Morphogenetic characters of the model ciliate Euplotes vannus (Ciliophora, Spirotrichea): Notes on cortical pattern formation during conjugational and postconjugational reorganization

Genes and proteins expressed at different life cycle stages in the model protist Euplotes vannus revealed by both transcriptomic and proteomic approaches

Sexual reproduction first appeared in unicellular protists and has continued to be an essential biological process in almost all eukaryotes. Ciliated protists, which contain both germline and somatic genomes within a single cell, have evolved a special form of sexual reproduction called conjugation that involves mitosis, meiosis, fertilization, nuclear differentiation, genome rearrangement, and the development of unique cellular structures. The molecular basis and mechanisms of conjugation vary dramatically among ciliates, and many details of the process and its regulation are still largely unknown. In order to better comprehend these processes and mechanisms from an evolutionary perspective, this study provides the first comprehensive overview of the transcriptome and proteome profiles during the entire life cycle of the newly-established marine model ciliate Euplotes vannus. Transcriptome analyses from 14 life cycle stages (three vegetative stages and 11 sexual stages) revealed over 26,000 genes that are specifically expressed at different stages, many of which are related to DNA replication, transcription, translation, mitosis, meiosis, nuclear differentiation, and/or genome rearrangement. Quantitative proteomic analyses identified 338 proteins with homologs associated with conjugation and/or somatic nuclear development in other ciliates, including dicer-like proteins, Hsp90 proteins, RNA polymerase II and transcription elongation factors, ribosomal-associated proteins, and ubiquitin-related proteins. Four of these homologs belong to the PIWI family, each with different expression patterns identified and confirmed by RT-qPCR, which may function in small RNA-mediated genome rearrangement. Proteins involved in the nonhomologous end-joining pathway are induced early during meiosis and accumulate in the developing new somatic nucleus, where more than 80% of the germline sequences are eliminated from the somatic genome. A number of new candidate genes and proteins likely to play roles in conjugation and its related genome rearrangements have also been revealed. The gene expression profiles reported here will be valuable resources for further studies of the origin and evolution of sexual reproduction in this new model species.

Three closely-related subclasses Phacodiniidia Small & Lynn, 1985, Protohypotrichia Shi et al., 1999, and Euplotia Jankowski, 1979 (Protista, Ciliophora): A new contribution to their phylogeny with reconsiderations on the evolutionary hypotheses

The huge variety of species and worldwide distribution of ciliated protists in class Spirotrichea continue to make it one of the most complicated and confused groups in Ciliophora, despite significant research interest in the unique molecular genetics of these organisms. In this study, the morphological and molecular information were integrated, and it is inferred from a new perspective for the evolutionary relationship among Phacodiniidia, Protohypotrichia, Hypotrichia and Euplotia. Our results indicate that Kiitricha and Caryotricha, two members in Protohypotrichia, may represent two parallel branches of evolution; Euplotidae and Aspidiscidae represent the most recently diverged taxa within Euplotida, followed by Certesiidae, Gastrocirrhidae, and Uronychidae. Further, representative morphological characters (e.g. fronto-ventral-transverse cirral anlagen, undulating membranes, marginal cirri and caudal cirri) were stochastically mapped on phylogenies to speculate evolutionary path and morphological characters of the evolutionary transition node groups were assumed.

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

Tetrahymenosis, caused by about 10 Tetrahymena species, is an emerging problem inflicting a significant economic loss on the aquaculture industry worldwide. However, in the order Tetrahymenida, there are many unresolved evolutionary relationships among taxa. Here we report 21 new sequences, including SSU-rRNA, ITS1-5.8S-ITS2 rRNA and LSU-rRNA, genes of 10 facultative parasitic Tetrahymena associated with tetrahymenosis, and conduct phylogenetic analyses based on each individual gene and a three-gene concatenated dataset. The main findings are: (1) All the parasitic and facultative parasitic species cluster in borealis group. (2) With the addition of new sequences, Tetrahymena is still divided into three groups, namely the "borealis group", the "australis group," and the "paravorax group." (3) the cluster pattern of all the newly sequenced facultative parasitic Tetrahymena species shows that members of the "borealis" group may be more susceptible to parasitism. (4) phylogeny based on concatenated genes show that T. pyriformis, T. setosa, and T. leucophrys have close relationship.

Doublets of the unicellular organism Euplotes vannus (Alveolata, Ciliophora, Euplotida): the morphogenetic patterns of the ciliary and nuclear apparatuses associated with cell division

Ciliated protists are one of the most diverse and highly differentiated group among unicellular organisms. Doublets occur in ciliates when two cells fuse into a single individual. Doublets contain two major cellular components (either cell in a doublet) and have traditionally been considered as developmental anomalies. Nevertheless, doublets can divide or even conjugate effectively, which may represent dispersal forms of the life stages. In addition, morphogenesis, as an important process in the life cycle, will provide important insights into the complex differentiation mechanism and various physiological phenomena. However, morphogenetic studies focusing on doublets of ciliates are very limited, which has become an obstacle to understand their complete life history. Here we isolated a doublet strain from the marine species Euplotes vannus (Müller, 1786) Diesing, 1850 and investigated its morphogenetic events during asexual reproduction. Our results indicate that: (1) the opisthe's oral primordium develops de novo beneath the cortex; (2) the frontoventral and transverse cirral anlagen, cirrus I/1, and marginal anlagen in both dividers develop de novo separately; (3) the dorsal kinety anlagen, the three rightmost ones of which produce three caudal cirri for the proter, occur within the parental structures in the mid-body region; (4) the opisthe acquires two caudal cirri, one from the end of each two rightmost kineties; and (5) there are two macronuclei and one micronucleus in the doublet and they divide amitotically and mitotically, respectively. Finally, we speculate that this special differentiation may be an adaptive form to adverse environments.

