Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes

BMC Genomics
Fabio GoriElena Marchiori

Abstract

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). 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 datas...Continue Reading

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Citations

Nov 26, 2014·Asian Pacific Journal of Cancer Prevention : APJCP·Zhuang YuShi-Hai Liu
Feb 23, 2019·Proteomics. Clinical Applications·Sophia DollMatthias Mann

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Methods Mentioned

BETA
Genome sequencing

Software Mentioned

Fosmid
454
Signature
Shotgun
BLASTX
PacBio

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