Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing 英文参考文献.docVIP
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Novel SNP Discovery in African Buffalo, Syncerus caffer, Using High-Throughput Sequencing 英文参考文献
NovelSNPDiscoveryinAfricanBuffalo,Synceruscaffer,
UsingHigh-ThroughputSequencing
NikkileRoex1,HarryNoyes2,AndrewBrass3,DanielG.Bradley4,StevenJ.Kemp2,5,SuzanneKay2,
PaulD.vanHelden1,EileenG.Hoal1*
1DST/NRFCentreofExcellenceforBiomedicalTuberculosisResearch/MRCCentreforMolecularandCellularBiology,DivisionofMolecularBiologyandHumanGenetics,
Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa, 2Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom,
3School of Computer Science, University of Manchester, Manchester, United Kingdom, 4Molecular Population Genetics, Smurfit Institute of Genetics, Trinity College
Dublin,Dublin,Ireland,5InternationalLivestockResearchInstitute,Nairobi,Kenya
Abstract
TheAfricanbuffalo,Synceruscaffer,isoneofthemostabundantandecologicallyimportantspeciesofmegafaunainthe
savannah ecosystem. It is an important prey species, as well as a host for a vast array of nematodes, pathogens and
infectiousdiseases,suchasbovinetuberculosisandcorridordisease.Large-scaleSNPdiscoveryinthisspecieswouldgreatly
facilitatefurtherresearchintotheareaofhostgeneticsanddiseasesusceptibility,aswellasprovideawealthofsequence
information for other conservation and genomics studies. We sequenced pools of Cape buffalo DNA from a total of 9
animals,onanABISOLiD4sequencer.TheresultingshortreadsweremappedtotheUMD3.1Bostaurusgenomeassembly
usingbothBWAandBowtiesoftwarepackages.Ameandepthof2.76coverageoverthemappedregionswasobtained.
Btau4geneannotation wasaddedtoallSNPsidentifiedwithingeneregions.BowtieandBWAidentifiedamaximumof
2,222,665 and 276,847 SNPs within the buffalo respectively, depending on analysis method. A panel of 173 SNPs was
validatedbyfluorescentgenotypingin87individuals.27SNPsfailedtoamplify,andoftheremaining146SNPs,43–54%of
theBowtieSNPsand57–58%oftheBWASNPswereconfirmedaspolymorphic.dN/dSratiosfoundnoevidenceofpositive
selection,andalthoughthereweregenesthatappearedtobeundernegativeselection,thesewerem
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