Browse > Article
http://dx.doi.org/10.23005/KSMLS.2021.6.1.38

Genome Survey and Microsatellite Marker Selection of Tegillarca granosa  

Kim, Jinmu (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
Lee, Seung Jae (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
Jo, Euna (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
Choi, Eunkyung (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
Kim, Hyeon Jin (Department of Aqualife Medicine, Chonnam National University)
Lee, Jung Sick (Department of Aqualife Medicine, Chonnam National University)
Park, Hyun (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
Publication Information
Journal of Marine Life Science / v.6, no.1, 2021 , pp. 38-46 More about this Journal
Abstract
The blood clam, Tegillarca granosa, is economically important in marine bivalve and is used in fisheries industry among western Pacific Ocean Coasts especially in Korea, China, and Japan. The number of chromosomes in the blood clam is known as 2n=38, but the genome size and genetic information of the genome are not still clear. In order to predict the genomic size of the T. granosa, the in-silico analysis analysed the genomic size using short DNA sequence information obtained using the NGS Illumina HiSeq platform. As a result, the genomic size of T. granosa was estimated to be 770.61 Mb. Subsequently, a draft genome assembly was performed through the MaSuRCA assembler, and a simple sequence repeat (SSR) analysis was done by using the QDD pipeline. 43,944 SSRs were detected from the genome of T. granosa and 69.51% di-nucleotide, 16.68% trinucleotide, 12.96% tetra-nucleotide, 0.82% penta-nucleotide, and 0.03% hexa-nucleotide were consisted. 100 primer sets that could be used for genetic diversity studies were selected. In the future, this study will help identify the genetic diversity of T. granosa and population genetic studies, and further identify the classification of origin between homogenous groups.
Keywords
Tegillarca granosa; Illumina HiSeq platform; MaSuRCA assembler, SSR; Homogeneous;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Meglecz E, Pech N, Gilles A, Dubut V, Hingamp P, Trilles A, Grenier R, Martin JF. 2014. "QDD version 3.1: a user-friendly computer program for microsatellite selection and primer design revisited: experimental validation of variables determining genotyping success rate." Mol Ecol Resour 14: 1302-1313.   DOI
2 Fernandez-Perez J, Nanton A, Arias-Perez A, Insua A, Mendez J. 2019. "Fifteen novel microsatellite loci, developed using nextgeneration sequencing, reveal the lack of genetic structure in Donax vittatus from Iberian Peninsula." Estuarine, Coastal and Shelf Science 217: 218-225.   DOI
3 Liu L, Hu N, Wang B, Chen M, Wang J, Tian Z, He Y, Lin D. 2011. "A brief utilization report on the Illumina HiSeq 2000 sequencer." Mycology 2: 169-191.
4 Lu R, Lin Z, Zhang Y, Chai X, Dong Y, Xiao G, Zhang J-M, Fang J, Hu L-H. 2008. "Comparison on the karyotypes of Scapharca subcrenata, Tegillarca granosa and Estellarca olivacea." Journal of Shanghai Fisheries University 17: 625-629.
5 Marcais G, Kingsford C. 2011. "A fast, lock-free approach for efficient parallel counting of occurrences of k-mers." Bioinformatics 27: 764-770.   DOI
6 Penaloza C, Bishop SC, Toro J, Houston RD. 2014. RAD Sequencing reveals genome-wide heterozygote deficiency in pair crosses of the Chilean mussel Mytilus spp. Proceedings of the World Congress on Genetics Applied to Livestock Production. Species Breeding: Breeding in Aquaculture Species: 275.
7 Rozen S, Skaletsky H. 2000. "Primer3 on the WWW for general users and for biologist programmers." Methods Mol Biol 132: 365-386.
8 Vurture GW, Sedlazeck FJ, Nattestad M, Underwood CJ, Fang H, Gurtowski J, Schatz MC. 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33: 2202-2204.   DOI
9 Katti MV, Ranjekar PK, Gupta VS. 2001. "Differential Distribution of Simple Sequence Repeats in Eukaryotic Genome Sequences." Molecular Biology and Evolution 18: 1161-1167.   DOI
10 Wang Y, Zeng Q, Xu L. 2013. "Population structure of the blood clam (Tegillarca granosa) in China based on microsatellite markers." Genet Mol Res 12: 892-900.   DOI
11 Su W, Zha S, Wang Y, Shi W, Xiao G, Chai X, Wu H, Liu G. 2017. "Benzo[a]pyrene exposure under future ocean acidification scenarios weakens the immune responses of blood clam, Tegillarca granosa." Fish Shellfish Immunol 63: 465-470.   DOI
12 Bai CM, Xin LS, Rosani U, Wu B, Wang QC, Duan XK, Liu ZH, Wang CM. 2019. "Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C." Gigascience 8.
13 Dong-li Z. 2011. Analysis of genetic variation in the fast growth families of Tegillarca granosa. Journal of Fisheries of China 35: 350-357
14 Liu B, Teng S, Shao Y, Chai X, Xiao G, Fang J, Zhang J, Wang C. 2017. "A Genetic Linkage Map of Blood Clam (Tegillarca granosa) Based on Simple Sequence Repeat and Amplified Fragment Length Polymorphism Markers." Journal of Shellfish Research 36: 31-40.   DOI
15 Manee MM, Al-Shomrani BM, Al-Fageeh MB. 2020. "Genome-wide characterization of simple sequence repeats in Palmae genomes." Genes Genomics 42: 597-608.   DOI
16 Mohamat-Yusuff F, Zulkarnain Z, Anuar NZA, Joni AAM, Kusin FM, Mohamed KN, Zulkeflee Z, Asha'ari ZH, Zulkifli SZ, Arshad A, Ismail A. 2020. "Impact of Diuron contamination on blood cockles (Tegillarca granosa Linnaeus, 1758)." Mar Pollut Bull 161: 111698.   DOI
17 Zimin AV, Marcais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. 2013. "The MaSuRCA genome assembler." Bioinformatics 29: 2669-2677.   DOI