ORF-based binarized structure network analysis of plasmids (OSNAp), a novel approach to core gene-independent plasmid phylogeny

• Published in: Plasmid 2020-03, Vol.108, p.102477-102477, Article 102477
• Main Authors: Suzuki, Masahiro, Doi, Yohei, Arakawa, Yoshichika
• Format: Article
• Language: English
• Subjects: clonal complex; Computational Biology - methods; Gene Order; Multilocus Sequence Typing; Neighbor-net; open reading frame; open reading frame-based binarized structure network analysis of plasmids; Open Reading Frames; ORF; OSNAp; Phylogenetic analysis; Phylogenetic network; Phylogeny; plasmid multilocus sequence typing; plasmid sequence type; Plasmids - classification; Plasmids - genetics; pMLST; pST
• ISSN: 0147-619X; 1095-9890
• DOI: 10.1016/j.plasmid.2019.102477

Systematic comparison of multiple plasmids remains challenging. We aimed to develop a new method for phylogenetic analysis of plasmids, open reading frame (ORF)-based binarized structure network analysis of plasmids (OSNAp). With the OSNAp, the genetic structures of plasmids in a given plasmid group are expressed as binary sequences based on the presence or absence of ORFs regardless of their positions or directions. As a proof-of-concept, ORFs were collected from 101 complete I1 plasmid sequences, and their corresponding binary sequences were generated. A tree was generated using the neighbor-net, an algorithm for constructing phylogenetic networks based on distance between taxa, to visualize the plasmid phylogeny drawn from binary sequences. The results were compared with those of plasmid sequence types (pSTs) defined by plasmid multilocus sequence typing (pMLST). All I1 plasmids were placed on the phylogenetic tree constructed from the binary sequences. Most plasmids belonging to the same pSTs had Dice indices of ≥0.95 and were placed in the same OSNAp split. On the other hand, pST12 plasmids were distributed on separate splits due to differences in ORFs not used in pMLST, suggesting improved differentiation of the plasmids with OSNAp compared with pMLST. OSNAp is a novel holistic approach to assess relatedness of a population of plasmids in a given plasmid group based on nucleotide sequence data. It provides higher discrimination than pMLST, which may prove useful in tracing bacteria that harbor plasmids of shared origins. •OSNAp, a new phylogenetic analysis method of plasmids was developed.•Plasmid structures are expressed as binary sequences based on their gene contents.•Phylogeny of plasmids are then visualized as a neighbor-net network.•OSNAp does not require the presence of common sequences among the plasmids.•Application of OSNAp is illustrated using I1 plasmids.