Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis

Nguyen, Thao T.B., Arimatsu, Yuji, Hong, Sung-Jong, Brindley, Paul J., Blair, David, Laha, Thewarach, and Sripa, Banchob (2015) Genome-wide characterization of microsatellites and marker development in the carcinogenic liver fluke Clonorchis sinensis. Parasitology Research, 114 (6). pp. 2263-2272.

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Abstract

Clonorchis sinensis is an important carcinogenic human liver fluke endemic in East and Southeast Asia. There are several conventional molecular markers that have been used for identification and genetic diversity; however, no information about microsatellites of this liver fluke is published so far. We here report microsatellite characterization and marker development for a genetic diversity study in C. sinensis, using a genome-wide bioinformatics approach. Based on our search criteria, a total of 256,990 microsatellites (a parts per thousand yen12 base pairs) were identified from a genome database of C. sinensis, with hexanucleotide motif being the most abundant (51 %) followed by pentanucleotide (18.3 %) and trinucleotide (12.7 %). The tetranucleotide, dinucleotide, and mononucleotide motifs accounted for 9.75, 7.63, and 0.14 %, respectively. The total length of all microsatellites accounts for 0. 72 % of 547 Mb of the whole genome size, and the frequency of microsatellites was found to be one microsatellite in every 2.13 kb of DNA. For the di-, tri-, and tetranucleotide, the repeat numbers redundant are six (28 %), four (45 %), and three (76 %), respectively. The ATC repeat is the most abundant microsatellites followed by AT, AAT, and AC, respectively. Within 40 microsatellite loci developed, 24 microsatellite markers showed potential to differentiate between C. sinensis and Opisthorchis viverrini. Seven out of 24 loci showed to be heterozygous with observed heterozygosity that ranged from 0.467 to 1. Four primer sets could amplify both C. sinensis and O. viverrini DNA with different sizes. This study provides basic information of C. sinensis microsatellites, and the genome-wide markers developed may be a useful tool for the genetic study of C. sinensis.

Item ID: 41823
Item Type: Article (Refereed Research - C1)
Keywords: Clonorchis sinensis, microsatellite, characterization, SciRoko, genetic diversity
ISSN: 1432-1955
Funders: Office of the Higher Education Commission, Thailand, Khon Kaen University, Thailand Research Fund (TRF), National Institute of Allergy and Infectious Disease (NIAID), United States Army Medical Research and Material Command (USAMRMC)
Projects and Grants: NIAID Award No. P50AI098639, USAMRMC W81XWH-12-C-0267
Date Deposited: 08 Dec 2015 18:41
FoR Codes: 11 MEDICAL AND HEALTH SCIENCES > 1117 Public Health and Health Services > 111799 Public Health and Health Services not elsewhere classified @ 50%
06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
SEO Codes: 92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920404 Disease Distribution and Transmission (incl. Surveillance and Response) @ 50%
92 HEALTH > 9204 Public Health (excl. Specific Population Health) > 920499 Public Health (excl. Specific Population Health) not elsewhere classified @ 50%
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