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Qiu B, Fang S, Ikhwanuddin M, Wong L, Ma H. Genome survey and development of polymorphic microsatellite loci for Sillago sihama based on Illumina sequencing technology. Mol Biol Rep 2020; 47:3011-3017. [PMID: 32124169 DOI: 10.1007/s11033-020-05348-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/25/2020] [Indexed: 10/24/2022]
Abstract
In this study, we first conducted a genome survey assay for Sillago sihama by Illumina sequencing platform, and then developed 15 polymorphic microsatellite loci in a wild population. A total of 129.46 Gb raw data were obtained, of which 115.07 Gb were clean data, with a sequencing depth of 179.3-folds. This genome was estimated to be 522.6 Mb in size, with the heterozygosity, repeat content and GC content being 0.63%, 21% and 44%. A total of 630,028 microsatellites were identified from the genome, of which, dinucleotide repeat was the most abundant (56.80%), followed by mononucleotide repeat (30.23%). Furthermore, 60 pairs of primers were designed and synthesized based on microsatellite sequences, of which 15 were polymorphic in a wild population. A total of 91 alleles were found, with an average of 6.07 per locus. Number of alleles, observed and expected heterozygosity per locus ranged from two to 13, from 0.250 to 0.862, and from 0.396 to 0.901, respectively. Twelve loci were highly informative (PIC > 0.5), and the others were medium informative (0.25 < PIC < 0.5). Seven loci deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0033). No significant linkage disequilibrium was detected between loci pairs. This study provided a large number of genomic resources and 15 polymorphic microsatellite loci that should be helpful for the further genetic studies in S. sihama.
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Affiliation(s)
- Bixun Qiu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China.,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Lilian Wong
- STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Sciences, Shantou University, 243 Daxue Road, Shantou, 515063, China. .,STU‑UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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