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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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Bacterial symbiont profile for the Canopy and Weevil samples. (A) Number of bacterial scaffolds (number of scaffolds) classified by their homology to different bacterial symbiont genera (given on x axis) for each of the four libraries (Weevil: blue bars; Canopy libraries: red bars). (B) Number of complete genomes (number of reference genomes) and nucleotides entries (number of nucleotide sequences) currently available in NCBI Chromosome (“other_genomic”) and nulceotide (“nt”) databases, respectively, for each symbiont genus (x axis).
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evv086-F3: Bacterial symbiont profile for the Canopy and Weevil samples. (A) Number of bacterial scaffolds (number of scaffolds) classified by their homology to different bacterial symbiont genera (given on x axis) for each of the four libraries (Weevil: blue bars; Canopy libraries: red bars). (B) Number of complete genomes (number of reference genomes) and nucleotides entries (number of nucleotide sequences) currently available in NCBI Chromosome (“other_genomic”) and nulceotide (“nt”) databases, respectively, for each symbiont genus (x axis).

Mentions: The portion of scaffolds identified as non-Hexapoda comprised between 0.6% (Canopy_Long) and 8.2% (Weevil). In Canopy, we identified 348 bacterial scaffolds and 429 eukaryote (non-Hexapoda) scaffolds (supplementary file S3, Supplementary Material online). Plant DNA was represented by dozens of long chloroplast scaffolds (up to 5 kb), of which 21 have a high similarity (up to 97%) to the genus Theobroma (cocoa), 8 other scaffolds were highly similar (up to 98%) to the genus Gossypium (cotton) and dozens of additional fragments showed a lower similarity to other known chloroplasts. A 7 kb scaffold had high homology to an unannotated genomic region of nematodes. Fungal identifications were rare but particularly interesting in the context of insect biology. For instance, we uncovered a 1 kb fungal scaffold 99.5% similar to Glarea lozoyensis, a fungal species linked to insect pathogenicity (Chen et al. 2013) and a 2 kb scaffold homologous to Phaeosphaeria nodorum (91% identity), another insect pathogen previously studied for its antibiotic synthesis pathway (Amnuaykanjanasin et al. 2009; supplementary file S3, Supplementary Material online). Bacterial scaffolds included potential symbiotic species in all libraries (fig. 3). In Canopy_Long, 108 scaffolds were homologous to the genera Wolbachia (42%), Rickettsia (50%), Spiroplasma, Hamiltonella, and Blattabacterium (3%). The Weevil pool, while comprising a similar proportion of Hexapoda scaffolds, contained more non-Hexapoda and potential symbionts scaffolds (fig. 3). In the latter, 89% were homologous to the genus Wolbachia (1,722 scaffolds). We noticed a tendency for lower representation of taxa with fewer available bacterial reference genomes or nucleotide sequences, thus sequences from these genera may be present in the samples but cannot be detected with the current database (fig. 3).Fig. 3.—


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)

Bacterial symbiont profile for the Canopy and Weevil samples. (A) Number of bacterial scaffolds (number of scaffolds) classified by their homology to different bacterial symbiont genera (given on x axis) for each of the four libraries (Weevil: blue bars; Canopy libraries: red bars). (B) Number of complete genomes (number of reference genomes) and nucleotides entries (number of nucleotide sequences) currently available in NCBI Chromosome (“other_genomic”) and nulceotide (“nt”) databases, respectively, for each symbiont genus (x axis).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv086-F3: Bacterial symbiont profile for the Canopy and Weevil samples. (A) Number of bacterial scaffolds (number of scaffolds) classified by their homology to different bacterial symbiont genera (given on x axis) for each of the four libraries (Weevil: blue bars; Canopy libraries: red bars). (B) Number of complete genomes (number of reference genomes) and nucleotides entries (number of nucleotide sequences) currently available in NCBI Chromosome (“other_genomic”) and nulceotide (“nt”) databases, respectively, for each symbiont genus (x axis).
Mentions: The portion of scaffolds identified as non-Hexapoda comprised between 0.6% (Canopy_Long) and 8.2% (Weevil). In Canopy, we identified 348 bacterial scaffolds and 429 eukaryote (non-Hexapoda) scaffolds (supplementary file S3, Supplementary Material online). Plant DNA was represented by dozens of long chloroplast scaffolds (up to 5 kb), of which 21 have a high similarity (up to 97%) to the genus Theobroma (cocoa), 8 other scaffolds were highly similar (up to 98%) to the genus Gossypium (cotton) and dozens of additional fragments showed a lower similarity to other known chloroplasts. A 7 kb scaffold had high homology to an unannotated genomic region of nematodes. Fungal identifications were rare but particularly interesting in the context of insect biology. For instance, we uncovered a 1 kb fungal scaffold 99.5% similar to Glarea lozoyensis, a fungal species linked to insect pathogenicity (Chen et al. 2013) and a 2 kb scaffold homologous to Phaeosphaeria nodorum (91% identity), another insect pathogen previously studied for its antibiotic synthesis pathway (Amnuaykanjanasin et al. 2009; supplementary file S3, Supplementary Material online). Bacterial scaffolds included potential symbiotic species in all libraries (fig. 3). In Canopy_Long, 108 scaffolds were homologous to the genera Wolbachia (42%), Rickettsia (50%), Spiroplasma, Hamiltonella, and Blattabacterium (3%). The Weevil pool, while comprising a similar proportion of Hexapoda scaffolds, contained more non-Hexapoda and potential symbionts scaffolds (fig. 3). In the latter, 89% were homologous to the genus Wolbachia (1,722 scaffolds). We noticed a tendency for lower representation of taxa with fewer available bacterial reference genomes or nucleotide sequences, thus sequences from these genera may be present in the samples but cannot be detected with the current database (fig. 3).Fig. 3.—

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