Systematics and Molecular Phylogeny of the Ciliate Genus Pseudokeronopsis (Ciliophora, Hypotrichia)

Abstract

A still challenging study on ciliate systematics is to clarify the taxonomic and phylogenetic confusions of the fascinating pigmented Pseudokeronopsis species because of their high interspecific similarities. We evaluated the identities and internal relationships within Pseudokeronopsis based on morphological descriptions in combination with the 18S and ITS-5.8S rDNA genetic distances, ITS2 secondary structures and phylogenetic analyses. Results showed that (1) Pseudokeronopsis pararubra, a species ever synonymized as Pseudokeronopsis carnea, is a valid species; (2) most Chinese populations identified as Pseudokeronopsis rubra represent a new species namely Pseudokeronopsis songi sp. nov.; (3) within Pseudokeronopsis, P. carnea branched early, while P. songi sp. nov., P. flava, and P. erythrina showed close relationships and formed a sister clade with P. pararubra; (4) compared to 18S and ITS2 rDNA, ITS-5.8S rDNA is more suitable for separating Pseudokeronopsis species, with pairwise distances of 0-0.0441 at the intraspecific level and 0.0635-0.1150 at the interspecific level; and (5) the core structure of Pseudokeronopsis ITS2 includes three helices, with helix III being the longest and showing an identical pattern in conspecific populations and small differences among species. Based on the evaluation, we clarify all misidentified and dubious 18S and ITS-5.8S rDNA sequences of Pseudokeronopsis in GenBank.

Constraints on Phylogenetic Interrelationships among Four Free-living Litostomatean Lineages Inferred from 18S rRNA gene-ITS Region sequences and Secondary Structure of the ITS2 molecule

“…Thus, there is a pyrimidine-pyrimidine mismatch in helix II of heterotricheans (Shazib et al 2016) and oligohymenophoreans (Coleman 2005;Miao et al 2008;Sun et al 2010Sun et al , 2013, as typical for eukaryotes (Coleman 2007;Schultz et al 2005). By contrast, this mismatch is not present in litostomateans and spirotricheans (Weisse et al 2008;Yi et al 2008;Li et al 2013Li et al , 2017. This indicates that the loss of the pyrimidine-pyrimidine mismatch is a molecular synapomorphy of litostomateans and spirotricheans, providing a further support for the SAL hypothesis based on extensive molecular data (Gentekaki et al 2014(Gentekaki et al , 2017.…”

“…Therefore, this molecule has become a popular tool in many phylogenetic studies, including those on ciliates (e.g. Coleman 2005;Miao et al 2008;Weisse et al 2008;Yi et al 2008;Sun et al 2010Sun et al , 2013Ponce-Gordo et al 2011;Li et al 2013;Shazib et al 2016;Li et al 2017).…”

“…Specifically, the length of ITS2 sequences varies from 168 to 169 nt within the genus Paramecium (Coleman 2005), from 168 to 217 nt in scuticociliates , and from 165 to 175 nt in peritrichs (Sun et al 2010(Sun et al , 2013. Spirotrichean ciliates exhibit the longest ITS2 sequences typically exceeding 200 nucleotides (Weisse et al 2008;Yi et al 2008;Li et al 2013Li et al , 2017. On the other hand, the genera Spirostomum and Anigsteinia from the class Heterotrichea of the subphylum Postciliodesmatophora display the shortest ITS2 sequences, being only 79-81 nt long, among all ciliates hitherto studied (Shazib et al 2016).…”

Further insights into the highly derived haptorids (Ciliophora, Litostomatea): Phylogeny based on multigene data

“…Phylogenetic analyses based on concatenation of multiple genes are increasingly used to give better interpretations evolutionary relationships within different ciliate groups (Antipa, Dolan, Lynn, Obolkina, & Strüder‐Kypke, ; Gao, Gao, Wang, Katz, & Song, ; Gao, Warren, et al., ; Gao et al., ; Gentekaki et al., ; Huang, Luo, Bourland, Gao, & Gao, ; Li, Liu, Gao, Warren, & Song, ; Li, Zhan, & Xu, ; Pan, Jiang, Fan, Al‐Farraj, & Gao, ; Sung, Sung, Hywel‐Jones, & Spatafora, ; Yan, Xu, Al‐Farraj, Al‐Rasheid, & Song, ; Yan, Fan, et al., ; Zhao, Gao, Fan, Strüder‐Kypke, & Huang, ). In this study, we broaden the taxon sampling of haptorians by adding 14 small subunit ribosomal RNA (SSU‐rRNA), 12 large subunit ribosomal RNA (LSU‐rRNA) and 12 ITS1‐5.8S‐ITS2 gene sequences.…”

Morphology and Molecular Phylogeny of Two New Terrestrial Ciliates, Australocirrus rubrus n. sp. and Notohymena gangwonensis n. sp. (Ciliophora: Oxytrichidae), from South Korea

“…The cortical granule type (color, size, shape, and arrangement) is an important feature in the classification of urostylid ciliate species (Berger ; Li et al. ). In our study, we found that A. australis and A. rubrus formed a clade, but the distance between them was relatively large (1.2% of sequences were dissimilar).…”