Faculty of Medicine, University of Southampton, Southampton, Hampshire, United Kingdom.
Molecular Microbiology Group, Clinical and Experimental Sciences, University Hospital Southampton, Southampton, Hampshire, United Kingdom.
PLoS One. 2020 May 29;15(5):e0233298. doi: 10.1371/journal.pone.0233298. eCollection 2020.
Evolutionary studies have been conducted that have investigated the chromosomal variance in the genus of Chlamydia. However, no all-encompassing genus-wide comparison has been performed on the plasmid. Therefore, there is a gap in the current knowledge on Chlamydia plasmid diversity.
This project is aimed to investigate and establish the nature and extent of diversity across the entire genus of Chlamydia, by comparing the sequences of all currently available plasmid carrying strains.
The PUBMED database was used to identify plasmid sequences from all available strains that met the set quality criteria for their inclusion in the study. Alignments were performed on the 51 strains that fulfilled the criteria using MEGA X software. Following that Maximum Likelihood estimation was used to construct 11 phylogenetic trees of the whole plasmid sequence, the individual 8 coding sequences, the iteron and a chromosomal gene ompA as a comparator.
The genus-wide plasmid phylogeny produced three distinct lineages labelled as alpha, beta and gamma. Nineteen genotypes were found in the initial whole plasmid analysis. Their distribution was allocated as six C. pecorum, two C. pneumoniae, one C. gallinacea, one C. avium, one C. caviae, one C. felis, two C. psittaci, one C. trachomatis, one C. muridarum, and two C. suis. The chromosomal comparative gene ompA supported this distribution, with the same number of primary clades with the same species distribution. However, ompA sequence comparison resulted in fewer genotypes due to a reduced amount of available sequences (33 out of 51). All results were statistically significant.
The results of this study indicate that the common bacterial ancestor of all the species had a plasmid, which has diverged over time. Moreover, it suggests that there is a strong evolutionary selection towards these species retaining their plasmids due to its high level of conservation across the genus, with the notable exception of C. pneumoniae. Furthermore, the evolutionary analysis showed that the plasmid and the chromosome have co-evolved.
已经进行了进化研究，调查了衣原体属的染色体变异。然而，尚未对质粒进行全面的属范围比较。因此，目前对衣原体质粒多样性的认识存在空白。
本项目旨在通过比较所有现有携带质粒的菌株的序列，调查并确定整个衣原体属的多样性的性质和程度。
使用 PUBMED 数据库从所有符合纳入研究标准的可用菌株中确定质粒序列。使用 MEGA X 软件对符合标准的 51 株菌进行比对。之后，使用最大似然估计构建了 11 个全质粒序列、11 个个体 8 个编码序列、内元和染色体基因 ompA 的系统发育树作为比较。
全属质粒系统发育树产生了三个不同的谱系，分别标记为 alpha、beta 和 gamma。在最初的全质粒分析中发现了 19 种基因型。它们的分布被分配为 6 种 C. pecorum、2 种 C. pneumoniae、1 种 C. gallinacea、1 种 C. avium、1 种 C. caviae、1 种 C. felis、2 种 C. psittaci、1 种 C. trachomatis、1 种 C. muridarum 和 2 种 C. suis。比较基因 ompA 的染色体支持这种分布，具有相同数量的主要分支和相同的物种分布。然而，由于可用序列数量减少（51 个中的 33 个），ompA 序列比较导致基因型数量减少。所有结果均具有统计学意义。
本研究结果表明，所有物种的共同细菌祖先都有一个质粒，随着时间的推移已经发生了分化。此外，这表明由于其在属内的高度保守性，这些物种保留质粒的进化选择很强，衣原体属中的 C. pneumoniae 是一个显著的例外。此外，进化分析表明质粒和染色体共同进化。
