Insights into the phylogeny of the ciliate of class Colpodea based on multigene data

Abstract

In the class Colpodea, there are many unresolved evolutionary relationships among taxa. Here, we report 30 new sequences including SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and the mitochondrial small subunit ribosomal RNA (mtSSU-rRNA) genes of five colpodeans, and conduct phylogenetic analyses based on each individual gene and a two-gene concatenated dataset. For the first time, multi-genes were used to analyze phylogenetic relationships in the class Colpodea. The main findings are: (1) SSU-rRNA, ITS1-5.8S-ITS2 rRNA, and mtSSU-rRNA gene sequences of C. reniformis and C. grandis are provided for the first time, and these two species group into the clade including C. inflata, C. lucida, C. cucullus, and C. henneguyi; (2) clustering pattern and morphological similarity indicate that Bresslauides discoideus has a close relation with Colpodidae spp.; (3) Emarginatophrya genus diagnosis is improved to be 'Hausmanniellidae with sharply shortened and isometric leftmost 1-4 ciliary rows' and Colpoda elliotti is transferred to Emarginatophrya; (4) the genus Colpoda is still non-monophyletic with the addition of 10 populations from five Colpoda species sequences, but there are only two Colpoda groups left based on the present work: Group I comprises C. inflata, C. lucida, C. cucullus, C. henneguyi, C. reniformis, and C. grandis, Group II comprises C. maupasi and C. ecaudata, and the presence of diagonal grooves and the way the vestibular opens might be the two key features that differentiates Colpoda species groups;(5) a close molecular relationship, and highly similar merotelokinetal mode, somatic ciliary pattern, and basic organization of the oral apparatus with P. steinii suggests Bromeliothrix metopoides should be temporarily assigned to Colpodidae.

Internal Transcribed Spacers as Phylogenetic Markers Enable Species-level Metataxonomic Analysis of Ciliated Protozoa

“…Being intrinsically more divergent than the flanking rRNA genes, ITS1 and ITS2 have been widely used in mycobiome (fungal microbiome) analysis for species identification and profiling [29,30], offering significantly enhanced taxonomic resolution. These two ITS regions have been used in studies of free-living ciliates to infer their evolution and refine their phylogeny among closely related ciliate species [31,32]. They have also facilitated the discovery of new ciliate species and genera [33][34][35].…”

Mitogenomic architecture and evolution of the soil ciliates Colpoda

“…Although mitochondria have traditionally been thought to be maternally inherited ( 17 ), reports from organisms such as Caenorhabditis elegans ( 18 ) and Daphnia ( 19 ) have confirmed the presence of considerable heteroplasmy within individual mitogenomes, which has spurred investigations into genome recombination and biparental inheritance in mitochondria ( 20 ). Up to now, mitogenomes have been widely studied in biogeography ( 21 ), ecology ( 22 ), epidemiology ( 23 ), and other fields, playing an increasing role in the study of interspecific evolutionary relationships ( 24 – 27 ), population structure, and dynamics ( 20 ).…”

“…As an ancient genus, Colpoda has a long evolutionary history. However, the phylogenetic relationships within the genus remain controversial ( 24 , 45 , 50 ). The exploration of Colpoda mitogenomes will provide a new perspective on the origin and evolutionary mechanisms of the genus.…”

“…The exploration of Colpoda mitogenomes will provide a new perspective on the origin and evolutionary mechanisms of the genus. However, except for several phylogenetic molecular markers such as cox1 , β-tubulin ( 24 ), and partial mito-SSU rDNA ( 50 ), mitogenome-level research in the class Colpodea has rarely been reported, which is essential to explore their evolutionary history.…”

Further insights into the phylogeny of facultative parasitic ciliates associated with tetrahymenosis (Ciliophora, Oligohymenophorea) based on multigene data

“…Ciliates are a highly differentiated group of microbial eukaryotes that inhabit virtually all environments in the world. They play an important role in the microbial food web through transfer of material and energy (Arregui et al, 2002 ; Azam & Malfatti, 2007 ; Bai et al, 2020 ; Caron et al, 2012 ; Ewa & Sebastian, 2018 ; Gao et al, 2020 ; Kathol et al, 2009 ; Lara et al, 2011 ; Li et al, 2022 ; Liu et al, 2020 ; Luo et al, 2021 ; Pan et al, 2020 ; Pilling et al, 2017 ; Song et al, 2021 ; Wang et al, 2020 ; Weisse, 2017 ; Wu et al, 2021 ).…”