Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.
Bottom Line: In addition to effect of taxonomic composition of the metagenomes, the number of mapped scaffolds also revealed structural differences between the two reference genomes, although the significance of this striking finding remains unclear.Finally, apparently exogenous sequences were recovered, including potential food plants, fungal pathogens, and bacterial symbionts.The "metagenome skimming" approach is useful for capturing the genomic diversity of poorly studied, species-rich lineages and opens new prospects in environmental genomics.
Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom.Show MeSH
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Mentions: The effect of different phyletic composition of the Canopy and Weevil metagenomes was further tested with genome coverage metrics against the two available Coleoptera genomes (see Materials and Methods). Figure 7 details the covered bases (bcovered) and the GMC values (coverage normalized for genome size, “+” symbol). Chromosome reconstruction was available only for Tc. Up to 5% of the Tc genome was covered by the hcn scaffolds of the Canopy (merged) metagenome (fig. 7A), but when excluding hcn scaffolds, the GMCTcCanopy_merged of various chromosomes was always less than 0.5%. This effect was particularly striking in chromosomes 3, 6, and 10, whereby the latter two are small chromosomes highly enriched in hcn sequences conserved between the Canopy metagenome and Tc.Fig. 7.—
Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom.