[논문]Development and validation of microsatellite markers for the endangered nerippe fritillary butterfly, Argynnis nerippe (Lepidoptera: Nymphalidae)

Jeong, Su Yeon; Kim, Min Jee; Kim, Sung Soo; Kim, Iksoo

doi:10.7852/ijie.2018.37.1.1

[국내논문] Development and validation of microsatellite markers for the endangered nerippe fritillary butterfly, Argynnis nerippe (Lepidoptera: Nymphalidae) 원문보기

International journal of industrial entomology, v.37 no.1, 2018년, pp.1 - 8

Jeong, Su Yeon (College of Agriculture & Life Sciences, Chonnam National University) , Kim, Min Jee (College of Agriculture & Life Sciences, Chonnam National University) , Kim, Sung Soo (Research Institute for East Asian Environment and Biology) , Kim, Iksoo (College of Agriculture & Life Sciences, Chonnam National University)

Abstract ▼ AI-Helper

The nerippe fritillary butterfly, Argynnis nerippe, is listed as an endangered species in Korea. Establishment of effective conservation strategies can be aided by the development and application of molecular markers that can be used to investigate the population genetics of the butterfly. Therefore, in this study, we identified ten microsatellite markers specific to A. nerippe using the Next-Seq 500 platform, and applied these markers to investigate the characteristics of five South Korean butterfly populations. Genotyping of 48 A. nerippe individuals from five localities showed that at each locus the number of alleles ranged from 4 to 14, and that the observed and expected heterozygosities were 0.324-0.863 and 0.138-0.985, respectively. Significant deviation from the Hardy-Weinberg equilibrium was not observed at any locus. Population structure analysis indicated that there are two genetic groups in Korea, but no population-based gene pool assignments were found. Analysis of $F_{ST}$, $R_{ST}$, and a principal coordinates analysis suggested that the Gureopdo and Yaecheon populations were isolated from other populations. Genetic isolation of the Gureopdo population may be a consequence of unequal population change between Gureopdo and inland populations and to the offshore habitat of Gureopdo. Genetic isolation of the Yaecheon population may be a consequence either of the southernmost location of the population or of the limited sample size available. Further studies with increased sample sizes will be necessary to draw robust conclusions on population isolation and to devise conservation strategies.

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표/그림 (9)

그림 Fig. 1. Sampling locations of Argynnis nerippe in South Korea. General locality names are as follows: locality 1, Anseong City, Gyeonggi-do Province (10 individuals); locality 2, Gureopdo, Incheon City (13 individuals); locality 3, Yaecheon, Gyeongsangbuk-do Province (5 individuals); locality 4, Jaecheon, Chungcheongbuk-do Province (10 individuals); and locality 5, Yangpyeong, Gyeonggi-do Province (10 individuals).
표 Table 1. Summary statistics of Illumina Next-Seq 500 pairedend( 2x150) read sequence data and de novo assembly of Argynnis nerippe genome
표 Table 2. Summary statistics of filtered scaffolds of Argynnis nerippe genome for microsatellite marker identifcation
표 Table 3. Ten microsatellite markers developed from Argynnis nerippe
표 Table 4. Characteristics of 10 microsatellite loci in Argynnis nerippe
그림 Fig. 2. Allelic patterns in the 10 microsatellite loci in five populations of Argynnis nerippe. Na, number of different alleles; Na (Freq. ≥5%), number of alleles with frequency greater than 5%; Ne, number of effective alleles; I, Shannon's Information Index; No. Private Alleles, number of alleles unique to a single population; No. LComm Alleles (≤25%), number of locally common alleles occurring in 25% or less in the populations; No. LComm Alleles (≤50%), number of locally common alleles occurring in 50% or less in the populations; HE, expected heterozygosity; HO, observed heterozygosity; and FIS, inbreeding coefficient. Vertical bars represent the standard error.
그림 Fig. 3. Clustering analysis of multilocus microsatellite data of Argynnis nerippe performed using STRUCTURE software. A, Plot of Delta K calculated with the formula Delta K = mean (|L''(K)|)/sd(L(K)), n = 48. B, Bar plot of estimated membership of each individual in K = 2 clusters. Black bars separate the five population sample groups. Different colors represent different gene pools.
그림 Fig. 4. Results of the principal coordinate analysis (PCoA). A, PCoA plot depicting allelic variance at 10 microsatellite loci in the 48 sampled individuals. B, PCoA plot depicting allelic variance at 10 microsatellite loci in the five sampled populations. The percentages variation explained by the 1st and 2nd axes are indicated.
표 Table 5. Analysis of genetic differentiation between pairs of Argynnis nerippe population

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제안 방법

In this study, we used Next-Generation Sequencing technology to identify ten microsatellite markers for A. nerippe. These markers represent the first available for this species.
After an initial test of candidate microsatellites for their availability of primer sites, amplification efficiency, degree of polymorphism, and specificity for target loci, 10 markers were selected for use in subsequent genotyping (Table 3).

대상 데이터

Argynnis nerippe adults (a total of 48 individuals) were sampled from five localities (Fig. 1) in South Korea in 2017. The precise coordinates of the sampling locations are omitted to ensure the protection of the species.

