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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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Related in: MedlinePlus

Variation in Weevil histone clusters. The top of the figure gives seven scaffolds homologous to D. melanogaster GenBank entry NP_001027366.1 containing the H2A gene. Histone domain signatures and their orientation are represented with colored boxes (H1: gray; H2A: light green; H2B: dark green; H3: purple; H4: red). The inter- and intrascaffold base variation are detailed at the bottom showing the alignment of the H2B ORFs and the alignment of the reads aggregated to generate the seventh scaffold (scf7180009777575, Weevil) (A: yellow; T: red; C: green; G: blue; gap: white).
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evv086-F6: Variation in Weevil histone clusters. The top of the figure gives seven scaffolds homologous to D. melanogaster GenBank entry NP_001027366.1 containing the H2A gene. Histone domain signatures and their orientation are represented with colored boxes (H1: gray; H2A: light green; H2B: dark green; H3: purple; H4: red). The inter- and intrascaffold base variation are detailed at the bottom showing the alignment of the H2B ORFs and the alignment of the reads aggregated to generate the seventh scaffold (scf7180009777575, Weevil) (A: yellow; T: red; C: green; G: blue; gap: white).

Mentions: The histone family represented the most frequently sampled protein-coding scaffolds, including 100 scaffolds of greater than 95% amino acid level similarity to Drosophila histones in the Weevil library. Figure 6 depicts 7 of the 18 Weevil scaffolds that had the same Drosophila histone best-hit in RefseqP. The scaffolds range from 2 to 7 kb in length and contain between 2 and 5 ORFs confirmed by the presence of histone domain signatures. The observed histone quintet (composed of four core histones H2A, H2B, H3, H4, and the H1 linker histone prevalent in insects) had a structure similar to that described in the boll weevil Anthonomus grandis (Roehrdanz et al. 2010). The seven scaffolds were used to generate an alignment centered on the first 100 bp of the H2B ORFs. The alignment consensus profile was typical for an exonic region, with the third codon base being less conserved between scaffolds, while there was additional intrascaffold variation on a small number of polymorphic sites (fig. 6, bottom). The fifth scaffold differed from the others by a duplication of the H2A gene and a 3 bp insertion in H2B.Fig. 6.—


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)

Variation in Weevil histone clusters. The top of the figure gives seven scaffolds homologous to D. melanogaster GenBank entry NP_001027366.1 containing the H2A gene. Histone domain signatures and their orientation are represented with colored boxes (H1: gray; H2A: light green; H2B: dark green; H3: purple; H4: red). The inter- and intrascaffold base variation are detailed at the bottom showing the alignment of the H2B ORFs and the alignment of the reads aggregated to generate the seventh scaffold (scf7180009777575, Weevil) (A: yellow; T: red; C: green; G: blue; gap: white).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv086-F6: Variation in Weevil histone clusters. The top of the figure gives seven scaffolds homologous to D. melanogaster GenBank entry NP_001027366.1 containing the H2A gene. Histone domain signatures and their orientation are represented with colored boxes (H1: gray; H2A: light green; H2B: dark green; H3: purple; H4: red). The inter- and intrascaffold base variation are detailed at the bottom showing the alignment of the H2B ORFs and the alignment of the reads aggregated to generate the seventh scaffold (scf7180009777575, Weevil) (A: yellow; T: red; C: green; G: blue; gap: white).
Mentions: The histone family represented the most frequently sampled protein-coding scaffolds, including 100 scaffolds of greater than 95% amino acid level similarity to Drosophila histones in the Weevil library. Figure 6 depicts 7 of the 18 Weevil scaffolds that had the same Drosophila histone best-hit in RefseqP. The scaffolds range from 2 to 7 kb in length and contain between 2 and 5 ORFs confirmed by the presence of histone domain signatures. The observed histone quintet (composed of four core histones H2A, H2B, H3, H4, and the H1 linker histone prevalent in insects) had a structure similar to that described in the boll weevil Anthonomus grandis (Roehrdanz et al. 2010). The seven scaffolds were used to generate an alignment centered on the first 100 bp of the H2B ORFs. The alignment consensus profile was typical for an exonic region, with the third codon base being less conserved between scaffolds, while there was additional intrascaffold variation on a small number of polymorphic sites (fig. 6, bottom). The fifth scaffold differed from the others by a duplication of the H2A gene and a 3 bp insertion in H2B.Fig. 6.—

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