Draft macronucleus genome of Euplotes crassus ciliate

Vinogradov, D. V.; Цой, О.В.; Zaika, A. V.; Lobanov, Alexey V.; Turanov, Anton A.; Gladishev, V. N.; Gelfand, Mikhail S.

doi:10.1134/s0026893312020197

Cited by 21 publications

(17 citation statements)

References 14 publications

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“…The MAC genome of Euplotes crassus (class Armophorea, genus Nyctotherus ) had also been sequenced, but its annotation is not complete [11]. The numbers of genes as well as the general principles of the genome organization have been shown to be dramatically different between the organisms.…”

Section: Introductionmentioning

confidence: 99%

Evolution of the Exon-Intron Structure in Ciliate Genomes

Bondarenko

Gelfand

2016

PLoS ONE

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A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus) possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n) are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively), but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33–35 bp, 47–51 bp, and 78–80 bp). In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short introns in various representatives of Ciliates.

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Section: Introductionmentioning

confidence: 99%

Evolution of the Exon-Intron Structure in Ciliate Genomes

Bondarenko

Gelfand

2016

PLoS ONE

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“…; Vinogradov et al. ). Lacking conventional TATA and CAAT boxes for the transcription regulation, these repetitions qualify as candidates for this regulation acting either independently, or in cooperation with the GAAAT motif located 21‐bp downstream the telomeric end (Ghosh et al.…”

Section: Resultsmentioning

confidence: 99%

Molecular Structures and Coding Genes of the Water‐Borne Protein Pheromones of Euplotes petzi, an Early Diverging Polar Species of Euplotes

Pedrini

Suter-Stahel²,

Vallesi

et al. 2016

J Eukaryotic Microbiology

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Euplotes is diversified into dozens of widely distributed species that produce structurally homologous families of water-borne protein pheromones governing self-/nonself-recognition phenomena. Structures of pheromones and pheromone coding genes have so far been studied from species lying in different positions of the Euplotes phylogenetic tree. We have now cloned the coding genes and determined the NMR molecular structure of four pheromones isolated from Euplotes petzi, a polar species which is phylogenetically distant from previously studied species and forms the deepest branching clade in the tree. The E. petzi pheromone genes have significantly shorter sequences than in other congeners, lack introns, and encode products of only 32 amino acids. Likewise, the three-dimensional structure of the E. petzi pheromones is markedly simpler than the three-helix up-down-up architecture previously determined in another polar species, Euplotes nobilii, and in a temperate-water species, Euplotes raikovi. Although sharing the same up-down-up architecture, it includes only two short α-helices that find their topological counterparts with the second and third helices of the E. raikovi and E. nobilii pheromones. The overall picture that emerges is that the evolution of Euplotes pheromones involves progressive increases in the gene sequence length and in the complexity of the three-dimensional molecular structure.

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“…Although Euplotes species have similar genome architectures to Oxytricha , to date they lack any evidence of scrambled genes (Prescott, 1994), although genome-wide micronuclear surveys are needed to be confident of this assertion. Similarly to Oxytricha and Stylonychia , the Euplotes crassus macronuclear genome is highly fragmented, containing ~10,000–20,000 gene-sized nanochromosomes (Vinogradov et al, 2012), each amplified to ~1,000 copies. The genetic content of the E. crassus macronucleus is ~40-fold reduced from the sequence complexity of its micronucleus (Baird et al, 1989), like that of Stylonychia .…”

Section: Searching For the Origin Of Scrambled Genes: Euplotes Chilomentioning

confidence: 99%

Genomes on the Edge: Programmed Genome Instability in Ciliates

Bracht

Fang

Goldman

et al. 2013

Cell

102

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Ciliates are an ancient and diverse group of microbial eukaryotes that have emerged as powerful models for RNA-mediated epigenetic inheritance. They possess extensive sets of both tiny and long noncoding RNAs that, together with a suite of proteins that includes transposases, orchestrate a broad cascade of genome rearrangements during somatic nuclear development. This Review emphasizes three important themes: the remarkable role of RNA in shaping genome structure, recent discoveries that unify many deeply diverged ciliate genetic systems, and a surprising evolutionary “sign change” in the role of small RNAs between major species groups.

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Draft macronucleus genome of Euplotes crassus ciliate

Cited by 21 publications

References 14 publications

Evolution of the Exon-Intron Structure in Ciliate Genomes

Evolution of the Exon-Intron Structure in Ciliate Genomes

Molecular Structures and Coding Genes of the Water‐Borne Protein Pheromones of Euplotes petzi, an Early Diverging Polar Species of Euplotes

Genomes on the Edge: Programmed Genome Instability in Ciliates

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