| In order to characterize the SSRs in hulless barley (Hordeum vulgare L. var. nudum HK. f.) transcriptome and annotate the SSR sequences based on bioinformatics analysis,the distribution frequency and basic repeat motifs of SSRs in hulless barley transcriptiome were screened by MISA software. The gene annotation of SSR sequences were obtained by BLASTX against nr,COG,Swiss-Prot and KEGG databases. A total of 11 930 SSRs with 119 kinds of repeat motifs were found in 58 065 Unigenes,distributed in 9 576 Unigenes,which accounted for 16.49% of all Unigenes,and the density of distribution was 6.63 kb per SSR. Among the SSRs in hulless barley transcriptome,the most abundant repeat motif was the tri-nucleotide (64.19%),followed by the di-nucleotide (24.05%). AG/CT and AGG/CCT,CCG/CGG and AGC/CTG were the superior type in di-,and tri-nucleotide repeat motif(s).Most of the repeat number of SSRs was from 5 to 12,and the length of the motif ranged from 12 to 25 bp,with an average of 21.15 bp. 9 576 SSR sequences were annotated with BLASTX against protein databases (nr,COG,Swiss-Prot and KEGG),of which,7 987,5 559,5 588 and 2 077 were annotated,respectively. The annotation of the SSR sequences in hulless barley suggested that they were mainly related to the basic biological metabolism. |
基本信息
