Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

Belkorchia, Abdel; Pombert, Jean‐François; Polonais, Valérie; Parisot, Nicolas; Delbac, Frédéric; Brugère, Jean-François; Peyret, Pierre; Gaspin, Christine; Peyretaillade, Éric

doi:10.1093/dnares/dsx002

Cited by 8 publications

(7 citation statements)

References 53 publications

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“…More recently, Belkorchia and colleagues developed a dedicated in silico approach based on genome prediction and transcriptome validation to survey the presence of ncRNAs in the genomes of four Encephalitozoon species E . cu niculi , Encephalitozoon intestinalis , Encephalitozoon hellem , and Encephalitozoon romaleae , and identified ten novel ncRNAs in the Encephalitozoon spp., including nine snoRNA-like genes and one U1 snRNA (Belkorchia et al 2017). They further investigated the genomes of three Nosema species N .…”

Section: Discussionmentioning

confidence: 99%

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First identification of long non-coding RNAs in fungal parasite Nosema ceranae

et al. 2018

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Nosema ceranae is a unicellular fungal parasite of honey bees and causes huge losses for apiculture. Until present, no study on N . ceranae long non-coding RNAs (lncRNAs) was documented. Here, we sequenced purified spores of N . ceranae using strand-specific library construction and high-throughput RNA sequencing technologies. In total, 83 novel lncRNAs were predicted from N . ceranae spore samples, including lncRNAs, long intergenic non-coding RNAs (lincRNAs), and sense lncRNAs. Moreover, these lncRNAs share similar characteristics with those identified in mammals and plants, such as shorter length and fewer exon number and transcript isoforms than protein-coding genes. Finally, the expression of 12 lncRNAs was confirmed with RT-PCR, confirming their true existence. To our knowledge, this is the first evidence of lncRNAs produced by a microsporidia species, offering novel insights into basic biology such as regulation of gene expression of this widespread taxonomic group.RNA-seq / long non-coding RNA / Nosema ceranae / honey bee

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Section: Discussionmentioning

confidence: 99%

“…bombycis , and identified most of the above-mentioned ncRNAs in Encephalitozoon spp. (Belkorchia et al 2017). However, the number of known ncRNAs in micrsporidia is very limited, and no report of lncRNAs in microsporidia was documented until now.…”

Section: Discussionmentioning

confidence: 99%

First identification of long non-coding RNAs in fungal parasite Nosema ceranae

et al. 2018

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“…2018), microsporidian parasites have low splicing efficiency and display variation in intron density and spliceosome completeness between species (Desjardins et al. 2015; Belkorchia et al. 2017).…”

Section: Resultsmentioning

confidence: 99%

Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae

Åsman

Curtis

Archibald

2019

Genome Biology and Evolution

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The regulation of gene expression and RNA maturation underlies fundamental processes such as cell homeostasis, development, and stress acclimation. The biogenesis and modification of RNA is tightly controlled by an array of regulatory RNAs and nucleic acid-binding proteins. While the role of small RNAs (sRNAs) in gene expression has been studied in-depth in select model organisms, little is known about sRNA biology across the eukaryotic tree of life. We used deep sequencing to explore the repertoires of sRNAs encoded by the miniaturized, endosymbiotically derived “nucleomorph” genomes of two single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans . A total of 32.3 and 35.3 million reads were generated from G . theta and B . natans , respectively. In G. theta , we identified nucleomorph U1, U2, and U4 spliceosomal small nuclear RNAs (snRNAs) as well as 11 C/D box small nucleolar RNAs (snoRNAs), five of which have potential plant and animal homologs. The snoRNAs are predicted to perform 2′- O methylation of rRNA (but not snRNA). In B . natans , we found the previously undetected 5S rRNA as well as six orphan sRNAs. Analysis of chlorarachniophyte snRNAs shed light on the removal of the miniature 18–21 nt introns found in B . natans nucleomorph genes. Neither of the nucleomorph genomes appears to encode RNA pseudouridylation machinery, and U5 snRNA cannot be found in the cryptophyte G. theta . Considering the central roles of U5 snRNA and RNA modifications in other organisms, cytoplasm-to-nucleomorph RNA shuttling in cryptophyte algae is a distinct possibility.

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“…A previous study failed to identify snoRNAs in microsporidia based on sequence similarity predictions (Gardner et al 2010). More recently, Belkorchia et al (2017) identified snoRNAs in Encephalitozoon and Nosema species but noted that the presence of intronic snoRNAs is unlikely due to very short intron lengths. Provocatively, C/D box snoRNAs (Makarova and Kramerov 2009) have similar motifs (CUGA and UGAUGA) as those found in the internal conserved region of the long introns (fig.…”

Section: Resultsmentioning

confidence: 99%

Microsporidian Introns Retained against a Background of Genome Reduction: Characterization of an Unusual Set of Introns

Whelan

Lee

et al. 2018

Genome Biology and Evolution

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Spliceosomal introns are ubiquitous features of eukaryotic genomes, but the mechanisms responsible for their loss and gain are difficult to identify. Microsporidia are obligate intracellular parasites that have significantly reduced genomes and, as a result, have lost many if not all of their introns. In the microsporidian Encephalitozoon cuniculi, a relatively long intron was identified and was spliced at higher levels than the remaining introns. This long intron is part of a set of unique introns in two unrelated genes that show high levels of sequence conservation across diverse microsporidia. The introns possess a unique internal conserved region, which overlaps with a shared, predicted stem–loop structure. The unusual similarity and retention of these long introns in reduced microsporidian genomes could indicate that these introns function similarly, are homologous, or both. Regardless, the significant genome reduction in microsporidia provides a rare opportunity to understand intron evolution.

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Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes

Cited by 8 publications

References 53 publications

First identification of long non-coding RNAs in fungal parasite Nosema ceranae

First identification of long non-coding RNAs in fungal parasite Nosema ceranae

Nucleomorph Small RNAs in Cryptophyte and Chlorarachniophyte Algae

Microsporidian Introns Retained against a Background of Genome Reduction: Characterization of an Unusual Set of Introns

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