이론/모형

Genotypic linkage disequilibrium (LD) between all pairs of loci, as well as deviation of genotypic frequencies from the Hardy–Weinberg equilibrium (HWE), were tested using GENEPOP Web ver. 4.2 (Raymond and Rousset, 1995; Rousset, 2008) by the Markov-chain approach modified from Guo and Thompson (1992) with 10,000 steps of dememorization and iteration.
The 95% significance levels for both HWE and LD tests were adjusted using Bonferroni’s correction (Rice, 1989).
Observed and expected heterozygosity (HO; Weir, 1990; H_E; Weir, 1990), F_IS (Hartl and Clark, 1997), the number of alleles, and the effective number of alleles were calculated using GenAlEx ver. 6.5 (Peakall and Smouse, 2012). Allelic richness (AR) standardized for variation in sample size was calculated using FSTAT 2.

성능/효과

005). The tests for genotypic LD showed no significant allele associations among the 10 loci after applying the Bonferroni correction, suggesting that all loci can be considered independent markers.
By contrast, the RST estimates showed a limited amount of divergence: five of the ten population pairs diverged significantly and the Gureopdo population diverged from other populations except that from Anseong; Yaecheon and Anseong populations diverged significantly; and, similarly, Yangpyeong and Yaecheon populations diverged significantly (Table 5).
In a test of pairwise F_ST estimates, seven of ten comparisons were found to be significant: Gureopdo diverged significantly from all other populations; Anseong and Yaecheon populations both diverged significantly from three populations, with the exception of that from Yangpyeong (Table 5). By contrast, the R_ST estimates showed a limited amount of divergence: five of the ten population pairs diverged significantly and the Gureopdo population diverged from other populations except that from Anseong; Yaecheon and Anseong populations diverged significantly; and, similarly, Yangpyeong and Yaecheon populations diverged significantly (Table 5).
By contrast, the R_ST estimates showed a limited amount of divergence: five of the ten population pairs diverged significantly and the Gureopdo population diverged from other populations except that from Anseong; Yaecheon and Anseong populations diverged significantly; and, similarly, Yangpyeong and Yaecheon populations diverged significantly (Table 5). Considering the results of the F_ST and R_ST analyses together, the Gureopdo population appeared to be the most divergent and the Yaecheon population the next most divergent. A PCoA based on the first two principal coordinates was performed to investigate population relationships based on genetic distances among individuals and among populations (Fig.
4). The first two components explained 16.99 and 87.30% of the individual- and population-based variation, respectively. The first component of individual-based analysis accounted for 9.
These are the first microsatellite markers for use in studies on the population genetic structure of this species. Our genotyping results indicate that A. nerippe populations in Gureopdo and Yaecheon are genetically isolated, although they are not currently inbred (Fig. 2). Given the limited access to this endangered species, the results of the population genetic analysis of A.
The selected microsatellite markers showed a high rate of successful genotyping, ranging from 0.896 to 1, with an average of 0.985 (Table 4).

후속연구

nerippe were of necessity based on examination of a limited number of individuals (48) from five South Korean localities. As more samples are collected from a diverse range of Asian countries, including South Korea, further analyses of the population genetics of this endangered species will be feasible using our newly developed set of microsatellite markers.

참고문헌 (25)

Earl DA (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4, 359-361.

상세보기
Faircloth BC (2008) Msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design. Mol Ecol Resour 8, 92-94.

상세보기
Fukuda H, Hama E, Kuzuya T, Takahashi A, Takahashi M, Tanaka B, et al. (1983) The life histories of butterflies in Japan II. Hoikusha Publishing Co.
Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci 108, 1513-1518

상세보기
Goudet J (1995) FSTAT (version 1.2): a computer program to calculate F-statistics. J Hered 86, 485-486.
Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportions for multiple alleles. Biometrics 48, 361-372.

상세보기
Hartl DL, Clark AG (1997) Principles of population genetics (3rd edition). Sinauer Associates, Sunderland.
Kim MJ, Jeong HC, Kim SR, Kim I (2011b). Complete mitochondrial genome of the nerippe fritillary butterfly, Argynnis nerippe (Lepidoptera: Nymphalidae). Mitochondrial DNA 22, 86-88.

상세보기
Kim MJ, Wang AR, Kim SS, An J, Kim I (2018) Development and validation of microsatellite markers for the tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), which is endangered in South Korea. Appl Entomol Zool 53, 151-156.

상세보기
Kim SS, Lee CM, Kwon TS (2011a) The butterfly community in Is. Guleopdo, Korea and the dominance of the endangered species Argynnis nerippe. Kor J Appl Entomol 50, 115-123.

원문보기 상세보기
Kim SS, Lee CM, Kwon TS, Joo HZ, Sung JH (2012) Korean butterfly atlas [1996-2011]. Korea Forest Research Institute.
Kim Y. 2002. Illustrated book of Korean butterflies in color. Seoul: Kyo-Hak Publishing Co.
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359.

상세보기
Moritz C (2002) Strategies to protect biological diversity and the evolutionary processes that sustain it. Syst Biol 51, 238-254.

상세보기
Nakamura Y (2011) Conservation of butterflies in Japan: status, actions and strategy. J Insect Conserv 15, 5-22.

상세보기
Palsboll PJ, Berube M, Allendorf FW (2007) Identification of management units using population genetic data. Trends Ecol Evol 22, 11-16.

상세보기
Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6, 288-295.

상세보기
Peng Y, Leung H, Yiu SM, Chin FY (2012) IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428.

상세보기
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959

상세보기
Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86, 248-249.

상세보기
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43, 223-225.

상세보기
Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8, 103-106.

상세보기
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365-386.
Weir SW (1990) Genetic data analysis II. Sinauer Associates, Sunderland.
Yue GH, Orban L (2000) Rapid isolation and characterization of microsatellites from the genome of Asian arowana (Scleropages formosus, Osteoglossidae, Pisces). Mol Ecol 9, 1007-1009.

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