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Scientia Silvae Sinicae ›› 2013, Vol. 49 ›› Issue (8): 43-50.doi: 10.11707/j.1001-7488.20130807

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Survey and Analysis of Microsatellites from DNA Sequences in Camellia Species Using 454 Pyrosequencing

Wen Qiang1,2, Xu Linchu2, Jiang Xiangmei2, Li Jiang2, Gu Yincong1, Xu Li'an1, Huang Minren1   

  1. 1. Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education Nanjing Forestry University Nanjing 210037;
    2. Jiangxi Forestry Academy Nanchang 330032
  • Received:2013-03-11 Revised:2013-04-23 Online:2013-08-25 Published:2013-08-17

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Abstract:

Abstract: By using 454 pyrosequencing, the simple sequence repeats (SSRs) from DNA sequences in three Camellia species, including C. oleifera, C. brevistyla and C. chekiangoleosa, were tapped with repeats of 2 to 6 bp by MISA. In all cases, the frequency of repeat motifs in the EST was similar, while the proportion in the EST of C. oleifera was higher than that of its genome. Comparisons of all SSRs, the dinucleotide repeat microsatellites (DNRs) were most dominant (>55%) and the most common DNRs was (AG)n. The most common trinucleotide repeat microsatellites (TNRs) was (AAG)n in EST, while the most common TNRs was (AAT)n in the genome of C. oleifera. Apart from the hexaucleotide repeat microsatellites (HXNRs), the abundance of the other four classes of microsatellites was negatively correlated with their repeat motif lengths. In the EST, apart from the HXNRs, diversification of microsatellite lengths (repeat number variation) was also negatively correlated with their repeat motif lengths, and we predicted that DNRs was the highest polymorphism and pentaucleotide repeat microsatellites (PTNRs) was the lowest. Subsequently, statistical analysis on SSRs within coding regions (CDS) and untranslated regions (UTR) in the Unigene showed that the ratio of motifs distribution was ranked as the following: 3'UTR>CDS>5'UTR. The DNRs were the dominant microsatellite in UTR, while the TNRs were dominant in CDS. The proportion of TNRs in the 5'UTR was higher than that in the 3'UTR, indicating that the SSRs in the 5'UTR were more conservative.

Key words: Camellia, 454 pyrosequencing, microsatellites

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