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Comparative Study
, 91 (5), 547-57

Comparisons With Caenorhabditis (Approximately 100 Mb) and Drosophila (Approximately 175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to Be Approximately 157 Mb and Thus Approximately 25% Larger Than the Arabidopsis Genome Initiative Estimate of Approximately 125 Mb

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Comparative Study

Comparisons With Caenorhabditis (Approximately 100 Mb) and Drosophila (Approximately 175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to Be Approximately 157 Mb and Thus Approximately 25% Larger Than the Arabidopsis Genome Initiative Estimate of Approximately 125 Mb

Michael D Bennett et al. Ann Bot.

Abstract

Recent genome sequencing papers have given genome sizes of 180 Mb for Drosophila melanogaster Iso-1 and 125 Mb for Arabidopsis thaliana Columbia. The former agrees with early cytochemical estimates, but numerous cytometric estimates of around 170 Mb imply that a genome size of 125 Mb for arabidopsis is an underestimate. In this study, nuclei of species pairs were compared directly using flow cytometry. Co-run Columbia and Iso-1 female gave a 2C peak for arabidopsis only approx. 15 % below that for drosophila, and 16C endopolyploid Columbia nuclei had approx. 15 % more DNA than 2C chicken nuclei (with >2280 Mb). Caenorhabditis elegans Bristol N2 (genome size approx. 100 Mb) co-run with Columbia or Iso-1 gave a 2C peak for drosophila approx. 75 % above that for 2C C. elegans, and a 2C peak for arabidopsis approx. 57 % above that for C. elegans. This confirms that 1C in drosophila is approx. 175 Mb and, combined with other evidence, leads us to conclude that the genome size of arabidopsis is not approx. 125 Mb, but probably approx. 157 Mb. It is likely that the discrepancy represents extra repeated sequences in unsequenced gaps in heterochromatic regions. Complete sequencing of the arabidopsis genome until no gaps remain at telomeres, nucleolar organizing regions or centromeres is still needed to provide the first precise angiosperm C-value as a benchmark calibration standard for plant genomes, and to ensure that no genes have been missed in arabidopsis, especially in centromeric regions, which are clearly larger than once imagined.

Figures

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Fig. 1. Relative DNA staining in nuclei of arabidopsis, drosophila, Gallus and Caenorhabditis. A, Arabidopsis has approx. 85 % of the 2C nuclear DNA fluorescence of drosophila. Relative red fluorescence of PI‐stained nuclei shows a ratio of approx. 0·85 : 1·00 between A. thaliana ecotype Columbia (2C mean = 201·6) and female D. melanogaster strain Iso‐1 (2C mean = 236·7). The arabidopsis 2C peak was identified as the lowest in its 2C (mean = 201·6), 4C (mean = 398·8), 8C (mean = 792·1), etc. doubling series. PI staining time = 4 h. B, Arabidopsis 16C nuclear DNA fluorescence exceeds that of 2C chicken. Relative red fluorescence of PI‐stained nuclei shows a ratio of approx. 1·15 : 1·00 between endopolyploid 16C nuclei of A. thaliana ecotype Columbia (16C peak mean = 390·9) and chicken erythrocyte nuclei (2C peak = 341·7). NB Arabidopsis is identified from its known doubling series 2C, 4C, 8C, 16C.) PI staining time = 2·8 h. C, Drosophila has approx. 175 % 2C nuclear DNA fluorescence of C. elegans. Relative red fluorescence of PI‐stained nuclei shows a ratio of approx. 1·00 : 1·74 between C. elegans variety Bristol N2 (2C mean = 95·9) and female D. melanogaster strain Iso‐1 (2C mean = 167·2). PI staining time = 9·3 h. D, Arabidopsis has approx. 157 % 2C nuclear DNA fluorescence of Caenorhabditis. Relative red fluorescence of PI‐stained nuclei shows a ratio of approx. 1·00 : 1·54 between C. elegans variety Bristol N2 (2C mean = 101·6) and A. thaliana ecotype Columbia (2C mean = 159·6). PI staining time = 4·1 h. NB Species were identified by varying the relative amounts of nuclei from one to the other between runs within each mixture.

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