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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

Inventory of rRNA gene scaffolds. Scaffolds identified to contain rRNA genes are classified into different life domains by using their closest rRNA homolog. The number of scaffolds holding a rRNA gene is reported for each library and each life domain (orange dots: bacterial rRNAs; green bars: Hexapoda rRNAs; purple dots: Metazoa; purple bars: other eukaryotes). For each library, the global number of rRNA scaffolds is also reported (red line) as well as the number of SSU and LSU rRNAs.
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evv086-F5: Inventory of rRNA gene scaffolds. Scaffolds identified to contain rRNA genes are classified into different life domains by using their closest rRNA homolog. The number of scaffolds holding a rRNA gene is reported for each library and each life domain (orange dots: bacterial rRNAs; green bars: Hexapoda rRNAs; purple dots: Metazoa; purple bars: other eukaryotes). For each library, the global number of rRNA scaffolds is also reported (red line) as well as the number of SSU and LSU rRNAs.

Mentions: Gene families recovered from the metagenomes correspond to multicopy and highly conserved elements (fig. 1, scenario D) and represent some of the lcn repeats mapped on the reference genomes (fig. 5C, red bars). Tandemly repeated rRNA genes were present in hundreds of scaffolds, with twice as many matches to the LSU than to the 2-fold shorter SSU gene (fig. 5). In all libraries, more than 80% of rRNA-containing scaffolds were homologous to Hexapoda, but other phyla were represented also (fig. 5). The Weevil and Canopy_Long libraries contained 2.3 and 0.95 rRNA scaffolds per morphospecies on average.Fig. 5.—


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)

Inventory of rRNA gene scaffolds. Scaffolds identified to contain rRNA genes are classified into different life domains by using their closest rRNA homolog. The number of scaffolds holding a rRNA gene is reported for each library and each life domain (orange dots: bacterial rRNAs; green bars: Hexapoda rRNAs; purple dots: Metazoa; purple bars: other eukaryotes). For each library, the global number of rRNA scaffolds is also reported (red line) as well as the number of SSU and LSU rRNAs.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

evv086-F5: Inventory of rRNA gene scaffolds. Scaffolds identified to contain rRNA genes are classified into different life domains by using their closest rRNA homolog. The number of scaffolds holding a rRNA gene is reported for each library and each life domain (orange dots: bacterial rRNAs; green bars: Hexapoda rRNAs; purple dots: Metazoa; purple bars: other eukaryotes). For each library, the global number of rRNA scaffolds is also reported (red line) as well as the number of SSU and LSU rRNAs.
Mentions: Gene families recovered from the metagenomes correspond to multicopy and highly conserved elements (fig. 1, scenario D) and represent some of the lcn repeats mapped on the reference genomes (fig. 5C, red bars). Tandemly repeated rRNA genes were present in hundreds of scaffolds, with twice as many matches to the LSU than to the 2-fold shorter SSU gene (fig. 5). In all libraries, more than 80% of rRNA-containing scaffolds were homologous to Hexapoda, but other phyla were represented also (fig. 5). The Weevil and Canopy_Long libraries contained 2.3 and 0.95 rRNA scaffolds per morphospecies on average.Fig. 5.—

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