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Tree Genetics and Molecular Breeding 2012, Vol.2, No.1, 1
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7
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1
A Letter Open Access
A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine, Poplar and
Eucalyptus
Maomao Yan , Xiaogang Dai , Shuxian Li , Tongming Yin
Jiangsu Key Laboratory Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, 210037, P.R. China
Corresponding author email:
tmyin@njfu.com.cn;
Authors
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
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)
Abstract
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.
Keywords
Microsatellites; Express sequence tag (EST); Repeat unit; Pine (
Pinus spp
.); Poplar (
Populus spp
.); Eucalyptus
(
Eucalyptus spp
.)
Background
Microsatellite, also known as Simple Sequence Repeats
(SSR), refers to short tandem repeating sequences of
2
-
6 base pairs nucleotide units (He, 1998). It is the
most rapid variable DNA sequence in genome, not
only with high polymorphism but also with high
conservation and universality among in the relatives
(Kashi and King, 2006). Therefore, microsatellite
markers would be one of the most effective genetic
tools for the integration of information among the
genomes of closely relative species (Li et al., 2009),
that has become the most widely applied molecular
markers in genetic research.
Microsatellite markers have been widely used for
genetic mapping and germplasm identification etc in
many plants. In recent years, microsatellite markers
were also rapidly developed in trees, having been
widely used in the tree studies of fingerprinting,
genetic map building and population genetic analyzing
etc. (González-Martínez et al., 2006). In the studies of
modern molecular genetics, microsatellite markers