used high-throughput sequencing technology to conduct a whole-genome survey of five Gobiidae fish species: Acanthogobius flavimanus, Acanthogobius stigmothonus, Favonigobius gymnauchen, Ctenotrypauchen microcephalus, and Tridentiger barbatus. De novo assembly of five fish genomes was performed, and genomic traits were compared through K-mer analysis. Among the five Gobiidae fish genomes, F. gymnauchen had the largest genome size (1601.98 Mb) and the highest heterozygosity (1.56%) and repeat rates (59.83%). Phylogenetic studies showed that A. flavimanus was most closely linked to A. stigmothonus, while Apogonidae and Gobiidae were closely related families. PSMC analysis revealed that C. microcephalus experienced a notable population expansion than the other four fish species in the Early Holocene. By using the KOG, GO, and KEGG databases to annotate single-copy genes, the annotated genes of the five fish were mainly classified as "signal transduction mechanisms", "cellular process", "cellular anatomical entity", and "translation". Acanthogobius flavimanus, A. stigmothonus, and T. barbatus had more genes classified as "response to stimulus" and "localization", which may have played an important role in their invasive processes. Our study also provides valuable material about Gobiidae fish genomics and genetic evolution.

Keywords: Gobiidae; PSMC; microsatellite; phylogenetic; whole-genome survey.

PubMed Disclaimer

Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
K-mer analysis of five Gobiidae species.
Figure 2
Figure 2
GC content and depth correlation evaluation of five Gobiidae fish.
Figure 3
Figure 3
The distribution and abundance of different SSR motifs. (a) Percentage distribution of various repeat types. (b) The number of SSR motifs in A. flavimanus. (c) The number of SSR motifs in A. stigmothonus. (d) The number of SSR motifs in F. gymnauchen. (e) The number of SSR motifs in C. microcephalus. (f) The number of SSR motifs in T. barbatus.
Figure 4
Figure 4
Frequency of mononucleotide, dinucleotide and trinucleotide repeats for five Gobiidae fish.
Figure 5
Figure 5
All predicted single-copy genes were aligned by BLAST to three information systems: (a) KOG annotation of predicted single-copy genes. (b) GO annotation of predicted single-copy genes. (c) KEGG annotation of predicted single-copy genes.
Figure 5
Figure 5
All predicted single-copy genes were aligned by BLAST to three information systems: (a) KOG annotation of predicted single-copy genes. (b) GO annotation of predicted single-copy genes. (c) KEGG annotation of predicted single-copy genes.
Figure 5
Figure 5
All predicted single-copy genes were aligned by BLAST to three information systems: (a) KOG annotation of predicted single-copy genes. (b) GO annotation of predicted single-copy genes. (c) KEGG annotation of predicted single-copy genes.
Figure 6
Figure 6
Venn diagram of annotated genes of five Gobiidae fish. Numbers represent the count of overlapping annotated genes.
Figure 7
Figure 7
Start and stop codons used in mitochondrial genomes of five Gobiidae fish. Different colors indicate different genes and codons.
Figure 8
Figure 8
The phylogenetic tree inferred the kinship of 26 species. (a) The phylogenetic relationship was constructed using 13 protein-coding genes from 26 species. Species from the same genus are represented by the same background colors. (b) Phylogenetic tree of 12 species using single-copy genes. The red lettering means the species in this study. The blue words indicate estimated divergence time of species (million years ago).
Figure 9
Figure 9
Historical demographic dynamics of five Gobiidae fish.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Agorreta A., Mauro D.S., Schliewen U., Van Tassell J.L., Kovačić M., Zardoya R., Rüber L. Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies. Mol. Phylogenet. Evol. 2013;69:619–633. doi: 10.1016/j.ympev.2013.07.017. - DOI - PubMed
    1. Winterbottom R., Emery A.R. A new genus and two new species of gobiid fishes (Perciformes) from the Chagos Archipelago, Central Indian Ocean. Environ. Biol. Fishes. 1981;6:139–149. doi: 10.1007/BF00002777. - DOI
    1. Froese R. FishBase. World Wide Web Electronic Publication. 2005. [(accessed on 2 January 2024)]. Available online: http://www.fishbase.org.
    1. Han D., Xue Y., Ji Y., Xu B., Liu H., Ma Q. Trophic and spatial niche of five gobiid fishes in Jiaozhou Bay. J. Fish. Sci. China. 2013;20:148–156. doi: 10.3724/SP.J.1118.2013.00148. - DOI
    1. Koonin E.V., Wolf Y.I. Constraints and plasticity in genome and molecular-phenome evolution. Nat. Rev. Genet. 2010;11:487–498. doi: 10.1038/nrg2810. - DOI - PMC - PubMed