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. 2024 Dec 23;14(24):3709.
doi: 10.3390/ani14243709.

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

Chao Peng  1 , Congqiang Luo  1 , Guangqing Xiang  2 , Jiezhen Huang  2 , Liye Shao  1 , Haihong Huang  1 , Sigang Fan  3
Affiliations

Genome-Wide Microsatellites in Acanthopagrus latus: Development, Distribution, Characterization, and Polymorphism

Chao Peng et al. Animals (Basel). .

Abstract

The yellowfin seabream (Acanthopagrus latus) is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of A. latus have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the A. latus genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 A. latus individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in Acanthopagrus schlegelii. These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of A. latus.

Keywords: Acanthopagrus latus; GO; KEGG; genome-wide; microsatellite.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Distribution of all SSR motif repeat numbers in A. latus genome.
Figure 2
Figure 2
Distribution of SSR repeats in A. latus genome. (a) All SSR repeats in genome. (b) Dinucleotide repeat. (c) Trinucleotide repeat. (d) Tetranucleotide repeat. (e) Pentanucleotide repeat. (f) Hexanucleotide repeat.
Figure 3
Figure 3
Chromosome-wide distribution of SSRs in A. latus genome. (a) Density of SSRs; (b) frequency of SSRs; (c) length of SSRs; (d) number of SSRs.
Figure 4
Figure 4
Percentage of SSR repeat numbers in different regions of A. latus genome.
Figure 5
Figure 5
Relative proportion of SSRs in different genomic regions of A. latus.
Figure 6
Figure 6
GO classifications of SSR-containing exons.
Figure 7
Figure 7
Bubble diagram of the top 30 KEGG pathways enriched by exons contained SSR.
Figure 8
Figure 8
Distribution of the number (shown as columnar) and frequency (shown as broken line) of SSR markers in each chromosome of A. latus.
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