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In silico comparative analysis of SSR markers in plants.

Victoria FC, da Maia LC, de Oliveira AC - BMC Plant Biol. (2011)

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil.

ABSTRACT

Background: The 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.

Results: In 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.

Conclusions: The 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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Distribuition of Physcomitrella patens SSR loci within sequences of known molecular function in Gene Onthology.
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Figure 7: Distribuition of Physcomitrella patens SSR loci within sequences of known molecular function in Gene Onthology.

Mentions: Regarding biological processes, the majority of SSR loci found were involved with metabolic (32.17%) and cellular (31.02%) processes (Figure 3). Comparing all P. patens genome sequences with Gene Ontology assignment and those containing SSRs (Figure 4), there was a concentration of SSRs in metabolic process genes. Biological adhesion, rhythmic processes, growth and cell killing processes had the lowest SSR contents among the P. patens transcripts. Similar results were found comparing P. patens and A. thaliana EST libraries [37]. This author suggested that genes that are involved in protein metabolism and biosynthesis are well conserved between mosses and vascular plants. These patterns were confirmed for mosses using Syntrichia ruralis and P. patens transcript databases, respectively [38,39]. For cellular components (Figure 5) the majority of SSRs found are related to intracellular component gene sequences (52.52%) and membrane elements (12.15%). This ontology levels were reported as the majority of GO assignments in for P. patens annotated sequences [39]. Currently, more than half of cellular component GO annotations for P. patens genome [32] are related with membrane structure (Figure 6). Our results show the enrichment of SSR occurrence mainly for genes related to this structural level. The whole genome molecular function assignment level in Gene Ontology revealed a predominance of binding genes (80.51%), suggesting these are representatively higher in P. patens genome (Figure 7). However, when EST sequences containing SSRs are assessed with the Gene Ontology assigned molecular function (Figure 8), a relative increase of other functions is revealed. Sequences associated with binding decrease (42.81%), and those related to catalytic activity (33.76%), and structural molecule activity (10.80%) increase. These findings agree to the expectations concerning the cellular function and are consistent with ratios observed for rice, Arabidopsis, and for the bryophytes Syntrichia ruralis and P. patens [32,38-41]. The higher occurrence of SSR loci in this ontology level indicate a good potential for using these molecular markers to saturate pathways associated to those functions described above.


In silico comparative analysis of SSR markers in plants.

Victoria FC, da Maia LC, de Oliveira AC - BMC Plant Biol. (2011)

Distribuition of Physcomitrella patens SSR loci within sequences of known molecular function in Gene Onthology.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037304&req=5

Figure 7: Distribuition of Physcomitrella patens SSR loci within sequences of known molecular function in Gene Onthology.
Mentions: Regarding biological processes, the majority of SSR loci found were involved with metabolic (32.17%) and cellular (31.02%) processes (Figure 3). Comparing all P. patens genome sequences with Gene Ontology assignment and those containing SSRs (Figure 4), there was a concentration of SSRs in metabolic process genes. Biological adhesion, rhythmic processes, growth and cell killing processes had the lowest SSR contents among the P. patens transcripts. Similar results were found comparing P. patens and A. thaliana EST libraries [37]. This author suggested that genes that are involved in protein metabolism and biosynthesis are well conserved between mosses and vascular plants. These patterns were confirmed for mosses using Syntrichia ruralis and P. patens transcript databases, respectively [38,39]. For cellular components (Figure 5) the majority of SSRs found are related to intracellular component gene sequences (52.52%) and membrane elements (12.15%). This ontology levels were reported as the majority of GO assignments in for P. patens annotated sequences [39]. Currently, more than half of cellular component GO annotations for P. patens genome [32] are related with membrane structure (Figure 6). Our results show the enrichment of SSR occurrence mainly for genes related to this structural level. The whole genome molecular function assignment level in Gene Ontology revealed a predominance of binding genes (80.51%), suggesting these are representatively higher in P. patens genome (Figure 7). However, when EST sequences containing SSRs are assessed with the Gene Ontology assigned molecular function (Figure 8), a relative increase of other functions is revealed. Sequences associated with binding decrease (42.81%), and those related to catalytic activity (33.76%), and structural molecule activity (10.80%) increase. These findings agree to the expectations concerning the cellular function and are consistent with ratios observed for rice, Arabidopsis, and for the bryophytes Syntrichia ruralis and P. patens [32,38-41]. The higher occurrence of SSR loci in this ontology level indicate a good potential for using these molecular markers to saturate pathways associated to those functions described above.

Bottom Line: 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.The 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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Genomics and Breeding Center, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, RS, Brasil.

ABSTRACT

Background: The 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.

Results: In 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus