Analysis of SSR Information in Transcriptome Sequences of Saxifraga sinomontana

doi:10.7525/j.issn.1673-5102.2018.06.018

Abstract

Abstract: MISA (MicroSatellite) software was used to analyze the microsatellites information from transcriptome sequences of Saxifraga sinomontana J.T.Pan & Gornall, intending to provide candidate sequences for the development of SSR markers and detection of genetic diversity. In total, 4 622 SSRs were detected in 63 763 unigenes, which was represented by 110 repeat motifs. The frequency of SSRs was detected to be 7.25%, with an average occurrence of per 10.00 kB in length. The tri-nucleotide was the most abundant repeat motif (55.50%), followed by di-nucleotide (30.23%). The dominant repeat motifs in di-nucleotide and tri-nucleotide were AG/TC and AAG/TTC, respectively. In SSRs, the di-nucleotide possessed the most abundant repeat types, the longest span, as well as higher polymorphism, followed by tri-nucleotide. However, for the tetra-nucleotide, penta-nucleotide and hexa-nucleotide, there were few repeat types. For S.sinomontana, the repeat numbers of SSRs were mainly from five to nine, of which the number gradually decreased along with the repeat numbers increased. Besides, the motif length mostly distributed in 12 to 30 bp, and the polymorphism of SSRs was above medium level.

Key words: Saxifraga sinomontana, transcriptome, SSR analysis

CLC Number:

Q949.751.2

LI Yan, GENGJI Zhuo-Ma, JIA Liu-Kun, WANG Zhi-Hua, CHEN Shi-Long, GAO Qing-Bo. Analysis of SSR Information in Transcriptome Sequences of Saxifraga sinomontana[J]. Bulletin of Botanical Research, 2018, 38(6): 939-947.

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