The Landscape of Genome-Wide and Gender-Specific Microsatellites in Indo-Pacific Humpback Dolphin and Potential Applications in Cetacean Resource Investigation

Abstract

Microsatellites are one of the important genome characterizations that can be a valuable resource for variety identification, genetic diversity, phylogenetic analysis, as well as comparative and conservation genomics research. Here, we developed comprehensive microsatellites through genome-wide mining for the threatened cetacean Indo-Pacific humpback dolphin (Sousa chinensis). We found 87,757 microsatellites with 2–6 bp nucleotide motifs, showing that about 32.5 microsatellites per megabase comprises microsatellites sequences. Approximately 97.8% of the markers developed in this study were consistent with the published identified markers. About 75.3% microsatellites were with dinucleotide motifs, followed by tetranucleotide motifs (17.4%), sharing the same composition pattern as other cetaceans. The microsatellites were not evenly distributed in the S. chinensis genome, mainly in non-coding regions, with only about 0.5% of the markers located in coding regions. The microsatellite-containing genes were mainly functionally enriched in the methylation process, probably demonstrating the potential impacts of microsatellites on biological functions. Polymorphic microsatellites were developed between different genders of S. chinensis, which was expected to lay the foundation for genetic diversity investigation in cetaceans. The specific markers for a male Indo-Pacific humpback dolphin will provide comprehensive and representative male candidate markers for sex identification, providing a potential biomolecular tool for further analysis of population structure and social behavior of wild populations, population trend evaluation, and species conservation management.

Genome‐wide development of intra‐ and inter‐specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…Therefore, they have been widely used in population genetics (Chen et al, 2022;Sapkota et al, 2022), genotyping, marker-assisted breeding, genome-wide association analysis (Jha et al, 2021;Kim et al, 2021;C. Li et al, 2014), forensic investigation (D. Li et al, 2021;, evolutionary studies (de Freitas et al, 2022;Nowicki et al, 2021;Song et al, 2021), and conservation genetics (Dong et al, 2022;Ming et al, 2022;Rodríguez-Peña et al, 2018).…”

“…SSRs are ubiquitous in the genome of higher organisms and exhibit genetic polymorphism at inter‐ and intra‐species levels (Amiteye, 2021; Bruford & Wayne, 1993; Ellegren, 2004). Therefore, they have been widely used in population genetics (Chen et al., 2022; Sapkota et al., 2022), genotyping, marker‐assisted breeding, genome‐wide association analysis (Jha et al., 2021; Kim et al., 2021; C. Li et al., 2014), forensic investigation (D. Li et al., 2021; J. Wang, Sun et al., 2022), evolutionary studies (de Freitas et al., 2022; Nowicki et al., 2021; Song et al, 2021), and conservation genetics (Dong et al., 2022; Ming et al., 2022; Rodríguez‐Peña et al., 2018).…”

Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

“…SSRs are ubiquitous in the genome of higher organisms and exhibit genetic polymorphism at inter- and intra-species levels (Bruford and Wayne 1993; Ellegren, 2004; Amiteye, 2021). Therefore, they have been widely used in population genetics (Chen et al, 2022; Sapkota et al, 2022;), genotyping, marker-assisted breeding, genome-wide association analysis (Li et al, 2014; Jha et al, 2021; Kim et al, 2021), forensic investigation (Li et al, 2021; Wang et al, 2022), evolutionary studies (Nowicki et al, 2021; Song et al, 2021; de Freitas et al, 2022), and conservation genetics (Rodríguez-Peña et al, 2018; Dong et al, 2022; Ming et al, 2022).…”