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Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.

ABSTRACT: BACKGROUND: Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conservation management, no species-specific microsatellite marker has been reported. METHODS: We adopted next-generation sequencing (NGS) to elucidate the microsatellite markers of Korean water deer and overcome these impediments on marker developments. We performed genotyping to determine the efficiency of this method as applied to population genetics. RESULTS: We obtained 98 Mbp of nucleotide information from 260,467 sequence reads. A total of 20,101 di-/tri-nucleotide repeat motifs were identified; di-repeats were 5.9-fold more common than tri-repeats. [CA](n) and [AAC](n)/[AAT](n) repeats were the most frequent di- and tri-repeats, respectively. Of the 17,206 di-repeats, 12,471 microsatellite primer pairs were derived. PCR amplification of 400 primer pairs yielded 106 amplicons and 79 polymorphic markers from 20 individual Korean water deer. Polymorphic rates of the 79 new microsatellites varied from 2 to 11 alleles per locus (H(e): 0.050-0.880; H(o): 0.000-1.000), while those of known microsatellite markers transferred from cattle to Chinese water deer ranged from 4 to 6 alleles per locus (H(e): 0.279-0.714; H(o): 0.300-0.400). CONCLUSIONS: Polymorphic microsatellite markers from Korean water deer were successfully identified using NGS without any prior sequence information and deposited into the public database. Thus, the methods described herein represent a rapid and low-cost way to investigate the population genetics of endangered/non-model species.

SUBMITTER: Yu JN

PROVIDER: S-EPMC3206051 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.

Yu Jeong-Nam JN Won Changman C Jun Jumin J Lim Youngwoon Y Kwak Myounghai M

PloS one 20111101 11

<h4>Background</h4>Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conser ...[more]

PMID: 22069476

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Project description:BACKGROUND:Anaplasma spp. are tick-borne Gram-negative obligate intracellular bacteria that infect humans and a wide range of animals. Anaplasma capra has emerged as a human pathogen; however, little is known about the occurrence and genetic identity of this agent in wildlife. The present study aimed to determine the infection rate and genetic profile of this pathogen in wild animals in the Republic of Korea. METHODS:A total of 253 blood samples [198 from Korean water deer (Hydropotes inermis argyropus), 53 from raccoon dogs (Nyctereutes procyonoides) and one sample each from a leopard cat (Prionailurus bengalensis) and a roe deer (Capreolus pygargus)] were collected at Chungbuk Wildlife Center during the period 2015-2018. Genomic DNA was extracted from the samples and screened for presence of Anaplasma species by PCR/sequence analysis of 429 bp of the 16S rRNA gene marker. Anaplasma capra-positive isolates were genetically profiled by amplification of a longer fragment of 16S rRNA (rrs) as well as partial sequences of citrate synthase (gltA), heat-shock protein (groEL), major surface protein 2 (msp2) and major surface protein 4 (msp4). Generated sequences of each gene marker were aligned with homologous sequences in the database and phylogenetically analyzed. RESULTS:Anaplasma capra was detected in blood samples derived from Korean water deer, whereas samples from other animal species were negative. The overall infection rate in tested samples was 13.8% (35/253) and in the water deer the rate was 17.8% (35/198), distributed along the study period from 2015 to 2018. Genetic profiling and a phylogenetic analysis based on analyzed gene markers revealed the occurrence of two distinct strains, clustered in a single clade with counterpart sequences of A. capra in the database. CONCLUSIONS:Anaplasma capra infection were detected in Korean water deer in the Republic of Korea, providing insight into the role of wildlife as a potential reservoir for animal and human anaplasmosis. However, further work is needed in order to evaluate the role of Korean water deer as a host/reservoir host of A. capra.

Dataset Information

Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.

Publications

Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.

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