Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research

Abstract

While nuclear small subunit ribosomal DNA (nSSU rDNA) is the most commonly-used gene marker in studying phylogeny, ecology, abundance, and biodiversity of microbial eukaryotes, mitochondrial small subunit ribosomal DNA (mtSSU rDNA) provides an alternative. Recently, both copy number variation and sequence variation of nSSU rDNA have been demonstrated for diverse organisms, which can contribute to misinterpretation of microbiome data. Given this, we explore patterns for mtSSU rDNA among 13 selected ciliates (representing five classes), a major component of microbial eukaryotes, estimating copy number and sequence variation and comparing to that of nSSU rDNA. Our study reveals: (1) mtSSU rDNA copy number variation is substantially lower than that for nSSU rDNA; (2) mtSSU rDNA copy number ranges from 1.0 × 104 to 8.1 × 105; (3) a most common sequence of mtSSU rDNA is also found in each cell; (4) the sequence variation of mtSSU rDNA are mainly indels in poly A/T regions, and only half of species have sequence variation, which is fewer than that for nSSU rDNA; and (5) the polymorphisms between haplotypes of mtSSU rDNA would not influence the phylogenetic topology. Together, these data provide more insights into mtSSU rDNA as a powerful marker especially for microbial ecology studies.

Cell-division pattern and phylogenetic analyses of a new ciliate genus Parasincirra n. g. (Protista, Ciliophora, Hypotrichia), with a report of a new soil species, P. sinica n. sp. from northwest China

“…Recent faunistic studies have revealed numerous new taxa of hypotrichous ciliates suggesting that this group is more diverse than previously supposed [1][2][3][4][5][6][7][8]. Furthermore, much work has been carried out on the morphogenesis and molecular phylogeny of hypotrichs, which has led to a better understanding of their systematics and evolutionary relationships [9][10][11][12][13][14][15][16][17].…”

Environmental Parameters and Substrate Type Drive Microeukaryotic Community Structure During Short-Term Experimental Colonization in Subtropical Eutrophic Freshwaters

“…As predators, producers, decomposer, and parasites, microeukaryotes represent the bulk of microbial diversity and play key roles in the ecological functioning and process of aquatic biological ecosystems ( Bik et al, 2012 ; Zhang et al, 2018 ; Zhao et al, 2018 ; Chen X. et al, 2019 ; Chi et al, 2019 ; Lu et al, 2019 ; Wang et al, 2020 ; Xu et al, 2020 ). Previous studies showed that several environmental factors play important roles in structuring microeukaryotic communities on biofilms.…”

Systematics and Multi-Gene Phylogeny of the Subfamily Nothoholostichinae (Ciliophora, Hypotrichia), With Integrative Description of a New Marine Species Nothoholosticha luporinii n. sp.

“…Ciliates (phylum Ciliophora Doflein, 1901), a highly diverse and ubiquitously distributed group of unicellular microbial eukaryotes, play substantial roles in various ecosystems. A lot of attention has been therefore paid to their diversity, function and evolution (e.g., Bharti et al, 2019;Hu et al, 2019;Jung and Berger, 2019;Kaur et al, 2019;Luo et al, 2019;Wang et al, 2019;Yan et al, 2019;Gong et al, 2020;Shao et al, 2020;Sheng et al, 2020;Wang Y. R. et al, 2020;Zhang et al, 2020). Hypotrichs (subclass Hypotrichia Stein, 1859) are not only among the most differentiated ciliate groups, but also among the most confused ones in terms of their systematics and phylogeny (for reviews, see Berger, 1999Berger, , 2006Berger, , 2008Berger, , 2011Luo et al, 2017;Song and Shao, 2017;Luo et al, 2018;Lyu et al, 2018;Kim and Min, 2019;Chen et al, 2020;Dong et al, 2020;Paiva, 2020;Park et al, 2020;Wang J. et al, 2020;Xu et al, 2020).…”