{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T13:23:53Z","timestamp":1778073833050,"version":"3.51.4"},"reference-count":61,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T00:00:00Z","timestamp":1593129600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004515","name":"Universiti Kebangsaan Malaysia","doi-asserted-by":"crossref","award":["GUP-2018-147"],"award-info":[{"award-number":["GUP-2018-147"]}],"id":[{"id":"10.13039\/501100004515","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Titan V GPU was donated by NVIDIA Corporation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>\n                    <jats:italic>Porphyromonas gingivalis<\/jats:italic>\n                    is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the\n                    <jats:italic>porR<\/jats:italic>\n                    gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (\n                    <jats:italic>porR<\/jats:italic>\n                    included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the\n                    <jats:italic>porR<\/jats:italic>\n                    gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that\n                    <jats:italic>porR<\/jats:italic>\n                    and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to\n                    <jats:italic>porR<\/jats:italic>\n                    because the intervening DNA segment that contains\n                    <jats:italic>porR<\/jats:italic>\n                    is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.\n                  <\/jats:p>","DOI":"10.7717\/peerj.9019","type":"journal-article","created":{"date-parts":[[2020,6,26]],"date-time":"2020-06-26T06:03:49Z","timestamp":1593151429000},"page":"e9019","source":"Crossref","is-referenced-by-count":6,"title":["Phylogenetic comparison between Type IX Secretion System (T9SS) protein components suggests evidence of horizontal gene transfer"],"prefix":"10.7717","volume":"8","author":[{"given":"Reeki","family":"Emrizal","sequence":"first","affiliation":[{"name":"Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nor Azlan","family":"Nor Muhammad","sequence":"additional","affiliation":[{"name":"Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, 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