Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis

AN Jun; ZHENG Cai-xia; YAO Yang; CHEN Bin-li

doi:10.13332/j.1000-1522.20150033

Journal of Beijing Forestry University > 2016 > 38(5): 77-83. > DOI: 10.13332/j.1000-1522.20150033

AN Jun, ZHENG Cai-xia, YAO Yang, CHEN Bin-li. Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis[J]. Journal of Beijing Forestry University, 2016, 38(5): 77-83. DOI: 10.13332/j.1000-1522.20150033

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Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis

College of Biological Sciences and Technology,Beijing Forestry University,Beijing,100083,P. R. China.

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Received Date: January 28, 2015
Revised Date: January 28, 2015
Published Date: May 30, 2016

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Abstract

Abstract

In order to understand the molecular mechanism of regulating ovule development of Pinus tabulae-formis thoroughly and clarify the influence of microsatellites in ovule development, we used the program MISA to mine and analyze the high-throughput sequencing in earlier experiments to seek the microsatellites of transcriptome, in an attempt to provide significant information and data for deeper research. A total of 1412 SSRs were identified in 1274 unigenes with one SSR per 2.15kb. Among 87 SSR repeat motifs of ovule transcriptome, (A/T)n was in the maximum proportion, accounting for 45.89%. Mononucleotide and trinucleotide repeats were the two more abundant in all repeat types, accounting for 46.88% and 34.99%, respectively. The microsatellites with length below 20 bp were in the majority and those over 20 bp amounted only 5.67%. It showed a negative relation between the frequency of occurrences and the length of microsatellites. Most of SSRs were in untranslated region, and only 232 SSRs were located in protein-coding regions, while 18 in both of them. Trinucleotide repeats were the richest in protein-coding regions (105, 45.26%).
- Pinus tabulaeformis,
- ovule,
- transcription,
- microsatellite

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References (67)

References

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Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis

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