Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to be 157 Mb and thus 25 % Larger than the Arabidopsis Genome Initiative Estimate of 125 Mb

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¯ow 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 con®rms 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 ®rst 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.

Extremely small genomes in two unrelated dipteran insects with shared early developmental traits

“…To estimate genome sizes, we used flow cytometry with D. melanogaster as standard (1C=175 Mb, Bennett et al 2003). We estimated haploid genome sizes of~100 Mb for C. fuscipes and P. cinerea, of~200 Mb for C. riparius, and of more than 300 Mb for C. albipunctata (Fig.…”

“…The coding genome of animals seems to impose a lower threshold at about 100 Mb for the haploid (1C) genome; smaller genomes may require a substantive reduction of the coding genome (Lynch 2007). The 100-Mb threshold coincides for example with the genome size of Caenorhabdites elegans (Bennett et al 2003), a very fast developing organism with about 19,000 protein-coding genes. The smallest insect genomes reported so far belong to highly specialized parasitic species including the louse Pediculus humanus (1C=105 Mb; Johnston et al 2007) and the strepsipteran Caenocholax fenyesi texensis (1C=108 Mb; Johnston et al 2004).…”

“…Genome sizes of C. fuscipes, P. cinerea, C. albipunctata, and C. riparius were estimated using brain nuclei and a propidium iodide flow cytometry protocol (Bennett et al 2003;DeSalle et al 2005;Gregory and Johnston 2008). Briefly, sample and standard were ground together and passed through a 50-µm filter, stained with 50 ppm of propidium iodide and run (after 30 min in the cold and dark) in a Beckman Coulter Elite flow cytometer with the laser emitting 25 mW of exciting light at 488 nm.…”

“…P. cinerea was prepared as above at the Jodrell Laboratory, RBG Kew, UK and run on a Partek CyFlow available at that laboratory (514-nm laser excitation, 25-mW, long pass filter). DNA content was determined by multiplying the ratio of the mean peak fluorescence of the 2C sample/mean peak of the standard with 175 Mb, the genome size of the sequenced strain of D. melanogaster anchored against the fully sequenced C. elegans strain (Bennett et al 2003).…”

The canine hookworm genome: Analysis and classification of Ancylostoma caninum survey sequences

“…While one would expect that the A. caninum genome size would be in the 53-59 MB range based on other clade V Strongylida species including Haemonchus contortus [9], our recent genome size estimate using flow sorted nuclei surprisingly revealed a genome more than six times this size. Genome size was estimated by prodidium iodide staining and flow cytometry of isolated nuclei following methods described in [10]. To prepare the nuclei, the A. caninum L3s were washed in cold Galbraith buffer pH 7.2 and then pipetted into a plastic petri dish along with 30-50 μl cold Galbraith buffer and chopped (50 times) with a fresh single edge razor blade.…”