Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of <i>Paramecium tetraurelia</i>

Chen, Chun-Long; Zhou, Hui; Liao, Jian-You; Qu, Liang‐Hu; Amar, Laurence

doi:10.1261/rna.1306009

Cited by 13 publications

(11 citation statements)

References 52 publications

(52 reference statements)

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“…The snoRNA USE (5′-AAACCCATAA) (Figure 1C) identified in this study was identical to the one identified previously upstream of Tetrahymena snRNA genes and in ncRNA genes of Paramecium (26,52). It was found upstream of 22 out of 27 intergenic monocistronic snoRNAs.…”

Section: Discussionsupporting

confidence: 83%

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila

Andersen¹,

Nielsen²

2011

Nucleic Acids Research

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The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during vegetative growth or sexual reorganization. In order to get an overview of medium-sized (40–500 nt) RNAs expressed from the Tetrahymena genome, we created a size-fractionated cDNA library from macronuclear RNA and analyzed 80 RNAs, most of which were previously unknown. The most abundant class was small nucleolar RNAs (snoRNAs), many of which are formed by an unusual maturation pathway. The modifications guided by the snoRNAs were analyzed bioinformatically and experimentally and many Tetrahymena-specific modifications were found, including several in an essential, but not conserved domain of ribosomal RNA. Of particular interest, we detected two methylations in the 5′-end of U6 small nuclear RNA (snRNA) that has an unusual structure in Tetrahymena. Further, we found a candidate for the first U8 outside metazoans, and an unusual U14 candidate. In addition, a number of candidates for new non-coding RNAs were characterized by expression analysis at different growth conditions.

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Section: Discussionsupporting

confidence: 83%

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila

Andersen¹,

Nielsen²

2011

Nucleic Acids Research

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“…Indeed, ~ 98% of P. tetraurelia introns are 20–30 nt in size, with a mean of 25 nt. A handful of significantly larger introns, ~ 80 nt in size, contain snoRNAs [ 18 ]. We therefore decided to train the highly configurable EuGene annotation software [ 12 ] for Paramecium , using gene models completely confirmed by RNA-Seq coverage (see Methods).…”

Section: Resultsmentioning

confidence: 99%

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

et al. 2017

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BackgroundThe 15 sibling species of the Paramecium aurelia cryptic species complex emerged after a whole genome duplication that occurred tens of millions of years ago. Given extensive knowledge of the genetics and epigenetics of Paramecium acquired over the last century, this species complex offers a uniquely powerful system to investigate the consequences of whole genome duplication in a unicellular eukaryote as well as the genetic and epigenetic mechanisms that drive speciation. High quality Paramecium gene models are important for research using this system. The major aim of the work reported here was to build an improved gene annotation pipeline for the Paramecium lineage.ResultsWe generated oriented RNA-Seq transcriptome data across the sexual process of autogamy for the model species Paramecium tetraurelia. We determined, for the first time in a ciliate, candidate P. tetraurelia transcription start sites using an adapted Cap-Seq protocol. We developed TrUC, multi-threaded Perl software that in conjunction with TopHat mapping of RNA-Seq data to a reference genome, predicts transcription units for the annotation pipeline. We used EuGene software to combine annotation evidence. The high quality gene structural annotations obtained for P. tetraurelia were used as evidence to improve published annotations for 3 other Paramecium species. The RNA-Seq data were also used for differential gene expression analysis, providing a gene expression atlas that is more sensitive than the previously established microarray resource.ConclusionsWe have developed a gene annotation pipeline tailored for the compact genomes and tiny introns of Paramecium species. A novel component of this pipeline, TrUC, predicts transcription units using Cap-Seq and oriented RNA-Seq data. TrUC could prove useful beyond Paramecium, especially in the case of high gene density. Accurate predictions of 3′ and 5′ UTR will be particularly valuable for studies of gene expression (e.g. nucleosome positioning, identification of cis regulatory motifs). The P. tetraurelia improved transcriptome resource, gene annotations for P. tetraurelia, P. biaurelia, P. sexaurelia and P. caudatum, and Paramecium-trained EuGene configuration are available through ParameciumDB (http://paramecium.i2bc.paris-saclay.fr). TrUC software is freely distributed under a GNU GPL v3 licence (https://github.com/oarnaiz/TrUC).Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3887-z) contains supplementary material, which is available to authorized users.

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“…Furthermore, the RWGD coincides with the explosion of speciation events that gave rise to the P. aurelia complex of 15 sibling species, while the old WGD (OWGD) probably occurred before the divergence of Paramecium and Tetrahymena. In addition, due to a very low rate of large-scale chromosomal rearrangements in P. tetraurelia, the sequenced Paramecium genome provides a unique system to identify an unprecedented large number of WGD paralogs of different ages and to study the mechanisms of genome evolution consequences on gene duplication (Chen et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome duplications contributed to the expansion of cytochrome b5 genes in Paramecium tetraurelia

Wang²,

Ding³

et al. 2013

Genet. Mol. Res.

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ABSTRACT. Cytochrome b 5 (cyt b 5 ) genes encode ubiquitous electron transport hemoproteins found in animals, plants, fungi, and purple bacteria. However, little is known about their evolutionary history in genomes so far. Here, we conducted an extensive genome-wide survey of cyt b 5 genes in 20 representative model species and identified 310 of these genes. Both the absolute number and relative proportion of cyt b 5 genes in Paramecium tetraurelia were significantly higher than those in other genomes. Our data also showed that whole-genome duplications (WGDs), especially the recent WGD, contributed to the species-specific expansion of cyt b 5 genes in the Paramecium genome. Furthermore, 24 cyt b 5 genes were identified as the minimal number of ancestral cyt b 5 in the ancestral Paramecium genome, which is also the largest number of these genes encountered in an organism. These results suggest that an excess of cyt b 5 genes were selectively retained in this species even before the three WGDs took place. Although more cyt b 5 genes were retained in P. tetraurelia than in other genomes, more cyt b 5 losses were

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Genome-wide evolutionary analysis of the noncoding RNA genes and noncoding DNA of Paramecium tetraurelia

Cited by 13 publications

References 52 publications

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila

Experimental identification and analysis of macronuclear non-coding RNAs from the ciliate Tetrahymena thermophila

Improved methods and resources for paramecium genomics: transcription units, gene annotation and gene expression

Whole-genome duplications contributed to the expansion of cytochrome b5 genes in Paramecium tetraurelia

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