Labella Alejandro M, Castro M Dolores, Manchado Manuel, Borrego Juan J
Department of Microbiology, Faculty of Sciences, Universidad de Malaga, 29071 Malaga, Spain.
Puerto de Santa María, Junta de Andalucía, IFAPA Centro El Toruño, 11500 Cadiz, Spain.
Microorganisms. 2018 Mar 12;6(1):24. doi: 10.3390/microorganisms6010024.
Phylogenetic relationships between species in the genus have been poorly studied despite pathogenic and ecological relevance of some of its members. This is the first phylogenetic study that includes new species of (validated or not) that have not been included in any of the previously described clades, using 16S rRNA sequences and multilocus sequence analysis (MLSA) in concatenated sequences of , , , and housekeeping genes. Sequence analysis has been implemented using Maximum-parsimony (MP), Neighbour-joining (NJ) and Maximum likelihood (ML) treeing methods and the predicted evolutionary relationship between the clades was established on the basis of bootstrap values of >75% for 16S rRNA sequences and MLSA. We have grouped 22 species of the genus into the following 5 clades: Phosphoreum (comprises , "," , , , "" and ""); clade Profundum (composed of , , , , , , "," and ); clade Damselae (two subspecies of , and ); and two new clades: clade Ganghwense (includes , , , , , and ); and clade Leiognathi (composed by , subsp. and " subsp. "). Two additional clades, Rosenbergii and Swingsii, were formed using a phylogenetic method based on 16S rRNA gene, although they are not confirmed by any MLSA methods. Only could not be included in none of the established clade, constituting an orphan clade.
尽管该属某些成员具有致病性和生态相关性，但对其物种间的系统发育关系研究甚少。这是首次进行的系统发育研究，使用16S rRNA序列以及atpA、gltA、gyrB和recA看家基因的串联序列进行多位点序列分析（MLSA），纳入了尚未包含在任何先前描述分支中的该属新物种（无论是否已得到验证）。已使用最大简约法（MP）、邻接法（NJ）和最大似然法（ML）构建树形图进行序列分析，并基于16S rRNA序列和MLSA的自展值>75%确定了各分支之间预测的进化关系。我们已将该属的22个物种分为以下5个分支：磷光分支（包括Photobacterium phosphoreum、“P. leiognathi”、“P. angustum”、P. kishitanii、P. iliopiscarium、“P. damselae”和“P. mandapamensis”）；深海分支（由P. profundum、P. fischeri、P. logei、P. iliopiscarium、P. profundum subsp. profundum、P. profundum subsp. piscinae、“P. leiognathi”和“P. angustum”组成）；少女分支（包含P. damselae的两个亚种，P. damselae subsp. damselae和P. damselae subsp. piscicida）；以及两个新分支：江华岛分支（包括P. ganghwense、P. iliopiscarium、P. profundum、P. leiognathi、P. angustum、P. kishitanii和P. mandapamensis）；以及颌针鱼分支（由P. leiognathi、P. leiognathi subsp. leiognathi和“P. leiognathi”subsp. kishitanii组成）。使用基于16S rRNA基因的系统发育方法形成了另外两个分支，罗森伯格分支和斯温斯分支，尽管它们未得到任何MLSA方法的证实。只有Photobacterium sp.无法归入已确定的任何一个分支，构成一个孤立分支。