Ultrastructure of Diophrys appendiculata and new systematic consideration of the euplotid family Uronychiidae (Protista, Ciliophora)

The ultrastructure of ciliates carries important cytological, taxonomical, and evolutionary signals for these single-celled eukaryotic organisms. However, little ultrastructural data have been accumulated for most ciliate groups with systematic problems. In the present work, a well-known marine uronychiid, Diophrys appendiculata, was investigated using electron microscopy and a comparison with, and a discussion considering, phylogenetic analyses were made. The new findings primarily show that: (i) this species lacks the typical alveolar plate, bears cortical ampule-like extrusomes, and has microtubular triads in the dorsal pellicle, and thus exhibits some ultrastructural features in common with most of its previously studied congeners; (ii) each adoral membranelle before the level of frontal cirrus II/2 contains three rows of kinetosomes and each membranelle after the level of frontal cirrus II/2 contains four rows, which might be related with morphogenesis and could be considered as a distinctive character of Diophrys; (iii) some structural details of the buccal field, such as the extra-pellicular fibrils, pellicle, pharyngeal disks and microtubular sheet, were documented. In addition, based on the ultrastructural comparison of representatives, we discuss the differentiation between the subfamilies Diophryinae and Uronychiinae. A hypothetical systematic relationship of members in the order Euplotida based on a wide range of data is also provided.

Timing and characteristics of nuclear events during conjugation and genomic exclusion in Paramecium multimicronucleatum

Ciliated protists are ideal material for studying the origin and evolution of sex, because of their nuclear dimorphism (containing both germline micronucleus and somatic macronucleus in the same cytoplasm), special sexual processes (conjugation and autogamy), and high diversity of mating-type systems. However, the study of sexual process is limited to only a few species, due to the difficulties in inducing or observing conjugation. In the present study, we investigate the conjugation process in Paramecium multimicronucleatum: (1) of the three prezygotic divisions, all micronuclei undergo the first two divisions (meiosis I, II), while a variable number of nuclei undergo the third division (mitosis); (2) the synkaryon divides three times after fertilization, giving rise to eight products that differentiate into four macronuclear anlagen and four micronuclei; (3) cells restore the vegetative stage after two successive cell fissions during which the macronuclear anlagen are distributed into daughter cells without division, while micronuclei divide mitotically; (4) the parental macronucleus begins to fragment following the first meiotic division and finally degenerates completely; (5) the entire process takes about 110 h, of which about 85 h are required for macronuclear development. In addition, we describe for the first time the process of genomic exclusion occurring between amicronucleate and micronucleate cells of P. multimicronucleatum, during which the micronucleate cell contributes a pronucleus to the amicronucleate cell, resulting in both exconjugants being homozygotes. These results provide new insights into the diversity of sexual processes and lay an important cytological basis for future in-depth studies of mating systems in ciliates.

How Ciliated Protists Survive by Cysts: Some Key Points During Encystment and Excystment

Forming cysts is a common and important bionomic strategy for microorganisms to persist in harsh environments. In ciliated protists, many species have been reported to form cysts when facing unfavorable conditions. Despite traditional studies on the morphological features of cysts and the chemical composition of cyst wall, recent research has focused more on the molecular mechanisms of encystment. The present work reviews studies on developmental features and molecular information of resting cysts in ciliates, and pays more attention to the following questions: what are the inducing factors of encystment and excystment? How does the cell change morphologically during these dynamic processes? And what molecular mechanisms underlie those changes? We also present and summarize the characteristics of cysts from diverse ciliate lineages in a phylogenetic framework, aiming to provide new perspectives for studies on adaptive evolution of unicellular eukaryotes.

