-

1. IDENTIFICATION OF PLASMID SEQUENCES IN
MICROCOCCUS AND EXIGUOBACTERIUM STRAINS
Padilla Franzotti, Carla L.; Kurth, Daniel G.
Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT-CONICET.
Tucumán, Argentina. E-mail: carlastembio@gmail.com
Conclusions
This preliminary analysis allowed the identification of potentially plasmid sequences in
different strains of the bacterial genera studied, which will serve as the basis for subsequent
analyzes, with the possibility of creating new genetic tools for the study of plasmidome.
Bibliography:
1. Galata, V., Fehlmann, T., Backes, C. & Keller, A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res. 47, D195–D202 (2019).
2. Arredondo-Alonso, S., Willems, R. J., van Schaik, W. & Schürch, A. C. On the (im)possibility of reconstructing plasmids from whole-genome short-read sequencing data. Microb. Genomics 3, 1–8 (2017).
3. Laczny, C. C., Galata, V., Plum, A., Posch, A. E. & Keller, A. Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates. Brief. Bioinform. 20, 857–865 (2017).
4. Dib, J. R., Wagenknecht, M., Farí
as, M. E. & Meinhardt, F. Strategies and approaches in plasmidome studies-uncovering plasmid diversity disregarding of linear elements? Front. Microbiol. 6, 463 (2015).
Exiguobacterium
Micrococcus
At distance of 0.3, the 9 Micrococcus strains showed plasmids sequences similar to DB
PLSDB, while only 3 Exiguobacterium strains showed any similarity. Five strains of
Micrococcus showed similar sequences at distances of 0.1. Plasmids sequences without
similarity to the sequences already known were found for most of the strains studied.
Background Methods
For each studied strain of the Micrococcus and Exiguobacterium
genera, contigs were generated by assembling short sequence
reads obtained from the SRA-NCBI database using SPAdes
3.11.0, which were evaluated by QUAST 2.3. These were
processed with four freely available high precision homology
independent plasmid detection tools: PlasFlow, cBar (working
from contigs), Recycler, and plasmidSPAdes (which reconstruct
plasmid sequences from the assembly diagram). We analyzed
our predictions with CATPAC and compared them with DB
PLSDB (to search for plasmid sequences with and without
similarity). We evaluated the topology,% GC and length of the
plasmid sequences resulting from the CATPAC analysis and
those already known for the two bacterial genera studied.
Results
These sequences averaged 2909.4 bp in length with a GC content of 59.4%. On the
other hand, of 6 Exiguobacterium strains analyzed, only 23 sequences were predicted,
where 10 could be circular elements. In this case, the sequences averaged 3838.2 bp in
length with a GC content of 41.1%. There are currently 9 complete plasmids described
for the genus Micrococcus, of which 4 are circular and 4 linear. For the Exiguobacterium
genus, 12 plasmids are known, all of circular topology. We found, in most of the strains
studied, plasmid sequences similar and without similarity to those described in the
PLSDB database, which we presumably determined as novel sequences.
Assembled genomes were generally fragmented. It
was found in 9 strains of Micrococcus, 130 sequences
that can be plasmids or fragments thereof, of which
78 would correspond to circular plasmids.
Bioinformatic workflow