Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

Ricard, Guénola; Graaf, R.M. de; Dutilh, Bas E.; Duarte, Isabel Margarida; Alen, Theo A. van; Hoek, Angela Ham van; Boxma, Brigitte; Staay, G.W.M. van der; Staay, S.Y. Moon-van der; Chang, Wei‐Jen; Landweber, Laura F.; Hackstein, J.H.P.; Huynen, Martijn A.

doi:10.1186/1471-2164-9-587

Cited by 30 publications

(28 citation statements)

References 77 publications

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“…Our results generally agree with previous findings in distantly related Euplotes spp. and these features may be conserved in all spirotrichous ciliates, or even in species in the classes Armophorea and Phyllopharyngea, which also contain gene-sized macronuclear chromosomes (Metenier and Hufschmid, 1988;Ricard et al, 2008;Riley and Katz, 2001).…”

Section: Discussionmentioning

confidence: 98%

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Doak

Lipps

et al. 2012

Gene

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Section: Discussionmentioning

confidence: 98%

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Doak

Lipps

et al. 2012

Gene

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“…Omics data are available for relatively few ciliate taxa (Abernathy et al, 2007;Aeschlimann et al, 2014;Aury et al, 2006;Gentekaki et al, 2014;Ricard et al, 2008;Swart et al, 2013) and no omics data of scuticociliates were available hitherto. In the present study, the transcriptomes of five ciliates, including two representatives (Pseudocohnilembus persalinus and Paralembus digitiformis) of the subclass Scuticociliatia, were sequenced and phylogenetically analysed with 24 other taxa.…”

Section: Discussionmentioning

confidence: 99%

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

Feng

Jiang

Warren

et al. 2015

Molecular Phylogenetics and Evolution

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“…Further credit to this concept now derives also from results of genome sequencing in Oxytricha trifallax [29,36] and Nyctotherus ovalis [25].…”

Section: Discussionmentioning

confidence: 99%

“…They bear the motif GAAAA (41 bp upstream the starting ATG codon) as presumptive site of initiation of transcription in the place of the more conventional TATA (or CAAT) boxes [22] and, as occurs in other ciliates [23][24][25], lack a polyadenylation signal represented by the canonical AATAAA motif. Good candidates to replace this motif are the sequences TTATTT and AATAA/G, that are shared by all the sequences in equivalent positions.…”

Section: Nucleotide Sequencesmentioning

confidence: 99%

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

Vallesi¹,

Alimenti²,

Terza³

et al. 2009

Marine Genomics

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Allelic genes encoding water-borne signal proteins (pheromones) were amplified and sequenced from the somatic (macronuclear) sub-chromosomic genome of Antarctic and Arctic strains of the marine ciliate, Euplotes nobilii. Their open reading frames appeared to be specific for polypeptide sequences of 83 to 94 amino acids identifiable with cytoplasmic pheromone precursors (pre-pro-pheromones), requiring two proteolytic steps to remove the pre-and pro-segments and secrete the mature pheromones. Differently from most of the macronuclear genes that have so far been characterized from Euplotes and other hypotrich ciliates, the 5' and 3' non-coding regions of all the seven E. nobilii pheromone genes are much longer than the coding regions (621 to 700 versus 214 to 285 nucleotides), and the 5' regions in particular show nearly identical sequences across the whole set of pheromone genes. These structural peculiarities of the non-coding regions are likely due to the presence of intron sequences and provide presumptive evidence that they are site of basic, conserved activities in the mechanism that regulates the expression of the E. nobilii pheromone genes. AbstractAllelic genes encoding water-borne signal proteins (pheromones) were amplified and sequenced from the somatic (macronuclear) sub-chromosomic genome of Antarctic and Arctic strains of the marine ciliate, Euplotes nobilii. Their open reading frames appeared to be specific for polypeptide sequences of 83 to 94 amino acids identifiable with cytoplasmic pheromone precursors (pre-propheromones), requiring two proteolytic steps to remove the pre-and pro-segments and secrete the mature pheromones. Differently from most of the macronuclear genes that have so far been characterized from Euplotes and other hypotrich ciliates, the 5' and 3' non-coding regions of all the seven E. nobilii pheromone genes are much longer than the coding regions (621 to 700 versus 214 to 285 nucleotides), and the 5' regions in particular show nearly identical sequences across the whole set of pheromone genes. These structural peculiarities of the non-coding regions are likely due to the presence of intron sequences and provide presumptive evidence that they are site of basic, conserved activities in the mechanism that regulates the expression of the E. nobilii pheromone genes.3

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Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

Cited by 30 publications

References 77 publications

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Copy number variations of 11 macronuclear chromosomes and their gene expression in Oxytricha trifallax

Phylogenomic analyses reveal subclass Scuticociliatia as the sister group of subclass Hymenostomatia within class Oligohymenophorea

Characterization of the pheromone gene family of an Antarctic and Arctic protozoan ciliate, Euplotes nobilii

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