DNA interference: DNA-induced gene silencing in the appendicularian
            <i>Oikopleura dioica</i>

Omotezako, Tatsuya; Onuma, Takeshi A.; Nishida, Hiroki

doi:10.1098/rspb.2015.0435

Cited by 21 publications

(29 citation statements)

References 19 publications

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“…In retrospect, conclusions about the mechanism(s) of homology-dependent silencing in Phytophthora may have been premature and based on too few target genes. In plants, fungi and some metazoans, silencing can occur through transcriptional and post-transcriptional processes (Vaucheret et al, 1998;Faugeron, 2000;Omotezako et al, 2015). Outcomes can be specific to the plasmid design, target gene and characteristics of the integration event (Lechtenberg et al, 2003).…”

Section: Current Silencing Model Does Not Apply To Pimadssilenced Strainmentioning

confidence: 99%

A MADS‐box transcription factor regulates a central step in sporulation of the oomycete Phytophthora infestans

Leesutthiphonchai

Judelson

2018

Molecular Microbiology

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MADS-box transcription factors play significant roles in eukaryotes, but have not yet been characterized in oomycetes. Here, we describe a MADS-box protein from Phytophthora infestans, which causes late blight of potato. P. infestans and most other oomycetes express a single MADS-box gene. PiMADS is not transcribed during vegetative growth, but is induced early during asexual sporulation. Its mRNA levels oscillate in response to light, which suppresses sporulation. The protein was not detected in nonsporulating mycelia, but was found in sporulating mycelia and spores. Both mRNA and protein levels decline upon spore germination. A similar expression pattern as well as nuclear localization was observed when the protein was expressed with a fluorescent tag from the native promoter. Gene silencing triggered by a construct expressing 478 nt of MADS sequences indicated that PiMADS is required for sporulation but not hyphal growth or plant colonization. A comparison of wild type to a silenced strain by RNA-seq indicated that PiMADS regulates about 3000 sporulation-associated genes, and acts before other genes previously shown to regulate sporulation. Analysis of the silenced strain also indicated that the native gene was not transcribed while the transgene was still expressed, which contradicts current models for homology-dependent silencing in oomycetes.

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Section: Current Silencing Model Does Not Apply To Pimadssilenced Strainmentioning

confidence: 99%

A MADS‐box transcription factor regulates a central step in sporulation of the oomycete Phytophthora infestans

Leesutthiphonchai

Judelson

2018

Molecular Microbiology

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“…Histochemical detection of alkaline phosphatase821 and acetylcholinesterase19 were carried out as previously described.…”

Section: Methodsmentioning

confidence: 99%

DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica

Omotezako

Matsuo

Onuma

et al. 2017

Sci Rep

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The maternal contribution to the oocyte cytoplasm plays an important role during embryogenesis because it is involved in early cell fate specification and embryonic axis establishment. However, screening projects targeting maternal factors have only been conducted in a limited number of animal models, such as nematodes, fruit flies, and zebrafish, while few maternal genes have been analysed because of difficulties encountered in inhibiting gene products already expressed in the ovaries. Therefore, simple and efficient methods for large-scale maternal screening are necessary. The appendicularian Oikopleura dioica is a planktonic tunicate member of the chordates. Gonadal microinjection and a novel gene knockdown method, DNA interference (DNAi), have been developed for use in this animal with the aim of inhibiting gene functions during oogenesis within the gonad. In this study, we adapted these methods for large-scale maternal factor screening, and observed malformation phenotypes related to some maternal factors. Approximately 2000 (56.9%) ovary-enriched gene products were screened, of which the knockdown of seven encoding genes resulted in various abnormalities during embryonic development. Most of these were related to microtubules and cell adhesion-related proteins. We conclude that DNAi is a potentially powerful screening tool for the identification of novel maternal factors in chordates.

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“…( (Onuma et al, 2017) and designing knockdown experiments (Omotezako et al, 2013(Omotezako et al, , 2015(Omotezako et al, , 2017. tunicate database, https://www.anise ed.cnrs.fr/).…”

Section: Reciprocal Searches Between Japanese and Norwegian O Dioimentioning

confidence: 99%

“…Here, we determined the genome sequence of Japanese O. dioica. Using the same population, we have developed tools for molecular, cellular, and genetic techniques, including gene knockdown methods (Omotezako et al, 2013(Omotezako et al, , 2015(Omotezako et al, , 2017, fluorescent live imaging of larvae (Kishi et al, 2014(Kishi et al, , 2017, and maternal and zygotic transcriptomes of the eggs and larvae (Wang et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

A genome database for a Japanese population of the larvacean Oikopleura dioica

et al. 2020

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The larvacean Oikopleura dioica is a planktonic chordate and is a tunicate that belongs to the closest relatives to vertebrates. Its simple and transparent body, invariant embryonic cell lineages, and short life cycle of 5 days make it a promising model organism for the study of developmental biology. The genome browser OikoBase was established in 2013 using Norwegian O. dioica. However, genome information for other populations is not available, even though many researchers have studied local populations. In the present study, we sequenced using Illumina and PacBio RSII technologies the genome of O. dioica from a southwestern Japanese population that was cultured in our laboratory for 3 years. The genome of Japanese O. dioica was assembled into 576 scaffold sequences with a total length and N50 length of 56.6 and 1.5 Mb, respectively. A total of 18,743 gene models (transcript models) were predicted in the genome assembly, named OSKA2016. In addition, 19,277 non‐redundant transcripts were assembled using RNA‐seq data. The OSKA2016 has global sequence similarity of only 86.5% when compared with the OikoBase, highlighting the sequence difference between the two far distant O. dioica populations on the globe. The genome assembly, transcript assembly, and transcript models were incorporated into ANISEED (https://www.aniseed.cnrs.fr/) for genome browsing and BLAST searches. Mapping of reads obtained from male‐ or female‐specific genome libraries yielded male‐specific scaffolds in the OSKA2016 and revealed that over 2.6 Mb of sequence were included in the male‐specific Y‐region. The genome and transcriptome resources from two distinct populations will be useful datasets for developmental biology, evolutionary biology, and molecular ecology using this model organism.

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DNA interference: DNA-induced gene silencing in the appendicularian Oikopleura dioica

Cited by 21 publications

References 19 publications

A MADS‐box transcription factor regulates a central step in sporulation of the oomycete Phytophthora infestans

A MADS‐box transcription factor regulates a central step in sporulation of the oomycete Phytophthora infestans

DNA interference-mediated screening of maternal factors in the chordate Oikopleura dioica

A genome database for a Japanese population of the larvacean Oikopleura dioica

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