Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comparative Study
. 2014 Aug 21:14:220.
doi: 10.1186/s12870-014-0220-8.

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

Sonali Sachin Ranade, Yao-Cheng Lin, Andrea Zuccolo, Yves Van de Peer, María del Rosario García-Gil
Comparative Study

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

Sonali Sachin Ranade et al. BMC Plant Biol. .

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.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Tautz D, Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 1984;12(10):4127–4138. doi: 10.1093/nar/12.10.4127. - DOI - PMC - PubMed
    1. Zane L, Bargelloni L, Patarnello T. Strategies for microsatellite isolation: a review. Mol Ecol. 2002;11(1):1–16. doi: 10.1046/j.0962-1083.2001.01418.x. - DOI - PubMed
    1. Gupta M, Chyi YS, Romeroseverson J, Owen JL. Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet. 1994;89(7–8):998–1006. - PubMed
    1. Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002;30(2):194–200. doi: 10.1038/ng822. - DOI - PubMed
    1. Berube Y, Zhuang J, Rungis D, Ralph S, Bohlmann J, Ritland K. Characterization of EST SSRs in loblolly pine and spruce. Tree Genet Genomes. 2007;3(3):251–259. doi: 10.1007/s11295-006-0061-1. - DOI

Publication types

MeSH terms

LinkOut - more resources