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Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

Basic information
Original title:Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability
Authors:Petr Šmarda, Petr Bureš, Jakub Šmerda, Lucie Horová
Further information
Citation:ŠMARDA, Petr, Petr BUREŠ, Jakub ŠMERDA and Lucie HOROVÁ. Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability. New Phytologist, New Phytologist Trust, 2012, vol. 193, No 2, p. 513-521. ISSN 0028-646X. doi:10.1111/j.1469-8137.2011.03942.x.Export BibTeX
@article{964789,
author = {Šmarda, Petr and Bureš, Petr and Šmerda, Jakub and Horová, Lucie},
article_number = {2},
doi = {http://dx.doi.org/10.1111/j.1469-8137.2011.03942.x},
keywords = {DNA base composition; flow cytometry; GC content; plant genomes; temperature DNA melting},
language = {eng},
issn = {0028-646X},
journal = {New Phytologist},
title = {Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability},
url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03942.x/abstract},
volume = {193},
year = {2012}
}
Original language:English
Field:Botany
WWW:link to a new windowstránka s abstraktem a pdf
Type:Article in Periodical
Keywords:DNA base composition; flow cytometry; GC content; plant genomes; temperature DNA melting

Knowledge of phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including plants) is poor. With the use of flow cytometry (FCM), the available data on the GC content in plants have nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. Here, we tested the reliability of FCM for estimating the GC content by comparison with the biochemical method of DNA melting temperature analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6–47.5%; FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. FCM and TMA data exhibited a high degree of correspondence that remained stable over the relatively wide range of binding lengths (3.39–4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM and the sequence data in Oryza, although the latter were consistently lower. Reliable estimates of the genomic base composition in plants by FCM are comparable with other alternative methods, and its wider application poses a challenge for future plant genomic research.

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