Analysis of SSR Information in ESTs Resource of Ipomoea trifida

doi:10.3969/j.issn.1000-7091.2012.z1.006

Abstract

Abstract: In the study， 1 458 ESTs of Ipomoea trifida in the database of NCBI were downloaded and analyzedby bioinformatics tools and method． The results showed that we got 868 non-redundant ESTs with total length about334． 368 kb after the preprocessed， some redundants and low qualities sequences were removed． Totally 35 SSRs( Simple sequence repeat) were screened and distributed in 35 ESTs， accounting for 4． 03 % of the non-redundantESTs， the average distribution distance of the EST-SSRs was about 9． 55 kb． In the different motifs ranging from 2 to6 nucleotides， except to mononucleotide， di-nucleotide and tri-nucleotide repeats were dominant repeat types and accounted for 68． 57% ， ftri-nucleotide repeats types accounted for 45． 71 % ． In addition， Among all repeat motifs ofSSRs， AT /AT was most high-frequent repeat motif and accounted for 14． 29% ， followed by TCT /AGA accounted for11 ． 43 % ， thirdly TAA /TTA accounted for 8． 57% ． Among all SSRs， SSRs which repeated overstep 5 times accounted for 37． 14% ， that of repeated 5 and 7 times accounted for 14． 29% ． The result in this paper indicated that theEST-SSR of Ipomoea trifida hadrevelance utility value in the study of sweetpotato genetic and breeding．

Key words: Ipomoea trifida, Bioinformatics, Expressed sequence tags, Simple sequence repeat

CLC Number:

S531

JIA Zhao-dong, MA Pei-yong, GUO Xiao-ding, XIE Yi-zhi. Analysis of SSR Information in ESTs Resource of Ipomoea trifida[J]. ACTA AGRICULTURAE BOREALI-SINICA, doi: 10.3969/j.issn.1000-7091.2012.z1.006.

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