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: In addition to mitochondrial genomes, nuclear repeat regions were expected to dominate in MGS (fig. 1, scenarios x and y). First, using RepeatMasker (see Materials and Methods, and supplementary file S4, Supplementary Material online), low complexity repeats (microsatellites, SSRs) constituted between 2.49% (Canopy_Next) and 6.08% (Canopy_Long) of all scaffolds (fig. 4A) and their number was correlated with the number of sequenced reads. The combined fraction of retroelements, DNA transposons, and small RNAs in Weevil, Canopy_Long, Canopy_Short, and Canopy_Next constituted 18.6%, 15.7%, 16.1%, and 21.8% of all scaffolds, respectively (fig. 4A). Despite its smaller size, Canopy_Next showed high proportions of repeats in all non-SSRs categories.Fig. 4.—
Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom.