Abstract
A novel computational approach shows a link between genome size and habitat from analysis of environmental metagenomic DNA reads.
Highlights
Because of its direct link with the functional repertoire, microbial genome size is an important ecologic parameter that is believed to be closely coupled to the functional complexity and environmental niche of an organism [1,2,3,4]
Ecologically more meaningful measure of genome size, we have developed a novel computational approach to predict effective genome size (EGS) directly from raw shotgun sequencing data, thereby avoiding experimental biases such as are mentioned above
Deriving a method for EGS prediction In brief, we use a set of marker genes that typically occur only once per genome to extrapolate the average genome size from the density of these genes found in the total set of sequence reads
Summary
Because of its direct link with the functional repertoire, microbial genome size is an important ecologic parameter that is believed to be closely coupled to the functional complexity and environmental niche of an organism [1,2,3,4]. For more than three decades, numerous studies have provided estimates of average microbial genome size for various environments, but results vary greatly. Estimates of the average DNA content per cell (converted to megabases [Mb] for comparison) range from 1.5 to 8.0 Mb for soil and from 1.5 to 9.5 Mb for aquatic environments (see Loferer-Krossbacher and coworkers [5] and Torsvik [6] for overviews of estimates). The diversity of techniques and parameters used (for example, sample filtering, DNA staining, and cell counting) greatly hampers the interpretation and comparison of these results. All currently used methods have several important drawbacks They have difficulties discriminating between the different ploidy levels of cells [7,8,9], and so any technique measuring DNA content does not necessarily measure genome size. Some estimates have been obtained in studies using cultured isolates only (for example, se the reports by Christensen [8] and Torsvik [13] and their groups), which does not reflect the actual environmental species composition
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