- Full list of author information is available at the end of the article. - 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - (SCCs), integrative and conjugative elements, accounting for up to 25% of the genome of S. - Similarly, Chassain et al. - Heilbronner et al. - Rossi et al. - aureus is the best characterized, particularly through the work of Schuster et al. - The core genome of the 3 species displays a similar evolution, and rapidly stagnates at close to 2000 genes. - lugdunensis genomes gave further evidence of the highly conserved genomes of the S. - For pan-genome development plot extrapolation: the red curve shows the fitted exponential Heaps ’ low function, and the blue and green curves indicate the upper and lower boundary of the 95% confidence interval. - For Core genome development plot extrapolation: the red curve shows the fitted exponential decay function, and the blue and green curves indicate the upper and lower boundary of the 95% confidence interval. - We did not identify pathogenicity islands in any of the 15 published genomes for S. - The phylogenetic tree was built based on the complete core genome of the analyzed strains. - Alignments of the each individual core gene set were generated using MUSCLE and subsequently concatenated to one large supermatrix. - Four of the 7 prophages exhibited a Zn 2+. - None of the plasmid sequences retrieved from the GenBank database carried any loci cod- ing for protease, PIN-like domain, T/AT, or CRISPR/Cas.. - Identification of CRISPR/Cas systems. - The CRISPR/Cas systems from HKU0901, N920143, VISLISI_27, VISLISI_33, and VISLISI_37 corre- sponded to a Class 1 Type IIIA system according to the classification of Koonin et al., with the conserved modular organization of this family [29]. - aureus, the CRISPR sequences are located downstream of the cas6 gene, as seen in most other Type IIIA CRISPR/Cas systems in CoNS [26, 28]. - No known origin was found in BLAST for any of the 12 spacers, whereas putative matches were found for 7 of them with sequences that might originate from known MGEs. - these could interact to form the typical hairpin structure involved in the initial processing of the CRISPR transcript.. - Unlike in the other 5 strains, the C33 complete CRISPR sequence was not associated with Type IIIA Cas coding loci but with Class 2 Type IIC cas genes (as classified according to Koonin et al. - CRISPR sequences were located upstream of the cas9 gene that displayed several stop codons, making it a pseudogene and the whole operon probably ineffective. - Nevertheless, when analyzing the possible BLAST matches of the 11 spacers, only 1 match for the. - We identified one recurrent DR sequence that does not match any of the 3 DRs identified in the Type IIIA complete CRISPR/Cas systems of S. - T/AT identification was performed on the available annotations of the 15 annotated S. - The mazEF genes are located upstream the of the sigB locus that comprises rsbU, rsbV, rsbW and sigB.. - All genes from the MazEF operon of the 15 S. - We did not identify any of the other T/AT systems that have been previously described in S. - Nevertheless, we found one locus with a predicted PIN-like domain in 13 of the 15 S. - The downstream gene encodes a member of the minimal acetyltransferase CG family (GCN5-related N-acetyl- transferase, Pfam family PF14542). - Table 3 Origin of the spacers of the 5 Type IIIA CRISPR/Cas systems from S. - 6 Genomic context of the PIN-like domain coding sequence of S. - lugdunensis, we ob- served that the essential motifs for DNA cleavage and translocation were highly conserved according to the amino acid sites identified by Roberts et al. - Although RM systems are widespread in staphylococci, according to the REBASE database, the identification of T/AT systems in 100% of the 15 S. - Indeed, in 2017 Rossi et al. - Indeed, Meric et al. - found evidence that homologous recombin- ation might have changed 40 and 24% of the core genome of S. - Interestingly, a pan-genome study of the sexual species S. - The openness of the pan-genomes of S. - lugdunensis speci- ation has occurred only recently, and we are only now experiencing the start of the emergence of new S. - Since its first description in 1988 by Freney et al., several phylogenetic studies have suggested that S. - The role of the MazEF T/AT system in S. - If the roles of plasmid T/AT systems have been only partially elucidated, those of chromosomal T/AT are even less well understood (Fernández-García et al. - Interestingly, Saavedra De Bast et al. - The widespread occurrence of the MazEF system and its highly conserved nucleic acid sequence do not support the hypothesis that it is a simple remnant of past evolutionary events, and its role needs now to be phenotypically elucidated. - However, the system could also be independent of the PIN protein, since the homologous operon is absent in other. - RM systems, particularly Type I, are one of the major mechanisms by which S. - lugdunensis constitutes a novel barrier for HGT, a situ- ation identified by Heilbronner et al. - The results of the present study suggest that such HGT might remain scarce and, if they can mobilize genetic elements between those species, and enrich the whole genome, they are probably too rare to enrich signifi- cantly S. - lugdunensis genomes, seven originated from a unique location over a 3 year period (VISLISI clinical trial), which might have limited, de facto, the genetic diversity of the genomes. - lugdunensis strain HKU0901 (NCBI accession number NC_013893), whose complete genome sequence was first published in 2010 by Tse et al., was used as a reference in the comparative analyses [56]. - The complete genome of this type strain was determined in 2015 by PacBio single- molecule real-time technology by Shiroma et al., and. - Identification of the core genome and pan-genome was per- formed using the EDGAR software platform [59]. - For the statistical extrapolation, it uses non-linear least- squares curve fitting of the observed core and pan genome sizes as function of the number of analyzed genomes.. - For the core genome extrapolation an exponential decay function is used as described by Tettelin et al., where c is the amplitude of the function, n is the genome number, Ω is the extrapolated size of the core genome for n. - Functional categories of the putative proteins encoded by S. - We compared the putative functions of the proteins encoded by the core genome of these three species as issued by EDGAR.. - Identification of CRISPR/Cas systems in S. - It does not focus on the genetic environment of the CRISPR sequences, and thus it does not identify the cas genes. - We set the limits to 15 kb upstream and downstream of the CRISPR sequences, since cas genes were expected to be found in very close proximity, and because CRISPR/Cas system operons are not expected to be larger than 15 kb, particularly type IIIA and II . - (DOCX 16 kb) Additional file 7: Pairwise alignment results according to EMBOSS Needle for the 3 loci of the Type I RM systems identified in S. - JL, SD and MPC analyzed phylogenic implications of the results. - All authors read, revised extensively, and gave final approval of the manuscript.. - Argemi X, Riegel P, Lavigne T, Lefebvre N, Grandpré N, Hansmann Y, et al.. - Argemi X, Prévost G, Riegel P, Keller D, Meyer N, Baldeyrou M, et al. - 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