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http://dx.doi.org/10.5352/JLS.2022.32.9.690

Analysis of Microsatellite Patterns in the Genome of Red Sea Cucumber  

Lee, Tae Wook (Department of Pharmaceutical Engineering, Gyeongsang National University)
Kim, Sam Woong (Agri-Food Bio Convergence Institute, Gyeongsang National University)
Kim, Jung Sun (Bios Co.)
Chi, Won-Jae (Microorganism Resources Division, National Institute of Biological Resources (NIBR), Environmental Research Complex)
Bang, Woo Young (Biological and Genetic Resources Utilization Division, National Institute of Biological Resources (NIBR), Environmental Research Complex)
Kim, Jang Hyeon (Lab of Aquatic Animal Diseases, College of Veterinary Medicine, Gyeongsang National University)
Yang, Chul Woong (Lab of Aquatic Animal Diseases, College of Veterinary Medicine, Gyeongsang National University)
Bang, Kyu Ho (Department of Pharmaceutical Engineering, Gyeongsang National University)
Gal, Sang Wan (Department of Pharmaceutical Engineering, Gyeongsang National University)
Publication Information
Journal of Life Science / v.32, no.9, 2022 , pp. 690-697 More about this Journal
Abstract
This study was conducted to analyze genome of red sea cucumber and to use it as basic data for the development of genetic markers for red sea cucumber. Microsatellite marker analysis of Ulleungdo_normal and Ulleungdo_native red sea cucumbers revealed that dinucleotide simple sequence repeats (SSRs) had the highest ratio, at 81.3~81.4%, and the number of the detected SSRs tended to decrease as the number of repeating sequence units in SSRs increased. In general, microsatellites with between 5 and 10 iterations were most common. As the size of the SSR repeating sequence units increased, the SSR iterations gradually decreased. The di-, tri-, and tetra-nucleotides in SSRs were detected in the highest numbers as (AT)5, (AAT)5, and (AAAT)5, respectively. (CG) and (CCG) had very low frequencies compared to the numbers of other repeating SSR units. The numbers of di-and tri-nucleotide repeats were up to 35 and 32, respectively, and then increased discontinuously up to 44 and 43 repeats, respectively. Tetra-, penta-, and hexa-nucleotides in SSRs occurred in numbers up to 25, 21 and 14, respectively. This analysis of red sea cucumber indicated that it maintains its own repetition sequence and repetition number; therefore, we suggest that using it as basic data for molecular marker will be possible in future research.
Keywords
Genomics; microsatellite; red sea cucumber; repeat number; repeat unit;
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