Welcome to Chinese Journal of Tropical Crops,

Chinese Journal of Tropical Crops ›› 2021, Vol. 42 ›› Issue (10): 2828-2833.DOI: 10.3969/j.issn.1000-2561.2021.10.011

• Omics & Biotechnology • Previous Articles     Next Articles

SSR, SNP and InDel Analysis Based on Tetrastichus brontispae Transcriptome

LIU Huawei1,2,3,4, LI Chaoxu1,3,4, LI Fen2, LYU Chaojun1,3,4, WU Shaoying2, QIN Weiquan1,3,4,*()   

  1. 1. Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571399, China
    2. Hainan University, Haikou, Hainan 570228, China
    3. Hainan Innovation Center of Academician Team (Integrated Management of Arecanut Yellow Leaf Disease), Wenchang, Hainan 571339, China
    4. Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang, Hainan 571399, China.
  • Received:2020-12-15 Revised:2021-02-18 Online:2021-10-25 Published:2021-11-25
  • Contact: QIN Weiquan

Abstract:

Tetrastichus brontispae is the pupal parasitic wasp of Brontispa longissima, an exotically invasive pest. The analysis of SSR, SNP and InDel sites in the transcriptome sequences of T. brontispae can provide data support for the development of new molecular markers and the in-depth study of its genetic diversity, population genetic structure and historical dynamics. Based on transcriptional data, MISA software and Varscan software were used to search the SSR, SNP and InDel sites of Unigenes. A total of 29 754 SSR sites were obtained in 11 802 Unigenes, with an average of 1 SSR per 1.72 kb, with an incidence of 39.96%. The length of the SSR fragments was 10-382 bp, with an average length of 23.91 bp. In the SSR segment, mononucleotide was dominant (60.82%), followed by dinucleotide (27.69%) and trinucleotide (10.79%). In all repeating motifs, the dominant repeating motif was A/T (59.32%), followed by AT/AT (15.28%). Among 6 895 Unigenes, 51 334 SNP sites were discovered, and each Unigene contained 7.45 SNP on average. There were 37 445 transition sites (72.94%) and 13 975 transversion points (27.22%). 15 644 InDel sites were also identified out of 6 040 Unigene, with an average of 2.59 InDel per Unigene.SSR, SNP and InDel sites are abundant in the transcriptome of T. brontispae, with a large number, high occurrence frequency, rich type and polymorphism potential.

Key words: Tetrastichus brontispae, transcriptome, SSR, SNP, InDel

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