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Bulletin of Botanical Research ›› 2016, Vol. 36 ›› Issue (1): 116-122.doi: 10.7525/j.issn.1673-5102.2016.01.016

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Distribution and Molecular Marker of SSR in EST Resource of Casuarinaceae

HU Pan1;ZHONG Chong-Lu1;ZHANG Yong1;JIANG Qing-Bin1;CHEN Yu1;CHEN Zhen1;HAN Qiang1;Khongsak Pinyopusarerk2;Didier Bogusz3   

  1. 1.Research Institute of Tropical Forestry,Chinese Academy of Forestry,Guangzhou 510520;
    2.CSIRO National Research Collections Australia,Acton,ACT 2600,Australia;
    3.Institut de Recherche pour le Développement(IRD),BP 64501,Montpellier,France
  • Online:2016-01-15 Published:2016-05-18

Abstract: There are 34 752 ESTs of Casuarinaceae in the database of NCBI, resulting in 12 062 non-redundant sequences(Unigene) with total length of 7 278.578 kb. 367 SSR were discovered to distribution on 353 Unigenes, the frequency and repeat motif types number of these EST-SSRs was 2.93% and 39, and the mean distance was 19.83 kb. Dinucleotide and trinucleotide repeats were the dominant types among the EST-SSRs, accounting for 57.77% and 34.06%, respectively. AG/CT(93.87%) and AAG/CTT(44.09%) were the most abundant motifs for dinucleotide and trinucleotide. There were 97 pairs of primers designed for the obtained EST-SSR, and 32 of all could be effectively amplified. By Blast analysis, 77.3% ESTs sequences containing SSR locus were homologous with functional sequences in non-redundant protein sequences databases. The homology with functions from Vitis vinifera had the greatest proportion(10.4%). By GO functional classification, 47.3% EST sequences containing SSR locus had at least one GO ontology, the sequences relevant to cellular components were most, and the functional items relevant to cytoplasm and nucleus were highest.

Key words: Casuarinaceae, EST, SSR