Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Jean-Pierre Flandrois 1, 2 Céline Brochier-Armanet 1, 2 Jérôme Briolay 3 Danis Abrouk 4 Guillaume Schwob 4 Philippe Normand 4 Maria P. Fernandez 4
1 BPGE - Bioinformatique, phylogénie et génomique évolutive
PEGASE - Département PEGASE [LBBE]
2 LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
3 UCBL - Université Claude Bernard Lyon 1
4 LEM - Laboratoire d'Ecologie Microbienne - UMR 5557
Abstract : The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for system-atics and, due to the boom in complete genome sequencing, their use has become widespread. Yet, in the case of uncultured strains, for which complete genome sequences cannot be easily obtained, sequencing many markers is complicated and time consuming. Taking the advantage of the organization of ribo-somal protein coding genes in large gene clusters, we amplified a 32 kb conserved region encompassing the spectinomycin (spc) operon using long range PCR from isolated and from uncultured nodular endophytic Frankia strains. The phylogenetic analysis of the 27 ribosomal protein genes contained in this region provided a robust phylogenetic tree consistent with phylogenies based on larger set of markers, indicating that this subset of ribosomal proteins contains enough phylogenetic signal to address systematic issues. This work shows that using long range PCR could break down the barrier preventing the use of ribosomal proteins as phylogenetic markers when complete genome sequences cannot be easily obtained.
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Journal articles
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https://hal-cnrs.archives-ouvertes.fr/hal-02327832
Contributor : Jean-Pierre Flandrois <>
Submitted on : Wednesday, October 23, 2019 - 8:02:25 AM
Last modification on : Thursday, February 20, 2020 - 7:21:11 PM

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Jean-Pierre Flandrois, Céline Brochier-Armanet, Jérôme Briolay, Danis Abrouk, Guillaume Schwob, et al.. Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon. Research in Microbiology, Elsevier, 2019, 170 (6-7), pp.280-287. ⟨10.1016/j.resmic.2019.06.005⟩. ⟨hal-02327832⟩

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