SSR,SNP,and InDel Characteristics of the Transcriptome During Seed Germination to Seedling Formation in Docynia delavayi
Based on the transcriptome data from the seed germination to seedling formation stages of Docynia delavayi,SSR,SNP,and InDel loci were identified using MISA and GATK3 software,followed by feature analysis.The results showed that from the 63782 non-redundant gene sequences(unigenes)in the transcriptome data,a total of 76981 SSR loci were mined,resulting in an occurrence frequency of 30.18%.Among the different types of repeat motifs,the most frequently oc-curring were mononucleotide repeats,while the least frequent were hexanucleotide repeats.In terms of all motifs,A/T mo-tifs had the highest occurrence frequency,accounting for 38.09%of the total SSR loci,followed by AG/GT motifs,which represented 27.63%of the total SSR loci.The number of repeats for various motifs ranged from 5 to 15 times,with SSR se-quence lengths between 10 to 66 bp.The number of SNP loci across 15 samples ranged from 202602 to 278026,with an average of 253064 SNPs per sample.The ratio of transition to transversion types was approximately 6:4 for each sample.The number of InDel loci varied from 35609 to 48977,with an average of 44642 InDel loci per sample.The SSR,SNP,and InDel loci in the transcriptome during the seed germination to seedling formation period of D.delavayi were found to be abundant and highly polymorphic.
Docynia delavayiSeed germination to seedling formationTranscriptomeSSRSNPInDel
万方数据
维普
