Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species

doi:10.1016/j.pld.2017.05.008

Abstract

Abstract: Microsatellites are highly polymorphic markers which have been used in a wide range of genetic studies. In recent years, various sources of next-generation sequencing data have been used to develop new microsatellite loci, but compared with the more common shotgun genomic sequencing or transcriptome data, the potential utility of RAD-seq data for microsatellite ascertainment is comparatively under-used. In this study, we employed MiddRAD-seq data to develop polymorphic microsatellite loci for the endangered yew species Taxus florinii. Of 8,823,053 clean reads generated for ten individuals of a population, 94,851 (~1%) contained microsatellite motifs. These corresponded to 2993 unique loci, of which 526 (~18%) exhibited polymorphism. Of which, 237 were suitable for designing microsatellite primer pairs, and 128 loci were randomly selected for PCR validation and microsatellite screening. Out of the 128 primer pairs, 16 loci gave clear, reproducible patterns, and were then screened and characterized in 24 individuals from two populations. The total number of alleles per locus ranged from two to ten (mean=4.875), and within-population expected heterozygosity from zero to 0.789 (mean=0.530), indicating that these microsatellite loci will be useful for population genetics and speciation studies of T. florinii. This study represents one of few examples to mine polymorphic microsatellite loci from ddRAD data.

Key words: MiddRAD-seq, Endangered species, Microsatellite, Next-generation sequencing, Taxus florinii

Hantao Qin, Guoqian Yang, Jim Provan, Jie Liu, Lianming Gao. Using MiddRAD-seq data to develop polymorphic microsatellite markers for an endangered yew species[J]. Plant Diversity, 2017, 39(05): 294-299.

