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

Chao Peng; Congqiang Luo; Guangqing Xiang; Jiezhen Huang; Liye Shao; Haihong Huang; Sigang Fan

doi:10.3390/ani14243709

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

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

Authors

Chao Peng¹, Congqiang Luo¹, Guangqing Xiang², Jiezhen Huang², Liye Shao¹, Haihong Huang¹, Sigang Fan³

Affiliations

¹ Changde Key Innovation Team for Wetland Biology and Environmental Ecology, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, China.
² Longshan Animal Husbandry and Fisheries Affairs Center, Xiangxi 416800, China.
³ Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.

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.

Grants and funding

This work was supported by the Central Public-Interest Scientific Institution Basal Research Fund (nos. 2023TD44 and 2021SD05), the Hunan Natural Science Foundation Youth Project (2024JJ6331), and the scientific research program of the Education Department of Hunan province (22A0495).