Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

Abstract

As a model organism for studies of cell and environmental biology, the free‐living and cosmopolitan ciliate Euplotes vannus shows intriguing features like dual genome architecture (i.e., separate germline and somatic nuclei in each cell/organism), “gene‐sized” chromosomes, stop codon reassignment, programmed ribosomal frameshifting (PRF) and strong resistance to environmental stressors. However, the molecular mechanisms that account for these remarkable traits remain largely unknown. Here we report a combined analysis of de novo assembled high‐quality macronuclear (MAC; i.e., somatic) and partial micronuclear (MIC; i.e., germline) genome sequences for E. vannus, and transcriptome profiling data under varying conditions. The results demonstrate that: (a) the MAC genome contains more than 25,000 complete “gene‐sized” nanochromosomes (~85 Mb haploid genome size) with the N50 ~2.7 kb; (b) although there is a high frequency of frameshifting at stop codons UAA and UAG, we did not observe impaired transcript abundance as a result of PRF in this species as has been reported for other euplotids; (c) the sequence motif 5′‐TA‐3′ is conserved at nearly all internally‐eliminated sequence (IES) boundaries in the MIC genome, and chromosome breakage sites (CBSs) are duplicated and retained in the MAC genome; (d) by profiling the weighted correlation network of genes in the MAC under different environmental stressors, including nutrient scarcity, extreme temperature, salinity and the presence of ammonia, we identified gene clusters that respond to these external physical or chemical stimulations, and (e) we observed a dramatic increase in HSP70 gene transcription under salinity and chemical stresses but surprisingly, not under temperature changes; we link this temperature‐resistance to the evolved loss of temperature stress‐sensitive elements in regulatory regions. Together with the genome resources generated in this study, which are available online at Euplotes vannus Genome Database (http://evan.ciliate.org), these data provide molecular evidence for understanding the unique biology of highly adaptable microorganisms.

Functional analysis of the methyltransferase SMYD in the single-cell model organism Tetrahymena thermophila

“…Interestingly, SMYD homologues of the four ciliates included in this study showed relatively low similarity (in the range of 10.4%-41%). This high diversity of ciliate SMYD is consistent with the fact that ciliates underwent radiation after their early branching and harbored a rich pool of morphological and genetic diversities (Chen et al 2014(Chen et al , 2018(Chen et al , 2019Guerin et al 2017;Hamilton et al 2016;…”

Morphology and Molecular Phylogeny of Two Freshwater Oligotrich Ciliates (Protozoa, Ciliophora, Oligotrichia), Pelagostrombidium fallax (Zacharias, 1895) Krainer, 1991 and Limnostrombidium viride (Stein, 1867) Krainer, 1995, with Brief Notes on Stomatogenesis

“…The PCR conditions and primers which were used to amplify the SSU rRNA gene follow previous studies (Chen et al. ; Gao et al. 2016a; Wang et al.…”

“…Genomic DNA was extracted using a DNeasy Tissue kit (Qiagen, Hilden, Germany). The PCR conditions and primers which were used to amplify the SSU rRNA gene follow previous studies (Chen et al 2019;Gao et al 2016a;Wang et al 2019). PCR products were sequenced without cloning.…”

Conjugation in Euplotes raikovi (Protista, Ciliophora): New Insights into Nuclear Events and Macronuclear Development from Micronucleate and Amicronucleate Cells

“…In each cell, a germline micronucleus (MIC), which is inactive during the vegetative life coexists with a somatic polyploid macronucleus (MAC), which controls the general functions of the cell [7]. The genome of the MIC is arranged into typical eukaryotic chromosomes, while the genome of the MAC is composed by centromere-less chromosomes amplified in hundreds of copies [7][8][9][10][11]. Because of these characters, ciliates are used as model organisms in a wide range of disciplines, including cytology, evolutionary biology, and genetics [12][13][14][15][16][17].…”