Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): Implications for structural evolution and phylogenetic reconstruction

Sun, Ping; Clamp, John C.; Xu, Dapeng

doi:10.1016/j.ympev.2010.02.030

Cited by 43 publications

(59 citation statements)

References 52 publications

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“…This, in turn, established the conserved structural models for sessile peritrichs that revealed evidence of homology useful for phylogenetic analysis [13]. The ITS2 sequences with homologous structures were synchronously aligned using 4SALE [36].…”

Section: (C) Predicting Secondary Structures Of Its2mentioning

confidence: 92%

“…Extraction of DNA from samples was carried out using methods described in [13]. Amplification of the ITS region and a fragment of approximately 150 bp comprising part of the internal H4 region was accomplished according to protocols in [31,32].…”

Section: Materials and Methods (A) Collection Isolation Fixation Andmentioning

confidence: 99%

“…Moreover, genetic distances between SSU rRNA sequences of morphospecies were small [12], and this high degree of conservation makes it difficult to resolve phylogenetic relationships within the genus and make a clear discrimination between morphospecies. Furthermore, the long-standing assumption that the family Vorticellidae was a distinct, stable taxon and that Vorticella was equally distinct and stable at the generic level was upset by convincing molecular evidence [12][13][14][15]. Given these important systematic uncertainties and the low resolution at the infrageneric level of phylogenies based on SSU rRNA sequences, molecular phylogenies of Vorticella that include a broader sample of taxa and additional genes are desirable.…”

Section: Introductionmentioning

confidence: 99%

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

Sun

Clamp

et al. 2013

Proc. R. Soc. B.

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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.

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Section: (C) Predicting Secondary Structures Of Its2mentioning

confidence: 92%

Section: Materials and Methods (A) Collection Isolation Fixation Andmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Sun

Clamp

et al. 2013

Proc. R. Soc. B.

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“…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).…”

Section: Putative Secondary Structure Of the Free-living Litostomateamentioning

confidence: 99%

“…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.…”

Section: Putative Secondary Structure Of the Free-living Litostomateamentioning

confidence: 99%

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

Rajter

Vďačný

2017

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Abstract. We investigated interrelationships between four free-living litostomatean lineages, using 18S rRNA gene and ITS region sequences as well as the secondary structure of the ITS2 molecules. Our phylogenetic analyses confirmed the deep split of free-living litostomateans into Rhynchostomatia and Haptoria represented here by Haptorida, Pleurostomatida, and Spathidiida. This bifurcation is also corroborated by the signature of the rhynchostomatian and haptorian ITS2 molecules. Specifically, the consensus stems of helices II and III are longer by one base pair in Rhynchostomatia, while the terminal loops of both helices are longer by one or two nucleotide/-s in Haptoria. A close relationship of Pleurostomatida and Haptorida is favored by quartet likelihood-mapping and supported by a 5'-AG vs. CU-3' motif in the variable part of helix II and by two morphological apomorphies, i.e., meridionally extending somatic kineties and a non-three-rowed dorsal brush. Although monophyletic origin of Spathidiida is poorly supported in phylogenetic trees, the unique motif 5'-GA vs. UC-3' present in the consensus helix II stem could be an important molecular synapomorphy of spathidiids, apart from the ancestrally anteriorly curved somatic kineties and the three-rowed dorsal brush. The peculiar family Pseudoholophryidae has very likely found its phylogenetic home among spathidiids, as an early branching lineage.

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Morphology and morphogenesis ofEpistylis plicatilisehrenberg, 1831 (Ciliophora, Peritrichia) from Wuhan, China

Shi

Meng

Liu

et al. 2014

Journal of Morphology

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A limnetic peritrichous ciliate, Epistylis plicatilis Ehrenberg, 1831, was collected from a freshwater ditch beside Moshan Hill, Wuhan, China. Its morphology, infraciliature, and morphogenesis were investigated based on specimens examined in vivo, following staining with protargol and by scanning electron microscopy. The characteristics of the Wuhan population of E. plicatilis are as follows: 1) colonial, each colony typically comprising 30-50 individuals, with a dichotomously branched, noncontractile stalk; 2) fully expanded zooids measure 90-155 × 30-50 µm in vivo; 3) a series of 6 or 7 conspicuous folds appear in the posterior region of the zooid when it contracts; 4) single horseshoe-shaped macronucleus oriented transversely; 5) single contractile vacuole located in peristomial region on dorsal wall of infundibulum; 6) myoneme system comprises 20-24 longitudinal fibers, peristomial disk fibers as a wreath-like net and peristomial ring fibers; 7) narrowly spaced transverse striations on the surface of the body; 8) infundibular polykineties 1 and 2 are three-rowed, infundibular polykinety 3 is two-rowed; and 9) stomatogenesis is of the buccokinetal type; in the new oral apparatus, infundibular polykineties 2 and 3, the haplokinety, and the germinal kinety all originate from the germinal kinety of the parental oral apparatus whereas the polykinety and infundibular polykinety 1 originate from the parental haplokinety. An improved diagnosis of E. plicatilis is supplied.

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Analysis of the secondary structure of ITS transcripts in peritrich ciliates (Ciliophora, Oligohymenophorea): Implications for structural evolution and phylogenetic reconstruction

Cited by 43 publications

References 52 publications

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

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

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

Morphology and morphogenesis ofEpistylis plicatilisehrenberg, 1831 (Ciliophora, Peritrichia) from Wuhan, China

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