Comparative in silicoanalysis of EST-SSRs in angiosperm and gymnosperm tree genera

BMC Plant Biology

Research Article

Yao-Cheng Lin¹  Yves Van de Peer²  Andrea Zuccolo³  Sonali Sachin Ranade⁴  María del Rosario García-Gil⁴ 

[1] Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium;Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium;Genomics Research Institute, University of Pretoria, Hatfield Campus, 0028, Pretoria, South Africa;Istituto di Genomica Applicata, Via J. Linussio 51, 33100, Udine, Italy;Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127, Pisa, Italy;Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83, Umeå, Sweden;

关键词: Angiosperms;    Gymnosperms;    Expressed sequence tags;    Simple sequence repeats (SSR);    Microsatellites;   

DOI  :  10.1186/s12870-014-0220-8

 received in 2014-04-07, accepted in 2014-08-05,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundSimple 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).ResultsOur 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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Ranade et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.