Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera

Show simple item record Ranade, Sonali Sachin Lin, Yao-Cheng Zuccolo, Andrea Van de Peer, Yves García-Gil, María del Rosario 2014-10-21T10:49:27Z 2014-10-21T10:49:27Z 2014
dc.description.abstract BACKGROUND: Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5′UTR, ORF and 3′UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS: Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS: Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species. en_US
dc.description.librarian am2014 en_US
dc.description.uri en_US
dc.identifier.citation Ranade, SS, Lin, YC, Zuccolo, A, Van de Peer, Y & Garcia-Gil, MD 2014 'Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera', BMC Plant Biology, vol. 14, art. 220, pp. 1-10. en_US
dc.identifier.issn 1471-2229
dc.identifier.other 10.1186/s12870-014-0220-8
dc.language.iso en en_US
dc.publisher BioMed Central en_US
dc.rights © 2014 Ranade et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License. en_US
dc.subject Angiosperms en_US
dc.subject Gymnosperms en_US
dc.subject Simple sequence repeats (SSR) en_US
dc.subject Microsatellites en_US
dc.subject Expressed sequence tags (ESTs) en_US
dc.subject EST-SSRs en_US
dc.title Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera en_US
dc.type Article en_US

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