Neisseria cinerea 346T whole genome sequence
Custodio, Rafael; Tang, Christoph; Exley, Rachel (2021), Neisseria cinerea 346T whole genome sequence, Dryad, Dataset, https://doi.org/10.5061/dryad.3ffbg79gx
Type VI Secretion Systems (T6SS) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can limit growth of related pathogens. We explored the impact of Tfp expression on N. cinerea T6SS-dependent killing and show that expression of Tfp by prey strains enhances their susceptibility to T6SS, by keeping them in close proximity of T6SS wielding attacker strains. Our findings have important implications for understanding how spatial constraints during contact-dependent antagonism can shape the evolution of microbial communities.
DNA Isolation and whole-genome sequencing (WGS)
Genomic DNA was extracted using the Wizard Genomic Kit (Promega), and sequenced by PacBio (Earlham Institute, Norwich) using single-molecule real-time (SMRT) technology; reads were assembled de novo with HGAP3 (Chin et al., 2013).
The README file contains an explanation of how to open and edit the whole genome sequence .dna files.
Upon further sequence analysis of the PacBio plasmid sequence file of Neisseria cinerea CCUG346T, a duplicated region of approximately 16 kb in the plasmid sequence was identified. Further analysis of genomic DNA from the isolate was performed using overlapping PCR and sequencing. As a result, a modified plasmid map was generated from the PacBio sequence to remove the duplicated region and eliminate 16507 bp from the original sequence file (125,648 bp) resulting in a plasmid sequence of 108,141 bp.