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Bulletin of Botanical Research ›› 2019, Vol. 39 ›› Issue (2): 294-302.doi: 10.7525/j.issn.1673-5102.2019.02.016

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Characteristic Analysis of Microsatellites in the Transcriptome of Phyllanthus emblica,an Important Edible and Medicinal Plant

LIU Xiong-Fang, LI Tai-Qiang, ZHANG Xu, LI Zheng-Hong, WAN You-Ming, AN Jing, LIU Xiu-Xian, MA Hong   

  1. Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224
  • Received:2018-08-27 Online:2019-03-05 Published:2019-03-20
  • Supported by:
    The Fundamental Research Funds for the Central Non-profit Research Institution of CAF(CAFYBB2016ZX003-2);Technology Innovation Talent Project of Yunnan Province(2016HB007)

Abstract: In order to comprehensively understand the characteristics of distribution and variation of the SSR loci in the transcriptome of Phyllanthus emblica L., transcriptome sequencing was conducted on young leaves of P.emblica by using Illumina Hiseq 4000. The SSR loci were studied using MISA software from the obtained unigenes. A total of 9 991 SSRs distributed on 9 538 unigenes were detected, with an average density of one SSR per 5.49 kB. Mononucleotide and dinucleotide repeats were the main SSR types, accounting for 42.3% and 30.79% of all SSRs, respectively. There were 1 731 SSR loci distributed across the protein-coding regions, with an overall density of 0.039 SSRs/kB. The dominant repeat type was trinucleotide repeat type. Among all the 169 repeat motifs, A/T(42.10%) was the richest motif, followed in order by AG/CT(22.91%) and AAG/CTT(5.02%). The number of repeats ranged from 4 to 75, most of them were concentrated on four to 20. The SSRs with repeat fragment length ≥20 bp accounted for 21.20%. There was significant negative correlation(P<0.01) between the frequency of SSRs and the repeat fragment length, with correlation coefficient of -0.561. The SSR loci in the transcriptome of P.emblica showed high frequency and density of distribution, rich low-level repeat motifs, large repeat number and long fragments, most of which exhibited high potential of polymorphisms in our study. These SSR loci would lay an important foundation for further developing a large number of EST-SSRs and studying on population genetics of P.emblica, and they would also provide a reference for conservation and rational exploitation of genetic resources of the species.

Key words: Phyllanthus emblica, edible and medicinal plant, transcriptome sequencing, microsatellite

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