0.1 [47]. The robustness of the ML topologies was evaluated using a recently developed Shimodaira-Hasegawa-like test for branches implemented in PhyML v3.0.1 [47]. For the sake of clarity, a small selection of the most relevant sequences was performed to show herein, based on the results MK-0518 of the phylogenetic analysis with the full set of homologous sequences. Sequencing of plasmid https://www.selleckchem.com/products/MK-2206.html pSfr64a Plasmid pSfr64a was purified by the Hirsch method [48], and

used to construct a shotgun library with inserts of approximately 1-2 kb. A total of 1970 high-quality readings were collected by using the ABI3730XL automatic DNA sequencing machine (Applied Biosystems, Foster City, CA). Gaps were filled in by performing appropriate PCR amplification.

Assemblages were obtained by the PhredPhrap-Consed software [49–51]. The quality of the final assembly was less than 1 error per 100,000 bases and had an average coverage of 6.5X. Annotation Open reading frames were predicted by using GLIMMER 3.0 [52, 53] and annotation was carried out with the help of BLASTX [54] comparisons against the GenBank nonredundant database [55], INTERPRO [56] searches, and manual curation by using ARTEMIS [57]. To compare partial genomic sequences with the nonredundant database of GenBank, BLASTX searches were performed, and the top hits were classified with respect to organisms with which they matched. Nucleotide sequence accesion number Thiazovivin cell line Plasmid pSfr64a accession number is GenBank: CP002245. GR64 nifH, recA, and rpoB accesion numbers are respectively GenBank: JN034672, JN034673, JN034674. Acknowledgements We are grateful to José Luis Fernández, Javier Rivera and Nadya Chaira for excellent technical assistance, and to Paul Gaytán and Eugenio López Rutecarpine for synthesis of oligonucleotides. This work was partially supported by grant IN203109 from DGAPA, UNAM. Electronic supplementary material Additional file 1: Similarity of pSfr64a ORFs to genes located in the chromosome of NGR234, pRet42a and pRet42d plasmids. Lists all the

ORFs of pSfr64a, their predicted function, e-value and % of identity to the corresponding ORFs with highest similarity, located on the chromosome of S. fredii NGR234, and R. etli plasmids pRet42a and pRet42d. (PDF 146 KB) References 1. Masson-Boivin C, Giraud E, Perret X, Batut J: Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends in Microbiol 2009, 17:458–466.CrossRef 2. Romero D, Brom S: The symbiotic plasmids of the Rhizobiaceae . In Plasmid biology. Edited by: Phillips G, Funell B. Washington DC, ASM Press; 2004:271–290. 3. Ding H, Hynes MF: Plasmid transfer systems in the rhizobia. Can J Microbiol 2009, 55:917–927.PubMedCrossRef 4. Danino VE, Wilkinson A, Edwards A, Downie JA: Recipient induced transfer of the symbiotic plasmid pRL1JI in Rhizobium leguminosarum bv. viciae is regulated by a quorum-sensing relay. Mol Microbiol 2003, 50:511–525.