Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences英文文献资料.docVIP

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Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences英文文献资料.doc

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Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences英文文献资料

HindawiPublishingCorporation AdvancesinBioinformatics Volume2010,ArticleID976792,7pages doi:10.1155/2010/976792 ResearchArticle ApplyingSmall-ScaleDNASignaturesasanAidinAssembling SoybeanChromosomeSequences MyronPeto,DavidM.Grant,RandyC.Shoemaker,andStevenB.Cannon USDA-ARS-CICGRUnitandDepartmentofAgronomy,IowaStateUniversity,Ames,IA50011,USA CorrespondenceshouldbeaddressedtoStevenB.Cannon,steven.cannon@ Received19November2009;Accepted28June2010 AcademicEditor:IzabelaMakalowska Copyright?2010MyronPetoetal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. Previousworkhasestablishedagenomicsignaturebasedonrelativecountsofthe16possibledinucleotides.Untilnow,ithasbeen generallyacceptedthatthedinucleotidesignatureischaracteristicofagenomeandisrelativelyhomogeneousacrossagenome. However,wefoundsomelocalregionsofthesoybeangenomewithasignaturedi?eringwidelyfromthatoftherestofthegenome. Thoseregionsweremostlycentromericandpericentromeric,andenrichedforrepetitivesequences.WefoundthatDNAbinding energyalsopresentedlarge-scalepatternsacrosssoybeanchromosomes.Thesetwopatternswerehelpfulduringassemblyand qualitycontrolofsoybeanwholegenomeshotgunsca?oldsequencesintochromosomepseudomolecules. 1.Introduction sequence overlap and (2) construction of chromosome pseudomoleculesbyplacingandorientingthesca?oldsusing other information (i.e., genetic and physical maps). We foundthatthegeneticmap,whilegenerallycollinearwiththe genomicsequence,showedwidelyvaryingratesofrecombi- nation.Figure1showschromosome6ofsoybean(formerly linkagegroupC2),whichillustratesthephenomenon.The horizontalsectioninthemiddleofthechromosomecovers thecentromericandpericentromericregionswherealarge physical distance corresponds to a small genetic distance. Therelativelackofrecombinationinthisregionresultsin poor resolution and di?culties in ordering and orienting thosesca?olds.Inco