An ITS-based phylogenetic framework for the genus Vorticella : finding the molecular and morphological gaps in a taxonomically difficult group

Abstract

Vorticella includes more than 100 currently recognized species and represents one of the most taxonomically challenging genera of ciliates. Molecular phylogenetic analysis of Vorticella has been performed so far with only sequences coding for small subunit ribosomal RNA (SSU rRNA); only a few of its species have been investigated using other genetic markers owing to a lack of similar sequences for comparison. Consequently, phylogenetic relationships within the genus remain unclear, and molecular discrimination between morphospecies is often difficult because most regions of the SSU rRNA gene are too highly conserved to be helpful. In this paper, we move molecular systematics for this group of ciliates to the infrageneric level by sequencing additional molecular markers-fast-evolving internal transcribed spacer (ITS) regions-in a broad sample of 66 individual samples of 28 morphospecies of Vorticella collected from Asia, North America and Europe. Our phylogenies all featured two strongly supported, highly divergent, paraphyletic clades (I, II) comprising the morphologically defined genus Vorticella. Three major lineages made up clade I, with a relatively well-resolved branching order in each one. The marked divergence of clade II from clade I confirms that the former should be recognized as a separate taxonomic unit as indicated by SSU rRNA phylogenies. We made the first attempt to elucidate relationships between species in clade II using both morphological and multi-gene approaches, and our data supported a close relationship between some morphospecies of Vorticella and Opisthonecta, indicating that relationships between species in the clade are far more complex than would be expected from their morphology. Different patterns of helix III of ITS2 secondary structure were clearly specific to clades and subclades of Vorticella and, therefore, may prove useful for resolving phylogenetic relationships in other groups of ciliates.

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

“…Regardless of the model used, the structure and motifs of helices II and III are conservative among various ciliate groups. 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.…”

“…Interestingly, this is the shortest ITS2 region among all already investigated ciliates from the subphylum Intramacronucleata. 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.…”

“…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).…”

Phylogenetic perspectives on diversification and character evolution in the species-rich genusErysimum(Erysimeae; Brassicaceae) based on a densely sampled ITS approach

“…To tackle this problem, we utilized secondary structure information using RNAsalsa (Stocsits et al ., ). Secondary structure information of rRNA data has been advocated to aid in multiple alignment (Parsch, Braverman & Stephan, ; Letsch & Kjer, ) and this approach is becoming more popular (Kjer, ; Mallatt & Winchell, ; Letsch & Kjer, ; Molina, Wen & Struwe, ; Sun et al ., ). RNAsalsa uses structural constraints as an input file.…”

Morphology and Phylogeny of Four New Vorticella Species (Ciliophora: Peritrichia) from Coastal Waters of Southern China

“…The SSU rDNA of three Vorticella species sequenced by Sun et al. (), namely, V. chlorostigma, V. striata and V. natans, were removed from the alignment after preliminary analysis because of their short lengths. The hymenostomes Tetrahymena bergeri and T. corlissi were selected as outgroup taxa.…”