Examining the efficacy of a genotyping-by-sequencing technique for population genetic analysis of the mushroom Laccaria bicolor and evaluating whether a reference genome is necessary to assess homology

Literature cited

• BallouxF. 2004. Heterozygote excess in small populations and the heterozygote-excess effective population size. Evolution 58:1891–1900, doi:10.1111/j.0014-3820.2004.tb00477.x
   Google Scholar
• BergemannSEDouhanGWGarbelottoMMillerSL. 2006. No evidence of population structure across three isolated subpopulations of Russula brevipes in an oak/pine woodland. New Phytol 170:177–184, doi:10.1111/j.1469-8137.2006.01654.x
   Google Scholar
• BergemannSEMillerSL. 2002. Size, distribution and persistence of genets in local populations of the late-stage ectomycorrhizal basidiomycete, Russula brevipes. New Phytol 156: 313–320, doi:10.1046/j.1469-8137.2002.00507.x
   PubMedGoogle Scholar
• BergemannSESmithMAParrentJLGilbertGSGarbelottoM. 2009. Genetic population structure and distribution of a fungal polypore, Datronia caperata (Polyporaceae), in mangrove forests of Central America. J Biogeography 36:266–279, doi:10.1111/j.1365-2699.2008.02006.x
   Google Scholar
• Cabrera-ToledoDGonzales-AstorgaJVolvidesAP. 2008. Heterozygote excess in ancient populations of the critically endangered Dioon caputoi (Zamiaceae, Cycadales) from central Mexico. Bot J Linn Soc 158:436–447, doi:10.1111/j.1095-8339.2008.00868.x
   Google Scholar
• CatchenJMAmoresAHohenlohePCreskoWPostlethwaitJH. 2011. Stacks: building and genotyping loci de novo from short-read aequences. G3: Genes, genomes, genet 1:171–182.
   Web of Science ®Google Scholar
• CoatesBSSumerfordDVMillerNJKimKSSappingtonTWSiegfriedBDLewisLC. 2009. Comparative performance of single nucleotide polymorphism and microsatellite markers for population genetic analysis. J Hered 100:556–564, doi:10.1093/jhered/esp028
   Google Scholar
• DaveyJWBlaxterML. 2011. RADSeq: next-generation population genetics. Briefings in Funct Genomics 9: 416–423, doi:10.1093/bfgp/elq031
   Google Scholar
• DaveyJWHohenlohePAEtterPDBooneJQCatchenJMBlaxterML. 2011. Genomewide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510, doi:10.1038/nrg3012
   PubMed Web of Science ®Google Scholar
• DeFaveriJViitaniemiHLederEMeriläJ. 2013. Characterizing genic and nongenic molecular markers: comparison of microsatellites and SNPs. Mol Ecol Res 13:377–392, doi:10.1111/1755-0998.12071
   Web of Science ®Google Scholar
• DouhanGWVincenotLGrytaHSelosseM-A. 2011. Population genetics of ectomycorrhizal fungi: from current knowledge to emerging directions. Fungal Biol 115:569–597, doi:10.1016/j.funbio.2011.03.005
   PubMed Web of Science ®Google Scholar
• DutechCEnjalbertJFournierEDelmotteFBarrésBCarlierJTharreauDGiraudT. 2007. Challenges of microsatellite isolation in fungi. Fungal Genet Biol 44: 933–949, doi:10.1016/j.fgb.2007.05.003
   PubMed Web of Science ®Google Scholar
• ElshireRJGlaubitzJCSunQPolandJAKawamotoKBucklerESMitchellSE. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379, doi:10.1371/journal.pone.0019379
   PubMed Web of Science ®Google Scholar
• EvannoGRegnautSGoudetJ. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Mol Ecol 14:2611–2620, doi:10.1111/j.1365-294X.2005.02553.x
   PubMed Web of Science ®Google Scholar
• GarvinMRSaitohKChurikovDYBrykovVAGharrettAJ. 2010. Single nucleotide polymorphisms in chum salmon (Oncorhynchus keta) mitochondrial DNA derived from restriction site haplotype information. Genome 53:501–507, doi:10.1139/G10-026
   Google Scholar
• GuichouxELagacheLWagnerSChaumeilPLÉGerPLepaisOLepoittevinCMalausaTRevardelESalinFPetitRJ. 2011. Current trends in microsatellite genotyping. Mol Ecol Res 11:591–611, doi:10.1111/j.1755-0998.2011.03014.x
   PubMed Web of Science ®Google Scholar
• HessJEMatalaAPNarumSR. 2011. Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of chinook salmon in the Columbia River Basin. Mol Ecol Res 11:137–149, doi:10.1111/j.1755-0998.2010.02958.x
