Tandem repeat distribution of gene transcripts in three plant families

Maia, Luciano Carlos da; Souza, Velci Queiróz de; Köpp, Maurício Marini; Carvalho, Fernando Irajâ Félix de; Oliveira, Antônio Costa de

doi:10.1590/s1415-47572009005000091

Cited by 24 publications

(31 citation statements)

References 38 publications

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“…The SSR frequency in PUTs of B. napus (one per 11.32 kb) was higher than that in its parents (one per 22.3 kb in B. oleracea and one per 24.58 kb in B. rapa). This agrees with the results of a previous study in which the frequency of SSRs was shown to increase with genome size (da Maia et al 2009). B. napus was derived originally from interspecific hybridization of B. rapa and B. oleracea and subsequent chromosome doubling (Nagaharu 1935).…”

Section: Discussionsupporting

confidence: 93%

Characterization and comparison of gene-based simple sequence repeats across Brassica species

et al. 2011

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Simple sequence repeats (SSRs) are important components of eukaryotic genomes and may play an important role in regulating gene expression. However, the characteristics of genic SSRs and the effect of interspecific hybridization and polyploidization on genic SSRs seem not to have received desired attention in terms of scientific investigations. To determine the features of genic SSRs and elucidate their role in polyploidization process of the Brassica family, we identified SSRs in Plant Genome Database-assembled unique transcripts (PUTs) of Brassica species. A higher density of SSRs and a greater number of compound motif SSRs and mononucleotide motif types with large average number of repeats were detected in allotetraploid Brassica napus than in the diploid parental species (Brassica rapa and Brassica oleracea). In addition, a greater proportion of SSR-PUTs were found to be associated with the stress response and developmental processes in B. napus than in the parents. A negative correlation between the repeat number and the motif type and the total length, and a positive correlation between the repeat number and the total length of SSRs were observed. PUT-SSR might be generated from A/T-rich regions. The successful development of 123 pairs of SSR primers for Brassica PUTs showed that SSR-PUTs could be exploited as gene-based SSR functional markers for application in Brassica breeding. These results indicate that interspecific hybridization and polyploidization could trigger the amplification of SSRs, and long SSRs might become shorter to enable the plant to adapt to environmental and artificial selection.

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Section: Discussionsupporting

confidence: 93%

Characterization and comparison of gene-based simple sequence repeats across Brassica species

et al. 2011

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“…More importantly, the physical distribution of microsatellites in different genomic regions (such as ends and middles of the chromosomes) was also highly nonuniform (Figure 6). In fact, similar results were also found in other studies that investigated the microsatellite frequency and distribution with respect to motif length and type in the different genomic/genic regions of several model and crop species [8], [9], [10], [14], [25]. These results strongly indicated that different patterns of microsatellite distribution across genomic regions exist and may be due to the different selective pressures acting on the microsatellites in different genomic regions [2], [4] owing to their different biological functions [1].…”

Section: Discussionsupporting

confidence: 89%

“…In addition, the physical positions of microsatellites were not analyzed in these previous studies, and the genomic distributions of microsatellites have been poorly characterized. More importantly, due to the lack of genomic information, a small number of plant species were analyzed in each of these previous reports [14], [15], and the evolutionary dynamics of microsatellite distribution in plants have therefore not yet been investigated.…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

Shi

Huang

et al. 2013

PLoS ONE

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Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules.

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“…The absence of a relationship between genome size and tandem repeat loci content were reported based in grass genome studies [11], where large genomes such as sugarcane ( Saccharum officinarum L.), maize and wheat did not present higher frequencies of SSR loci.…”

Section: Resultsmentioning

confidence: 99%

In silicocomparative analysis of SSR markers in plants

2011

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BackgroundThe adverse environmental conditions impose extreme limitation to growth and plant development, restricting the genetic potential and reflecting on plant yield losses. The progress obtained by classic plant breeding methods aiming at increasing abiotic stress tolerances have not been enough to cope with increasing food demands. New target genes need to be identified to reach this goal, which requires extensive studies of the related biological mechanisms. Comparative analyses in ancestral plant groups can help to elucidate yet unclear biological processes.ResultsIn this study, we surveyed the occurrence patterns of expressed sequence tag-derived microsatellite markers for model plants. A total of 13,133 SSR markers were discovered using the SSRLocator software in non-redundant EST databases made for all eleven species chosen for this study. The dimer motifs are more frequent in lower plant species, such as green algae and mosses, and the trimer motifs are more frequent for the majority of higher plant groups, such as monocots and dicots. With this in silico study we confirm several microsatellite plant survey results made with available bioinformatics tools.ConclusionsThe comparative studies of EST-SSR markers among all plant lineages is well suited for plant evolution studies as well as for future studies of transferability of molecular markers.

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Tandem repeat distribution of gene transcripts in three plant families

Cited by 24 publications

References 38 publications

Characterization and comparison of gene-based simple sequence repeats across Brassica species

Characterization and comparison of gene-based simple sequence repeats across Brassica species

Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

In silicocomparative analysis of SSR markers in plants

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