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While <jats:italic>C. abortus<\/jats:italic> is recognized as descended from <jats:italic>C. psittaci<\/jats:italic> species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of <jats:italic>C. abortus<\/jats:italic>. Such strains include <jats:italic>C. psittaci<\/jats:italic> strain 84\/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both <jats:italic>C. abortus<\/jats:italic> and <jats:italic>C. psittaci<\/jats:italic>.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84\/2334 clustered with <jats:italic>C. abortus<\/jats:italic> species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to <jats:italic>C. abortus<\/jats:italic> in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with <jats:italic>C. abortus<\/jats:italic> strains. The analysis also suggested a closer evolutionary relationship between this strain and the major <jats:italic>C. abortus<\/jats:italic> clade, than to two other intermediary avian <jats:italic>C. abortus<\/jats:italic> strains or <jats:italic>C. psittaci<\/jats:italic> strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced <jats:italic>C. abortus<\/jats:italic> genomes as well as similar features to both <jats:italic>C. abortus<\/jats:italic> and <jats:italic>C. psittaci<\/jats:italic> species. The strain also possesses an extrachromosomal plasmid, as found in most <jats:italic>C. psittaci<\/jats:italic> species but absent from all sequenced classical <jats:italic>C. abortus<\/jats:italic> strains.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Overall, the results show that <jats:italic>C. psittaci<\/jats:italic> strain 84\/2334 clusters very closely with <jats:italic>C. abortus<\/jats:italic> strains, and are consistent with the strain being a recent <jats:italic>C. abortus<\/jats:italic> ancestral species. This suggests that the strain should be reclassified as <jats:italic>C. abortus<\/jats:italic>. Furthermore, the identification of a <jats:italic>C. abortus<\/jats:italic> strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from <jats:italic>C. abortus<\/jats:italic> infection.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07477-6","type":"journal-article","created":{"date-parts":[[2021,3,6]],"date-time":"2021-03-06T19:03:57Z","timestamp":1615057437000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84\/2334 should be reclassified as Chlamydia abortus species"],"prefix":"10.1186","volume":"22","author":[{"given":"David","family":"Longbottom","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morag","family":"Livingstone","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Ribeca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delphine Sylvie Anne","family":"Beeckman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arie","family":"van der Ende","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Pannekoek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daisy","family":"Vanrompay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,3,6]]},"reference":[{"key":"7477_CR1","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1053\/jcpa.2002.0629","volume":"128","author":"D Longbottom","year":"2003","unstructured":"Longbottom D, Coulter LJ. 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