References

Anderson, T.J.C., Su, X.Z., Roddam, A.W., et al., 2000. Complex mutations in a high proportion of microsatellite loci from the protozoan parasite Plasmodium falciparum. Mol. Ecol. 9, 1599-1608.
Angers, B., Bernatchez, L., 1997. Complex evolution of a salmonid microsatellite locus and its consequences in inferring allelic divergence from size information.Mol. Biol. Evol. 14, 230-238.
Baird, N.A., Etter, P.D., Atwood, T.S., et al., 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3, e3376.
Bonatelli, I.A., Carstens, B.C., Moraes, E.M., 2015. Using next generation RAD sequencing to isolate multispecies microsatellites for Pilosocereus (Cactaceae).PLoS ONE 10, e0142602.
Catchen, J., Hohenlohe, P.A., Bassham, S., et al., 2013. Stacks: an analysis tool set for population genomics. Mol. Ecol. 22, 3124-3140.
Davey, J.W., Hohenlohe, P.A., Etter, P.D., et al., 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12, 499-510.
Dubreuil, M., Sebastiani, F., Mayol, M., et al., 2008. Isolation and characterization of polymorphic nuclear microsatellite loci in Taxus baccata L. Conserv. Genet. 9, 1665-1668.
Elbers, J.P., Clostio, R.W., Taylor, S.S., 2016. Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Mol. Ecol.Resour. http://dx.doi.org/10.1111/1755-0998.12591.
Elshire, R.J., Glaubitz, J.C., Sun, Q., et al., 2011. A robust, simple genotyping-bysequencing (GBS) approach for high diversity species. PLoS ONE 6, e19379.
Gao, L.M., Möller, M., Zhang, X.M., et al., 2007. High variation and strong phylo-geographic pattern among cpDNA haplotypes in Taxus wallichiana (Taxaceae) in China and North Vietnam. Mol. Ecol. 16, 4684-4698.
Guichoux, E., Lagache, L., Wagner, S., et al., 2011. Current trends in microsatellite genotyping. Mol. Ecol. Resour. 11, 591-611.
Hodel, R.G.J., Segovia-Salcedo, M.C., Landis, J.B., et al., 2016. The report of my death was an exaggeration: a review for researchers using microsatellites in the 21st century. Appl. Plant Sci. 4, 1600025.
Jansson, E., Taggart, J.B., Wehner, S., et al., 2016. Development of SNP and microsatellite markers for goldsinny wrasse (Ctenolabrus rupestris) from ddRAD sequencing data. Conserv. Genet. Resour. 8, 201-206.
Jarne, P., Lagoda, P.J., 1996. Microsatellites, from molecules to populations and back.Trends Ecol. Evol. 11, 424-429.
Jeffries, D.L., Copp, G.H., Lawson, H.L., et al., 2016. Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius. L. Mol. Ecol. 25, 2997-3018.
Kingston, D.G., Newman, D.J., 2007. Taxoids: cancer-fighting compounds from nature. Curr. Opin. Drug Discov. Dev. 10, 130-144.
Leitch, I.J., Hanson, L., Winfield, M., et al., 2001. Nuclear DNA C-values complete familial representation in gymnosperms. Ann. Bot. 88, 843-849.
Li, Y.C., Korol, A.B., Fahima, T., et al., 2002. Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11, 2453-2465.
Liu, J., Gao, L.M., 2011. Comparative analysis of three different methods of total DNA extraction used in Taxus. Guihaia 31, 244-249.
Liu, J., Gao, L.M., Li, D.Z., et al., 2011a. Cross-species amplification and development of new microsatellite loci for Taxus wallichiana (Taxaceae). Am. J. Bot. 98, e70-e73.
Liu, J., Moeller, M., GAO, L.M., et al., 2011b. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species. Mol.Ecol. Resour. 11, 89-100.
Liu, J., Moeller, M., Provan, J., et al., 2013. Geological and ecological factors drive cryptic speciation of yews in a biodiversity hotspot. New Phytol. 199, 1093-1108.
Ma, J.Q., Huang, L., Ma, C.L., et al., 2015. Large-scale SNP discovery and genotyping for constructing a high-density genetic map of tea plant using specific-locus amplified fragment sequencing (SLAF-seq). PLoS ONE 10, e0128798.
Meglécz, E., Costedoat, C., Dubut, V., et al., 2010. QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26, 403-404.
Möller, M., Gao, L.M., Mill, R.R., et al., 2013. A multidisciplinary approach reveals hidden taxonomic diversity in the morphologically challenging Taxus wallichiana complex. Taxon 62, 1161-1177.
Peakall, R.O.D., Smouse, P.E., 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes 6, 288-295.
Peterson, B.K., Weber, J.N., Kay, E.H., et al., 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and nonmodel species. PLoS ONE 7, e37135.
Poudel, R.C., Gao, L.M., Möller, M., et al., 2013. Yews (Taxus) along the Hindu KushHimalayan region: exploring the ethnopharmacological relevance among communities of Mongol and Caucasian origins. J. Ethnopharmacol. 147, 190-203.
Rousset, F., 2008. genepop' 007: a complete re-implementation of the genepop software for Windows and Linux. Mol. Ecol. Resour. 8, 103-106.
Schuelke, M., 2000. An economic method for the fluorescent labeling of PCR fragments. Nat. Biotechnol. 18, 233-234.
Selkoe, K.A., Toonen, R.J., 2006. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers. Ecol. Lett. 9, 615-629.
Spjut, R.W., 2007. Taxonomy and nomenclature of Taxus (Taxaceae). J. Bot. Res. Inst.Tex. 1, 203-289.
Taylor, S.A., White, T.A., Hochachka, W.M., et al., 2014. Climate-mediated movement of an avian hybrid zone. Curr. Biol. 24, 671-676.
Vera, M., Díez-del-Molino, D., García-Marín, J.L., 2016. Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Mol. Ecol. 25, 1089-1105.
Wang, X., Wang, L., 2016. GMATA: an integrated software package for genome-scale SSR mining, marker development and viewing. Front. Plant Sci. 7, 1350.
Wei, N., Bemmels, J.B., Dick, C.W., 2014. The effects of read length, quality and quantity on microsatellite discovery and primer development: from Illumina to PacBio. Mol. Ecol. Resour. 14, 953-965.
Yang, G.Q., Chen, Y.M., Wang, J.P., et al., 2016. Development of a universal and simplified ddRAD library preparation approach for SNP discovery and genotyping in angiosperm plants. Plant Meth. 12, 39.
Yang, J.B., Li, H.T., Li, D.Z., et al., 2009. Isolation and characterization of microsatellite markers in the endangered species Taxus wallichiana using the FIASCO method.HortScience 44, 2043-2045.
Zalapa, J.E., Cuevas, H., Zhu, H., et al., 2012. Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences. Am.J. Bot. 99, 193-208.

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