Two new species of Ripella (Amoebozoa, Vannellida) and unusual intragenomic variability in the SSU rRNA gene of this genus

Abstract

Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.

A diversity of amoebae colonise the gills of farmed Atlantic salmon (Salmo salar) with amoebic gill disease (AGD)

“…Both the Tubulinea and Discosea 18S rRNA analysis were congruent with former Amoebozoa analysis (Kang et al, 2017;Kudryavtsev and Gladkikh, 2017;Tyml and Dyková, 2017), as many typical higher taxa were found grouped within the trees presented. All the newly sequenced strains within Tubulinea had high homology with sequences representative of genus Nolandella, (Clade 1 (C1) in Fig.…”

“…group. The most recent phylogenetic models were used as the backbone to the analysis, which included those of Tyml and Dyková (2017) for Tubulinea, Sibbald et al, (2017), Kudryavtsev and Gladkikh, (2017) and Udalov et al, (2016) The sequence datasets were aligned in MAFFT v. 7 (Katoh et al, 2017) using the G-INS-I algorithm for the Tubulinea dataset, and the E-INS-I algorithm for the Discosea dataset. The alignments were trimmed using trimAl v.12 (Capella-Gutiérrez et al, 2009) with -gt 0.3 -st 0.001 restrictions for both the Tubulinea and Discosea analysis.…”

Tracing the Origin of Planktonic Protists in an Ancient Lake

“…However, concerted evolution should eliminate different copies of the rRNA gene within genomes in evolutionary times [73]. Still, certain protist lineages may keep different copies of the 18S rDNA in a single genome [74,75]. Indeed, we found 192 OTUs in Lake Baikal, which were similar to the dinoflagellate Gyrodinium helveticum.…”

Tracing the Origin of Planktonic Protists in an Ancient Lake

“…However, concerted evolution should eliminate different copies of the rRNA gene within genomes in evolutionary times [77]. Still, certain protist lineages may keep different copies of the 18S rDNA in their genomes [78,79]. Indeed, we found 192 OTUs in Lake Baikal, which were similar to the dinoflagellate Gyrodinium helveticum.…”