Crops ›› 2016, Vol. 32 ›› Issue (3): 171-174.doi: 10.16035/j.issn.1001-7283.2016.03.032

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SSR Information in Transcriptome of White Ginger (Zingiber officinale Roscoe)

Zou Yong1,2,Huang Ke1,2,Jiang Yusong1,2,Liu Yiqing1,2   

  1. 1Forestry and Life Sciences,Chongqing University of Sciences and Arts,Chongqing 402160,China
    2Engineering Research Center for Special Plant Seedlings of Chongqing,Chongqing 402160,China
  • Received:2016-02-24 Revised:2016-04-25 Online:2016-06-15 Published:2018-08-26
  • Contact: Yiqing Liu

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Abstract:

The Trinity software was applied in de novo transcriptome assembly of the white giner (Zingiber officinale Roscoe). The redundant contigs were filtered and removed by the CAP3 software. Meanwhile, the non-redundant unigenes were examined by the tool of MISA to detect SSRs. Finally, 16 593 SSRs were found, and these SSRs were distributed in 14 436 unigenes in the examined sequences. Frequency of occurrences for SSRs was 9.39%, and density of distribution was on average 1/9.26kb. The most abundant type of repeat motif was dinucleotide (37.59%) and trinucleotide (45.24%).The most frequent motifs in dinucleotide and trinucleotide were AG/CT (22.47%) and AGG/CCT (11.79%). 85.06% motifs in the length ranged from 12bp to 20bp. The SSR sites in the transcriptome of white giner had high frequency of occurrences, high density, and various types. These data might be applied in the study on marker-assisted selection, genetic diversity of Zingiber officinale Roscoe.

Key words: Zingiber officinale Roscoe, Transcriptome, SSR, Information of loci

Table 1

The distribution frequency of SSRs in white ginger transcriptome"

重复类型
Type of repeat		 SSR数量
Number of SSRs		 比例(%)
Rate		 平均长度(bp)
Average length		 平均分布距离(kb)
Average distance		 频率(%)
Frequency
二核苷酸Dinucleotide 6 237 37.59 15.07 28.87 4.06
三核苷酸Trinucleotide 7 507 45.24 16.70 23.98 4.88
四核苷酸Tetranucleotide 1 656 9.98 17.23 108.73 1.08
五核苷酸Pentanucleotide 739 4.45 20.60 243.66 0.48
六核苷酸Hexanucleotide 454 2.74 25.12 396.61 0.30
合计Total 16 593 100 18.94 9.26 10.79

Fig.1

The distribution frequency of SSRs on major repeat types in white ginger transcriptome"

Table 2

The number of SSR repeats in white ginger transcriptome"

基序长度(bp) SSR重复次数Number of SSR repeats
4 5 6 7 8 9 10 11 12 13 14 15 16 17
2 - - 2183 1421 937 829 576 269 9 4 9 - - -
3 - 4448 1969 1035 47 - 3 1 2 - - - - 2
4 1239 355 43 17 1 - - - - - - - - -
5 658 74 6 1 - - - - - - - - - -
6 411 21 8 9 4 - 1 - - - - - - -
总计 2308 4898 4209 2483 989 829 580 270 11 5 9 - - 2
比例(%) 13.91 29.52 25.37 14.96 5.96 5.00 3.50 1.63 0.07 0.03 0.05 0 0 0.01

Fig.2

The length frequency of SSR motifs in white ginger transcriptome"

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