A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine, Poplar and Eucalyptus
Jiangsu Key Laboratory Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, P.R. China
Tree Genetics and Molecular Breeding, 2012, Vol. 2, No. 1 doi: 10.5376/tgmb.2012.02.0001
Received: 16 Dec., 2011 Accepted: 18 Jan., 2012 Published: 01 Feb., 2012
© 2012 BioPublisher Publishing Platform
This article was first published in Genomics and Applied Biology in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:
Yan et al., 2012, A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine, Poplar and Eucalyptus, Tree Genetics and Molecular Breeding, Vol.2, No.1 1-7 (doi: 10.5376/tgmb.2012.02.0001)
Microsatellites are the kinds of sequences in the genome of living organism that have the fastest variation frequency. The variations of numbers of microsatellite repeat units in the structure gene cause frame-shift mutation of the gene, resulting in gene expressing in fully difference or expressing truncated protein. Thus, in the evolutionary process, microsatellite within the gene region would be influenced by a strong selection. In order to study the variations of microsatellite within the of gene s in different tree species, we performed a meta-analysis by using SPUTNIK program to analyze the 30 000 express sequence tag (EST) sequences of pine (Pinus spp.), Poplar (Populus spp.) and eucalyptus (Eucalyptus spp.) downloaded from NCBI database.
The results showed that the proportion of EST sequences containing microsatellites was 18.7% in eucalyptus and 15.3% in poplar, whereas only 8.2% occurred in pine tree that exhibited bigger differentiation. The study found that three-base repeat unit was is a major repeat type of microsatellite in the coding sequence of these three tree species. In addition to three-base repeat microsatellite, the abundance of other types of microsatellites in EST sequences of eucalyptus and poplar was decreased with increase of the repeat unit length, but in the pine tree occurring in the opposite situation. It was worth noticeable that the amount of microsatellite with fast frequency of variation of EST sequences in pine (>20 bp) was significantly less than that in eucalyptus and poplar. The study also found that the rate of repeating unit losing or gaining decreased with increases of the repeating units in the microsatellite of three tree species. In this study, we reported the comparative studies of microsatellites within the gene region in different tree species, revealing the similarities and differences in abundance and variation frequency of microsatellites in the EST sequences in pine, poplar and eucalyptus. Microsatellite sequence would have an important influence on the function of the gene containing the microsatellite. The results of this study would provide some parameters for understanding the characteristics of microsatellites with the gene region in the the different species, as well as useful references for developing microsatellite markers with high polymorphism by using the EST sequence of the studying tree species.
Microsatellites; Express sequence tag (EST); Repeat unit; Pine (Pinus spp.); Poplar (Populus spp.); Eucalyptus (Eucalyptus spp.)