Genetic Diversity and Phylogeny of the Genus Euplotes (Protozoa, Ciliophora) Revealed by the Mitochondrial CO1 and Nuclear Ribosomal Genes

Nuclear ribosomal and mitochondrial genes have been utilized individually or in combination to identify known species and discriminate closely related species. However, compared with metazoans, genetic diversity within the ciliate order Euplotida is poorly known. The aim of this study is to investigate how much nucleotide sequence divergence occurs within Euplotes. A total of 14 new gene sequences, comprising four SSU rDNA and 10 CO1 (including three species for the first time) were obtained. Phylogenetic analyses were carried out based on sequences of two DNA fragments from the same 27 isolates. We found that CO1 revealed a larger interspecific divergence than the SSU rRNA gene, thus demonstrating a higher resolution for separating congeners. Genetic distances differ significantly at the species level. Euplotes balteatus was revealed to have a large intraspecific variation at two loci, while E. vannus showed different levels of haplotype variability, which appeared as a polyphyletic cluster on the CO1 tree. These high genetic divergences suggest the presence of more cryptic species. By contrast, the CO1 gene showed low variability within E. raikovi, appearing as monophyletic clusters, which indicates that this species could be identified based on this gene. Conclusively, CO1 is a suitable marker for the study of genetic diversity within Euplotes, and increased taxon sampling gives an opportunity to screen relationships among members of this genus. Additionally, current data present no clear biogeographical pattern for Euplotes.

New Contributions to the Diversity of Hypotrichous Ciliates: Description of a New Genus and Two New Species (Protozoa, Ciliophora)

Ciliated protists (ciliates) are extremely diverse and play important ecological roles in almost all kinds of habitats. In this study, two new hypotrichs, Wilbertophrya sinica n. g. and n. sp. and Bakuella xianensis n. sp., from China are investigated. Wilbertophrya n. g. can be separated from related genera mainly by the combination of lacking a buccal cirrus, pretransverse cirri, and caudal cirri, while possessing frontoterminal cirri. Analyses based on morphological and molecular data confirm the validity of the species, W. sinica n. sp., which is characterized as follows: body 50-115 μm × 15-35 μm in vivo; midventral complex comprises four or five cirral pairs only and terminates above mid-body; three frontal, two frontoterminal cirri, and two to four transverse cirri; about 15 macronuclear nodules; colorless cortical granules sparsely distributed. Another new species, B. xianensis n. sp., was isolated from a freshwater wetland and is defined as follows: body 115-150 μm × 40-65 μm in vivo; about 70 macronuclear nodules; dark-brownish cortical granules in groups; midventral complex comprises 8-12 cirral pairs forming a row that terminates posteriorly in mid-body region and two or three short midventral rows that are continuous with the row of midventral pairs; three frontal, four to six frontoterminal, and three to five fine transverse cirri; three bipolar dorsal kineties. Phylogenetic analyses based on small subunit ribosomal DNA (SSU rDNA) sequence data suggest that the new genus Wilbertophrya n. g. belongs to an isolated clade, which might represent an undescribed taxon at the family level, whereas B. xianensis n. sp. groups with several congeners and members of other related genera are within the core urostylids.

Case Study of the Response of N6-Methyladenine DNA Modification to Environmental Stressors in the Unicellular Eukaryote Tetrahymena thermophila

Rediscovered as a potential epigenetic mark, N⁶-methyladenine DNA modification (6mA) was recently reported to be sensitive to environmental stressors in several multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. Here, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Single-molecule, real-time (SMRT) sequencing reveals that DNA 6mA levels in starved cells are significantly reduced, especially symmetric 6mA, compared to those in vegetatively growing cells. Despite a global 6mA reduction, the fraction of asymmetric 6mA with a high methylation level was increased, which might be the driving force for stronger nucleosome positioning in starved cells. Starvation affects expression of many metabolism-related genes, the expression level change of which is associated with the amount of 6mA change, thereby linking 6mA with global transcription and starvation adaptation. The reduction of symmetric 6mA and the increase of asymmetric 6mA coincide with the downregulation of AMT1 and upregulation of AMT2 and AMT5, which are supposedly the MT-A70 methyltransferases required for symmetric and asymmetric 6mA, respectively. These results demonstrated that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes.

IMPORTANCE Increasing evidence indicated that 6mA could respond to environmental stressors in multicellular eukaryotes. As 6mA distribution and function differ significantly in multicellular and unicellular organisms, whether and how 6mA in unicellular eukaryotes responds to environmental stress remains elusive. In the present work, we characterized the dynamic changes of 6mA under starvation in the unicellular model organism Tetrahymena thermophila. Our results provide insights into how Tetrahymena fine-tunes its 6mA level and composition upon starvation, suggesting that a regulated 6mA response to environmental cues is evolutionarily conserved in eukaryotes.

Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms

Evolutionary developmental biology, or Evo-Devo for short, has become an established field that, broadly speaking, seeks to understand how changes in development drive major transitions and innovation in organismal evolution. It does so via integrating the principles and methods of many subdisciplines of biology. Although we have gained unprecedented knowledge from the studies on model organisms in the past decades, many fundamental and crucially essential processes remain a mystery. Considering the tremendous biodiversity of our planet, the current model organisms seem insufficient for us to understand the evolutionary and physiological processes of life and its adaptation to exterior environments. The currently increasing genomic data and the recently available gene-editing tools make it possible to extend our studies to non-model organisms. In this review, we review the recent work on the regulatory signaling of developmental and regeneration processes, environmental adaptation, and evolutionary mechanisms using both the existing model animals such as zebrafish and Drosophila, and the emerging nonstandard model organisms including amphioxus, ascidian, ciliates, single-celled phytoplankton, and marine nematode. In addition, the challenging questions and new directions in these systems are outlined as well.