Journal: Scientific Reports

Article Title: Influence of mobile genetic elements and insertion sequences in long- and short-term adaptive processes of Acidithiobacillus ferrooxidans strains

doi: 10.1038/s41598-023-37341-4

Figure Lengend Snippet: Location, occurrence, and mapping of MGE-associated genes from validated and candidate iMGEs in the draft genome of A. ferrooxidans CCM 4253. ( A ) Location of experimentally validated and bioinformatically predicted iMGEs (candidate) present in the two query genomes and their correlative order (iMGE1 to iMGE9). Query iMGEs were classified as Tra- or Trb-type Integrative Conjugative Elements (ICEs), Genomic Islands (GIs), or Tn7 transposons (Tnp) and their integration sites were identified (detailed in Table ). ( B ) Occurrence and coverage of validated and candidate iMGEs of A. ferrooxidans ATCC 23270 T and ATCC 53993 in an extended set of draft genomes of the species. Strains were clustered based on the coverage patterns of the MGE-associated gene products (cut-off: e-value -10; detailed in Supplementary Table ). ( C ) Identification of novel iMGEs and iMGE-fragments in strain CCM 4253. Colored elements in the outer layer are known and candidate iMGEs in ATCC 23270 T and ATCC 53993 genomes. Some iMGEs are strain-exclusive, such as iMGE1 and iMGE3 . Others are conserved in two reference strains used as queries. Dark blue elements correspond to CCM 4253 strain genomic assembly contigs (GCA_003233765). Additional information layers, from the center of the figure outwards, correspond to (a) the TBlastN hits found in the CCM 4253 genome using either query strains MGEs; (b) the G + C content skew of the position; (c) the deep local coverage at the position; (d–f) the exclusive, flexible, or core pangenome compartment to which a given CCM 4253 gene pertains and (g) the prediction of MGE features using a combination of tools as previously described in Gonzalez et al. and Moya-Beltrán et al. . ( D ) PCR validation of novel and partially conserved candidate iMGEs identified in the genome of strain CCM 4253. PCR products correspond to specific attL , attR , attP , and attB sites (the scheme of experimental design is shown in Supplementary Table D and primer sequences are listed in Supplementary Table E) of the following iMGEs: iMGE1 (partial ICE integrated into the rimO gene); iMGE10 (integrated at tRNA Thr-TGT); iMGE11 (integrated at tRNA Arg-CCT); iMGE12 (integrated at tRNA Arg-TCT); iMGE13 (integrated at tRNA Ala-GGC); iMGE4 (partial ICE integrated at tRNA Ala-CGC). PCR of attP and attB sites were evaluated on DNA recovered after incubation of A. ferrooxidans CCM 4253 cells with mitomycin C. Lane M represents the 100 bp DNA ladder; lanes L, R, P, and B represent the attL , attR , attP , and attB specific sites in the individual iMGEs, respectively. The gel image has been cropped for display. The original gel image is shown in Supplementary Table F.

Article Snippet: Colored elements in the outer layer are known and candidate iMGEs in ATCC 23270 T and ATCC 53993 genomes.

Techniques: Incubation