Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes (Articolo in rivista)

Type
Label
  • Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes (Articolo in rivista) (literal)
Anno
  • 2013-01-01T00:00:00+01:00 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi
  • 10.1186/1471-2164-14-7 (literal)
Alternative label
  • Gori, Fabio; Tringe, Susannah G.; Folino, Gianluigi; van Hijum, Sacha A. F. T.; den Camp, Huub J. M. Op; Jetten, Mike S. M.; Marchiori, Elena (2013)
    Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes
    in BMC genomics
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Gori, Fabio; Tringe, Susannah G.; Folino, Gianluigi; van Hijum, Sacha A. F. T.; den Camp, Huub J. M. Op; Jetten, Mike S. M.; Marchiori, Elena (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#numeroVolume
  • 14 (literal)
Rivista
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#pagineTotali
  • 9 (literal)
Note
  • ISI Web of Science (WOS) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • Radboud University Nijmegen; United States Department of Energy (DOE); Consiglio Nazionale delle Ricerche (CNR); Radboud University Nijmegen; Radboud University Nijmegen; Delft University of Technology (literal)
Titolo
  • Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes (literal)
Abstract
  • Background: Sequencing technologies have different biases, in single-genome sequencing and metagenomic sequencing; these can significantly affect ORFs recovery and the population distribution of a metagenome. In this paper we investigate how well different technologies represent information related to a considered organism of interest in a metagenome, and whether it is beneficial to combine information obtained using different technologies. We analyze comparatively three metagenomic datasets acquired from a sample containing the anammox bacterium Candidatus 'Brocadia fulgida' (B. fulgida). These datasets were obtained using Roche 454 FLX and Sanger sequencing with two different libraries (shotgun and fosmid). (literal)
  • Results: In each dataset, the abundance of the reads annotated to B. fulgida was much lower than the abundance expected from available cell count information. This was due to the overrepresentation of GC-richer organisms, as shown by GC-content distribution of the reads. Nevertheless, by considering the union of B. fulgida reads over the three datasets, the number of B. fulgida ORFs recovered for at least 80% of their length was twice the amount recovered by the best technology. Indeed, while taxonomic distributions of reads in the three datasets were similar, the respective sets of B. fulgida ORFs recovered for a large part of their length were highly different, and depth of coverage patterns of 454 and Sanger were dissimilar. (literal)
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