Phylogenomic analysis ofBalantidium ctenopharyngodoni(Ciliophora, Litostomatea) based on single-cell transcriptome sequencing

Abstract

In this paper, we present transcriptome data for Balantidium ctenopharyngodoni Chen, 1955 collected from the hindgut of grass carp (Ctenopharyngodon idella). We evaluated sequence quality and de novo assembled a preliminary transcriptome, including 43.3 megabits and 119,141 transcripts. Then we obtained a final transcriptome, including 17.7 megabits and 35,560 transcripts, by removing contaminative and redundant sequences. Phylogenomic analysis based on a supermatrix with 132 genes comprising 53,873 amino acid residues and phylogenetic analysis based on SSU rDNA of 27 species were carried out herein to reveal the evolutionary relationships among six ciliate groups: Colpodea, Oligohymenophorea, Litostomatea, Spirotrichea, Heterotrichea and Protocruziida. The topologies of both phylogenomic and phylogenetic trees are discussed in this paper. In addition, our results suggest that single-cell sequencing is a sound method of obtaining sufficient omics data for phylogenomic analysis, which is a good choice for uncultivable ciliates. The transcriptome data for Balantidium ctenopharyngodoni are the first omics data within the subclass Trichostomatia, and provide a good basis for ciliate phylogenomic analysis, as well as related omics analysis.

Molecular occurrence and risk factors for Toxoplasma gondii infection in equids in Jilin, China

“…2 ) 18 . The methods of maximum likelihood (ML) (MEGA v.7.0) and Bayesian (MrBayes 3.2) were executed for phylogenetic analysis 19 . In the ML analysis, the substitution model Kimura-2-parameter accompanying with 1000 replicates of bootstrapping was performed using MEGA 7.0.…”

Incorporating mitogenome sequencing into integrative taxonomy: The multidisciplinary redescription of the ciliate Thuricola similis (Peritrichia, Vaginicolidae) provides new insights into the evolutionary relationships among Oligohymenophorea subclasses

“…The evolutionary relationships among the subclasses of Oligohymenophorea, i.e., Hymenostomatia, Peniculia, Peritrichia, and Scuticociliatia, have been increasingly debated, since their phylogenetic positions are unstable both in works based on 18S rDNA phylogenies (e.g., Li et al, 2006;Miao et al, 2004;Miao et al, 2001;Strüder-Kypke et al, 2000;Utz and Eizirik, 2007;Utz et al, 2010) and concatenated rDNA sequences phylogenetic analyses (e.g., Gao et al, 2013;Gao et al, 2016). Phylogenomic analyses have been proved to generally improve the robustness of molecular phylogenetic reconstructions, untangling many previously debated phylogenies in various taxa (Feng et al, 2015;Gentekaki et al, 2014;Gentekaki et al, 2017;Jiang et al, 2019;Lasek-Nesselquist and Johnson, 2019;Lynn and Kolisko, 2017;Lynn et al, 2018;Pan et al, 2019;Sheng et al, 2018;Sun et al, 2017b;Wang et al, 2019). Until now, there are only a few phylogenomic analyses on the class Oligohymenophorea and all of them use nuclear gene datasets.…”

“…Indeed, only few complete mitochondrial genomes of ciliates are available online (Barth and Berendonk, 2011;Brunk et al, 2003;Burger et al, 2000;Coyne et al, 2011; de Graaf et al, 2011;de Graaf et al, 2009;Gao et al, 2018;Li et al, 2018;Moradian et al, 2007;Park et al, 2019a;Serra et al, 2020;Swart et al, 2012), and none of them come from peritrichs. In the last few years, the evolutionary relationships among and within the classes of Ciliophora have been investigated through phylogenomic studies using transcriptomes (Feng et al, 2015;Gentekaki et al, 2014;Gentekaki et al, 2017;Grant et al, 2012;Jiang et al, 2019;Lasek-Nesselquist and Johnson, 2019;Lynn and Kolisko, 2017;Lynn et al, 2018;Pan et al, 2019;Sheng et al, 2018;Sun et al, 2017b;Wang et al, 2019). The availability of ciliates' mitogenomes would allow to compare these two approaches, i.e., phylogenomic using nuclear transcriptomes versus phylogenomic using mitogenomes, to test evolutionary relationship with two sets of genes that evolve rather independently.…”

First report of genetic diversity and risk factor analysis of equine piroplasm infection in equids in Jilin, China

“…2) [16]. Phylogenetic trees were constructed using the maximum likelihood (ML) (MEGA v.7.0) and Bayesian (MrBayes 3.2) methods [17]. For the ML analysis, a Tamura-3-parameter model and bootstrapping of 1000 replicates were selected to calculate the evolutionary relationship using MEGA v.7.0 software.…”