Characterization of Genome-Wide Microsatellites of Saccharina japonica Based on a Preliminary Assembly of Illumina Sequencing Reads-中国期刊网

摘要 Microsatellitesorsimplesequencerepeats（SSR）functionwidelyandlocatedependentlyingenome.However,theircharacteristicsareoftenignoredduetothelackofgenomicsequencesofmostspecies.Kelp（Saccharinajaponica）,abrownmacroalga,isextensivelyculturedinChina.Inthisstudy,thegenomeofS.japonicawassurveyedusinganIlluminasequencingplatform,anditsmicrosatelliteswerecharacterized.Thepreliminarilyassembledgenomewas469.4Mbinsize,withascaffoldN50of20529bp.Amongthe128370identifiedmicrosatellites,90671,25726and11973werefoundinintergenicregions,intronsandexons,averaging339.3,178.8and205.4microsatellitesperMb,respectively.ThesemicrosatellitesdistributedunevenlyinS.japonicagenome.Mononucleotidemotifswerethemostabundantinthegenome,whiletrinucleotideoneswerethemostprevalentinexons.Themicrosatelliteabundancedecreasedsignificantlywiththeincreaseofmotifrepeatnumbers,andthemicrosatelliteswithasmallnumberofrepeatsaccountedforahigherproportionoftheexonsthanthoseoftheintergenicregionsandintrons.C/G-richmotifsweremorecommoninexonsthaninintergenicregionsandintrons.ThesecharacteristicsofmicrosatellitesinS.japonicagenomemayassociatewiththeirfunctions,andultimatelytheiradaptationandevolution.Amongthe120140pairsofdesignedmicrosatelliteprimers,approximately75%werepredictedtobeabletoamplifyS.japonicaDNA.Thesemicrosatellitemarkerswillbeextremelyusefulforthegeneticbreedingandpopulationevolutionstudiesofkelp.

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Characterization of Genome-Wide Microsatellites of Saccharina japonica Based on a Preliminary Assembly of Illumina Sequencing Reads

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Characterization of Genome-Wide Microsatellites of Saccharina japonica Based on a Preliminary Assembly of Illumina Sequencing Reads

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