Advanced search
1 file | 278.42 KB

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

Author
Organization
Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
GENOME SIZE, WEB SERVER, DNA METHYLATION, GENETIC DIVERSITY, LENGTH VARIATION, Microsatellites, TRANSPOSON ASSOCIATIONS, LOBLOLLY-PINE, EXPRESSED SEQUENCE TAGS, MICROSATELLITE MARKERS, PLANTS, Simple sequence repeats (SSR), Expressed sequence tags, Gymnosperms, Angiosperms

Downloads

  • Ranade et al. 2014 BMC Plant Biology 14 220.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 278.42 KB

Citation

Please use this url to cite or link to this publication:

Chicago
Ranade, Sonali Sachin, Yao-Cheng Lin, Andrea Zuccolo, Yves Van de Peer, and Maria del Rosario Garcia-Gil. 2014. “Comparative in Silico Analysis of EST-SSRs in Angiosperm and Gymnosperm Tree Genera.” Bmc Plant Biology 14.
APA
Ranade, S. S., Lin, Y.-C., Zuccolo, A., Van de Peer, Y., & Garcia-Gil, M. del R. (2014). Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY, 14.
Vancouver
1.
Ranade SS, Lin Y-C, Zuccolo A, Van de Peer Y, Garcia-Gil M del R. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY. 2014;14.
MLA
Ranade, Sonali Sachin, Yao-Cheng Lin, Andrea Zuccolo, et al. “Comparative in Silico Analysis of EST-SSRs in Angiosperm and Gymnosperm Tree Genera.” BMC PLANT BIOLOGY 14 (2014): n. pag. Print.
@article{5723091,
  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.},
  articleno    = {220},
  author       = {Ranade, Sonali Sachin and Lin, Yao-Cheng and Zuccolo, Andrea and Van de Peer, Yves and Garcia-Gil, Maria del Rosario},
  issn         = {1471-2229},
  journal      = {BMC PLANT BIOLOGY},
  keyword      = {GENOME SIZE,WEB SERVER,DNA METHYLATION,GENETIC DIVERSITY,LENGTH VARIATION,Microsatellites,TRANSPOSON ASSOCIATIONS,LOBLOLLY-PINE,EXPRESSED SEQUENCE TAGS,MICROSATELLITE MARKERS,PLANTS,Simple sequence repeats (SSR),Expressed sequence tags,Gymnosperms,Angiosperms},
  language     = {eng},
  pages        = {10},
  title        = {Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera},
  url          = {http://dx.doi.org/10.1186/s12870-014-0220-8},
  volume       = {14},
  year         = {2014},
}

Altmetric
View in Altmetric
Web of Science
Times cited: