Characterization of microsatellites in the coding regions of the Populus genome

Li, Shuxian; Yin, Tongming; Wang, Mingxiu; Tuskan, Gerald A.

doi:10.1007/s11032-010-9413-5

Cited by 18 publications

(20 citation statements)

References 23 publications

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“…Microsatellite locus size (10.03 and 11.10 repeats in E. plorans and L. migratoria, respectively) and distance between loci (4.16 kb in E. plorans and 3.53 kb in L. migratoria on average) also support SSR association with noncoding sequences because exonic regions use to bear microsatellite repeats at low density (3 or less units at about 40 kb distance) (Li et al 2002(Li et al , 2011. However, the presence of more distant microsatellite loci with less than five repeats, located in coding regions, would have gone unnoticed with our search criterion.…”

Section: Discussionmentioning

confidence: 96%

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

et al. 2014

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Simple sequence repeats (SSRs), also known as microsatellites, are one of the prominent DNA sequences shaping the repeated fraction of eukaryotic genomes. In spite of their profuse use as molecular markers for a variety of genetic and evolutionary studies, their genomic location, distribution, and function are not yet well understood. Here we report the first thorough joint analysis of microsatellite motifs at both genomic and chromosomal levels in animal species, by a combination of 454 sequencing and fluorescent in situ hybridization (FISH) techniques performed on two grasshopper species. The in silico analysis of the 454 reads suggested that microsatellite expansion is not driving size increase of these genomes, as SSR abundance was higher in the species showing the smallest genome. However, the two species showed the same uneven and nonrandom location of SSRs, with clear predominance of dinucleotide motifs and association with several types of repetitive elements, mostly histone gene spacers, ribosomal DNA intergenic spacers (IGS), and transposable elements (TEs). The FISH analysis showed a dispersed chromosome distribution of microsatellite motifs in euchromatic regions, in coincidence with chromosome location patterns previously observed for many mobile elements in these species. However, some SSR motifs were clustered, especially those located in the histone gene cluster.

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Section: Discussionmentioning

confidence: 96%

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

et al. 2014

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“…However, microsatellite analysis of bioinformatics mainly focused on fungi, human beings and mode of plant (Brinkmann et al, 1998;Lothe, 1997;Toth et al, 2000). For forest tree species, most of microsatellite analysis were yet limited to be experimental analysis on a small number of microsatellite loci (Wyman et al, 2003), whereas a large number of microsatellite bioinformatics analysis were also limited to a single species, such as whole genome sequenced poplar (Tuskan et al, 2004;Li et al, 2009). So far, it is yet to report comparative study of the characteristics of microsatellite more than one species, which might be due to lack of the genomic sequence resources.…”

Section: Discussionmentioning

confidence: 99%

“…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.…”

Section: Introductionmentioning

confidence: 99%

“…The studies on the microsatellite in the exon sequence of the poplar genome revealed that the microsatellites with three-base repeat units in the exons of poplar genome were far more than other types of microsatellites (Li et al, 2009). Comparing to microsatellites with other repeat types, the microsatellite with three-base repeat unit had minimum impacts on open reading frame of gene, enrichment of three-base repeat microsatellite showed that microsatellite in the exon region were influenced by the selection of genetic code in the evolutionary process.…”

Section: Introductionmentioning

confidence: 99%

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A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine, Poplar and Eucalyptus

Yan¹,

Dai²,

Li³

et al. 2012

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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.

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“…SSRs are highly abundant and exhibit extensive levels of polymorphism in both eukaryotic and prokaryotic genomes. They are found in both proteincoding and in noncoding regions of genomes, but are more abundant in noncoding regions than in exons (Tóth et al, 2000;Li et al, 2011). Compared with an average mutation rate of approximately 10 -9 single nucleotide substitutions per generation for eukaryotic genomes, SSR locus mutation rates are high, ranging from 10 -3 to 10 -6 per generation (Schug et al, 1997;Xu et al, 2000).…”

Section: Introductionmentioning

confidence: 99%

Survey of simple sequence repeats in woodland strawberry (Fragaria vesca)

Guan¹,

Huang²,

Feng³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. The use of simple sequence repeats (SSRs), or microsatellites, as genetic markers has become popular due to their abundance and variation in length among individuals. In this study, we investigated linkage groups (LGs) in the woodland strawberry (Fragaria vesca) and demonstrated variation in the abundances, densities, and relative densities of mononucleotide, dinucleotide, and trinucleotide repeats. Mononucleotide, dinucleotide, and trinucleotide repeats were more common than longer repeats in all LGs examined. Perfect SSRs were the predominant SSR type found and their abundance was extremely stable among LGs and chloroplasts. Abundances of mononucleotide, dinucleotide, and trinucleotide repeats were positively correlated with LG size, whereas those of tetranucleotide and hexanucleotide SSRs were not. Generally, in each LG, the abundance, relative abundance, relative density, and the proportion of each unique SSR all declined rapidly as the repeated unit increased. Furthermore, the lengths and frequencies of SSRs varied among different LGs.

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Characterization of microsatellites in the coding regions of the Populus genome

Cited by 18 publications

References 23 publications

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

A Meta-Analysis of EST-SSR Sequences in the Genomes of Pine, Poplar and Eucalyptus

Survey of simple sequence repeats in woodland strawberry (Fragaria vesca)

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