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Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.

Linard B, Crampton-Platt A, Gillett CP, Timmermans MJ, Vogler AP - Genome Biol Evol (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom.

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Genome coverage estimations. GMC values are reported for the Weevil and Canopy metagenomes mapped on Tc and Dp. (A) GMCCanopyTc is detailed for the ten Tc chromosomes. Bars with parallel lines: GMC value based on both high-copy number and low-copy number repeats (top x axis). Bars with dots: GMC value based on low-copy number repeats only. Also given is the size for each chromosome (bottom x axis). (B) GMCs calculated for the different Dp/Tc and Canopy/Weevil combinations (x axis). Right y axis: GMC normalizations. Left y axis: Genome base covered by low-copy number scaffolds (bcovered, vertical bars). (C) A typical cluster profile is illustrated for the chromosome scaffold KB741028.1 (Dp genome). The y axis presents the cluster size, as the number of metagenomic scaffolds similar to the same reference genome region, along the linear genome assembly. Green bars correspond to intergenic regions, and red bars represent regions annotated as genes. The gray background indicates a region for which the sequence is known (bases ATCG in the genome assembly), and white background represents unknown bases (N in assembly).
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evv086-F7: Genome coverage estimations. GMC values are reported for the Weevil and Canopy metagenomes mapped on Tc and Dp. (A) GMCCanopyTc is detailed for the ten Tc chromosomes. Bars with parallel lines: GMC value based on both high-copy number and low-copy number repeats (top x axis). Bars with dots: GMC value based on low-copy number repeats only. Also given is the size for each chromosome (bottom x axis). (B) GMCs calculated for the different Dp/Tc and Canopy/Weevil combinations (x axis). Right y axis: GMC normalizations. Left y axis: Genome base covered by low-copy number scaffolds (bcovered, vertical bars). (C) A typical cluster profile is illustrated for the chromosome scaffold KB741028.1 (Dp genome). The y axis presents the cluster size, as the number of metagenomic scaffolds similar to the same reference genome region, along the linear genome assembly. Green bars correspond to intergenic regions, and red bars represent regions annotated as genes. The gray background indicates a region for which the sequence is known (bases ATCG in the genome assembly), and white background represents unknown bases (N in assembly).

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.—


Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics.

Linard B, Crampton-Platt A, Gillett CP, Timmermans MJ, Vogler AP - Genome Biol Evol (2015)

Genome coverage estimations. GMC values are reported for the Weevil and Canopy metagenomes mapped on Tc and Dp. (A) GMCCanopyTc is detailed for the ten Tc chromosomes. Bars with parallel lines: GMC value based on both high-copy number and low-copy number repeats (top x axis). Bars with dots: GMC value based on low-copy number repeats only. Also given is the size for each chromosome (bottom x axis). (B) GMCs calculated for the different Dp/Tc and Canopy/Weevil combinations (x axis). Right y axis: GMC normalizations. Left y axis: Genome base covered by low-copy number scaffolds (bcovered, vertical bars). (C) A typical cluster profile is illustrated for the chromosome scaffold KB741028.1 (Dp genome). The y axis presents the cluster size, as the number of metagenomic scaffolds similar to the same reference genome region, along the linear genome assembly. Green bars correspond to intergenic regions, and red bars represent regions annotated as genes. The gray background indicates a region for which the sequence is known (bases ATCG in the genome assembly), and white background represents unknown bases (N in assembly).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4494052&req=5

evv086-F7: Genome coverage estimations. GMC values are reported for the Weevil and Canopy metagenomes mapped on Tc and Dp. (A) GMCCanopyTc is detailed for the ten Tc chromosomes. Bars with parallel lines: GMC value based on both high-copy number and low-copy number repeats (top x axis). Bars with dots: GMC value based on low-copy number repeats only. Also given is the size for each chromosome (bottom x axis). (B) GMCs calculated for the different Dp/Tc and Canopy/Weevil combinations (x axis). Right y axis: GMC normalizations. Left y axis: Genome base covered by low-copy number scaffolds (bcovered, vertical bars). (C) A typical cluster profile is illustrated for the chromosome scaffold KB741028.1 (Dp genome). The y axis presents the cluster size, as the number of metagenomic scaffolds similar to the same reference genome region, along the linear genome assembly. Green bars correspond to intergenic regions, and red bars represent regions annotated as genes. The gray background indicates a region for which the sequence is known (bases ATCG in the genome assembly), and white background represents unknown bases (N in assembly).
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.—

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Life Sciences, Natural History Museum, London, United Kingdom.

Show MeSH
Related in: MedlinePlus