   PubMed Web of Science ®Google Scholar
• HohenlohePABasshamSEtterPDStifflerNJohnsonEACreskoWA. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genet 6:e1000862, doi:10.1371/journal.pgen.1000862
   PubMed Web of Science ®Google Scholar
• KeirleMRAvisPGFeldheimKAHemmesDEMuellerGM. 2011. Investigation the allelic evolution of an imperfect microsatellite locus in the Hawaiian mushroom Rhodocollybia laulaha. J Hered 102:727–734, doi:10.1093/jhered/esr099
   Google Scholar
• LabbéJMuratCMorinELe TaconFMartinF. 2011. Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Curr Genet 57:75–88, doi:10.1007/s00294-010-0328-9
   Google Scholar
• LangmeadBTrapnellCPopMSalzbergSL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25, doi:10.1186/gb-2009-10-3-r25
   PubMed Web of Science ®Google Scholar
• MartinFAertsAAhrenDBrunADanchinEGJDuchaussoyFGibonJKohlerALindquistEPeredaVSalamovAShapiroHJWuytsJBlaudezDBueeMBroksteinPCanbackBCohenDCourtyPECoutinhoPMDelaruelleCDetterJCDeveauADiFazioSDuplessisSFraissinet-TachetLLucicEFrey-KlettPFourreyCFeussnerIGayGGrimwoodJHoeggerPJJainPKilaruSLabbeJLinYCLegueVLe TaconFMarmeisseRMelayahDMontaniniBMuratetMNehlsUNiculita-HirzelHSecqMPO-LPeterMQuesnevilleHRajashekarBReichMRouhierNSchmutzJYinTChalotMHenrissatBKuesULucasSVan de PeerYPodilaGKPolleAPukkilaPJRichardsonPMRouzePSandersIRStajichJETunlidATuskanGGrigorievIV. 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88–92, doi:10.1038/nature06556
   PubMed Web of Science ®Google Scholar
• MillerMRDunhamJPAmoresACreskoWAJohnsonEA. 2007. Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248, doi:10.1101/gr.5681207
   PubMed Web of Science ®Google Scholar
• MorrisGPGrabowskiPPBorevitzJO. 2011. Genomic diversity in switchgrass (Panicum virgatum): from the continental scale to a dune landscape. Mol Ecol 20: 4938–4952, doi:10.1111/j.1365-294X.2011.05335.x
   Google Scholar
• MuellerGMGardesM. 1991. Intra- and interspecific relations within the Laccaria bicolor sensu lato. Mycol Res 95:592–601, doi:10.1016/S0953-7562(09)80073-7
   Google Scholar
• NarumSRBanksMBeachamTDBellingerMRCampbellMRDekoningJElzAGuthrie IiiCMKozfkayCMillerKMMoranPPhillipsRSeebLWSmithCTWarheitKYoungSFGarzaJC. 2008. Differentiating salmon populations at broad and fine geographical scales with microsatellites and single nucleotide polymorphisms. Mol Ecol 17:3464–3477.
   PubMed Web of Science ®Google Scholar
• PritchardJKStephensMDonnellyP. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945–959.
   PubMed Web of Science ®Google Scholar
• RengmarkAHSlettanASkaalaϕLieϕLingaasF. 2006. Genetic variability in wild and farmed Atlantic salmon (Salmo salar) strains estimated by SNP and microsatellites. Aquaculture 253:229–237, doi:10.1016/j.aquaculture.2005.09.022
   Google Scholar
• RoyMDuboisM-PProffitMVincenotLDesmaraisESelosseM-A. 2008. Evidence from population genetics that the ectomycorrhizal basidiomycete Laccaria amethystina is an actual multihost symbiont. Mol Ecol 17:2825–2838, doi:10.1111/j.1365-294X.2008.03790.x
   PubMed Web of Science ®Google Scholar
• StorferAMurphyMASpearSFHoldereggerRWaitsLP. 2010. Landscape genetics: Where are we now? Mol Ecol 19:3496–3514, doi:10.1111/j.1365-294X.2010.04691.x
   PubMed Web of Science ®Google Scholar
• VincenotLNaraKSthultzCLabbéJDuboisM-PTedersooLMartinFSelosseM-A. 2012. Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex. Mol Ecol 21: 281–299, doi:10.1111/j.1365-294X.2011.05392.x
   PubMed Web of Science ®Google Scholar
• WillingE-MDreyerCvan OosterhoutC. 2012. Estimates of genetic differentiation measured by FST do not necessarily require large sample sizes when using many SNP markers. PLoS ONE 7:e42649, doi:10.1371/journal.pone.0042649
   PubMed Web of Science ®Google Scholar
• WilsonAWHosakaKPerryBAMuellerGM. 2013. Laccaria (Agaricomycetes, Basidiomycota) from Tibet (Xizang Autonomous Region, China). Mycoscience 54: 406–419, doi:10.1016/j.myc.2013.01.006
   Web of Science ®Google Scholar