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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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Genomic repeats inventory. (A) Proportion of base pairs (%) identified as genomic repeats by RepeatMasker, plotted separately for short simple repeats (SSR) all non-SSR repeats which include retroelements, DNA retrotransposons and small RNAs. Low complexity repeats are presented for all scaffolds. Other repeats are given only for the Hexapoda scaffolds, as the proportions represent only previously known repeats having a definition in RepBase. (B) Part of an aligned matrix covering 461 copies of the Dp reference genome identified by their similarity to a paralogous scaffold (scf7180004984182; Canopy_Long). The corresponding regions are aligned, showing a similar 200 bp motif (A: yellow; T: red; C: green; G: blue; gap: white).
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evv086-F4: Genomic repeats inventory. (A) Proportion of base pairs (%) identified as genomic repeats by RepeatMasker, plotted separately for short simple repeats (SSR) all non-SSR repeats which include retroelements, DNA retrotransposons and small RNAs. Low complexity repeats are presented for all scaffolds. Other repeats are given only for the Hexapoda scaffolds, as the proportions represent only previously known repeats having a definition in RepBase. (B) Part of an aligned matrix covering 461 copies of the Dp reference genome identified by their similarity to a paralogous scaffold (scf7180004984182; Canopy_Long). The corresponding regions are aligned, showing a similar 200 bp motif (A: yellow; T: red; C: green; G: blue; gap: white).

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.—


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)

Genomic repeats inventory. (A) Proportion of base pairs (%) identified as genomic repeats by RepeatMasker, plotted separately for short simple repeats (SSR) all non-SSR repeats which include retroelements, DNA retrotransposons and small RNAs. Low complexity repeats are presented for all scaffolds. Other repeats are given only for the Hexapoda scaffolds, as the proportions represent only previously known repeats having a definition in RepBase. (B) Part of an aligned matrix covering 461 copies of the Dp reference genome identified by their similarity to a paralogous scaffold (scf7180004984182; Canopy_Long). The corresponding regions are aligned, showing a similar 200 bp motif (A: yellow; T: red; C: green; G: blue; gap: white).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv086-F4: Genomic repeats inventory. (A) Proportion of base pairs (%) identified as genomic repeats by RepeatMasker, plotted separately for short simple repeats (SSR) all non-SSR repeats which include retroelements, DNA retrotransposons and small RNAs. Low complexity repeats are presented for all scaffolds. Other repeats are given only for the Hexapoda scaffolds, as the proportions represent only previously known repeats having a definition in RepBase. (B) Part of an aligned matrix covering 461 copies of the Dp reference genome identified by their similarity to a paralogous scaffold (scf7180004984182; Canopy_Long). The corresponding regions are aligned, showing a similar 200 bp motif (A: yellow; T: red; C: green; G: blue; gap: white).
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.—

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