Neotypification of Pleurocapsa fuliginosa and epitypification of P. minor (Pleurocapsales): resolving a polyphyletic cyanobacterial genus

Strains with complete morphological match to Pleurocapsa fuliginosa and P. minor were isolated from Oahu (Hawaii, USA), with another strain matching P. minor isolated from a wet rock face in Utah (USA). Phylogenetically these baeocyte and pseudofilament producing strains fell in a single well-supported clade among a number of pleurocapsalean strains. They were sister to a clade of baeocyte-producing strains that lack the ability to form pseudofilaments and likely belong in an as-yet-to- be-described genus. Strains putatively named Pleurocapsa are scattered throughout the Pleurocapsales and Chroococcales, indicating a need for clear definition of the genus so that revisionary work and alpha-level taxonomy can move forward. To satisfy this need, P. fuliginosa HA4302-MV1 and P. minor HA4230-MV1 were chosen as neotype and epitype, respectively, establishing the genus based on molecular sequence data. In addition to the distinctive morphology of the genus, all Pleuro- capsa species for which 16S-23S ITS regions are available have an unusually long, branched D5 helix at the termination of the ITS region. The sister clade of strains that lack the ability to form pseudofilaments also possess an unusually long and branched D5 helix as well, suggesting that this feature of the ITS region may be a family-level synapomorphy

Multilocus genetic characterization of phytoplasmas

Classification of phytoplasmas into 16S ribosomal groups and subgroups and \u2018Candidatus Phytoplasma\u2019 species designation have been primarily based on the conserved 16S rRNA gene. However, distinctions among closely related \u2018Ca. Phytoplasma\u2019 species and strains based on 16S rRNA gene alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence heterogeneous, copies of this gene. Thus, in recent years, moderately conserved genes have been used as additional genetic markers with the aim to enhance the resolving power in delineating distinct phytoplasma strains among members of some 16S ribosomal subgroups. The present chapter is divided in two parts: the first part describes the non-ribosomal single-copy genes less conserved (housekeeping genes) such as ribosomal protein (rp), secY, secA, rpoB, tuf, and groEL genes, which have been extensively used for differentiation across the majority of phytoplasmas; the second part describes the differentiation of phytoplasmas in the diverse ribosomal groups using multiple genes including housekeeping genes and variable genes encoding surface proteins

Multilocus genetic characterization of phytoplasmas

Classification of phytoplasmas into 16S ribosomal groups and subgroups and \u2018Candidatus Phytoplasma\u2019 species designation have been primarily based on the conserved 16S rRNA gene. However, distinctions among closely related \u2018Ca. Phytoplasma\u2019 species and strains based on 16S rRNA gene alone have limitations imposed by the high degree of rRNA nucleotide sequence conservation across diverse phytoplasma lineages and by the presence in a phytoplasma genome of two, sometimes sequence heterogeneous, copies of this gene. Thus, in recent years, moderately conserved genes have been used as additional genetic markers with the aim to enhance the resolving power in delineating distinct phytoplasma strains among members of some 16S ribosomal subgroups. The present chapter is divided in two parts: the first part describes the non-ribosomal single-copy genes less conserved (housekeeping genes) such as ribosomal protein (rp), secY, secA, rpoB, tuf, and groEL genes, which have been extensively used for differentiation across the majority of phytoplasmas; the second part describes the differentiation of phytoplasmas in the diverse ribosomal groups using multiple genes including housekeeping genes and variable genes encoding surface proteins