Genome-wide mRNA and miRNA analysis in the early stages of germ tube outgrowth in Coprinopsis cinerea

Lau, Amy Yuet Ting; Xie, Yichun; Cheung, Man Kit; Cheung, Peter Chi Keung; Kwan, Hoi Shan

doi:10.1016/j.fgb.2020.103416

Cited by 13 publications

(15 citation statements)

References 81 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We found virtually no evidence for RNA editing, whereas allele specific expression was abundant, which supports a previous report of ASE in CM fungi (Gehrmann et al, 2018). RNA editing has been recently reported in the Agaricomycetes (Zhu et al, 2014), however, in contrast to the Ascomycota (Lau et al, 2020;Liu et al, 2016;Teichert et al, 2017), it displayed no clear-cut enrichment of A-to-I compatible variants in three previous studies (Bian et al, 2019;Teichert, 2020;Zhu et al, 2014) or in this study.…”

Section: Discussionsupporting

confidence: 89%

“…We found virtually no evidence for RNA editing, whereas ASE was abundant, which supports a previous report of ASE in CM fungi ( Gehrmann et al, 2018 ). RNA editing has been recently reported in the Agaricomycetes ( Zhu et al, 2014 ); however, in contrast to the Ascomycota ( Lau et al, 2020 ; Liu et al, 2016 ; Teichert et al, 2017 ), it displayed no clear-cut enrichment of A-to-I-compatible variants in three previous studies ( Bian et al, 2019 ; Teichert, 2020 ; Zhu et al, 2014 ) or in this study. Rather, our final candidate RNA-editing sites merely alluded to potential polyA site- and/or read alignment inaccuracies, leading us to conclude that RNA editing is not abundant in P. ostreatus .…”

Section: Resultscontrasting

confidence: 78%

See 1 more Smart Citation

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

Merényi

Virágh

Gluck‐Thaler

et al. 2022

eLife

View full text Add to dashboard Cite

Multicellularity has been one of the most important innovations in the history of life. The role of gene regulatory changes in driving transitions to multicellularity is being increasingly recognized; however, factors influencing gene expression patterns are poorly known in many clades. Here we compared the developmental transcriptomes of complex multicellular fruiting bodies of eight Agaricomycetes and Cryptococcus neoformans, a closely related human pathogen with a simple morphology. In-depth analysis in Pleurotus ostreatus revealed that allele-specific expression, natural antisense transcripts and developmental gene expression, but not RNA editing or a 'developmental hourglass' act in concert to shape its transcriptome during fruiting body development. We found that transcriptional patterns of genes strongly depend on their evolutionary ages. Young genes showed more developmental and allele-specific expression variation, possibly because of weaker evolutionary constraint, suggestive of non-adaptive expression variance in fruiting bodies. These results prompted us to define a set of conserved genes specifically regulated only during complex morphogenesis by excluding young genes and accounting for deeply conserved ones shared with species showing simple sexual development. Analysis of the resulting gene set revealed evolutionary and functional associations with complex multicellularity, which allowed us to speculate they are involved in complex multicellular morphogenesis of mushroom fruiting bodies.

show abstract

Section: Discussionsupporting

confidence: 89%

Section: Resultscontrasting

confidence: 78%

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

Merényi

Virágh

Gluck‐Thaler

et al. 2022

eLife

View full text Add to dashboard Cite

show abstract

“…We found virtually no evidence for RNA editing, whereas allele specific expression was abundant, which supports the only previously available report of ASE in CM fungi (Gehrmann et al, 2018). RNA editing has been recently reported in the Agaricomycetes (Wu et al, 2019(Wu et al, , 2018Zhu et al, 2014), however, in contrast to the Ascomycota (Lau et al, 2020;Liu et al, 2016;Teichert et al, 2017), it displayed no clear-cut enrichment of A-to-I compatible variants in three previous studies (Bian et al, 2019;Teichert, 2020;Zhu et al, 2014) or in this study. Rather, our final candidate RNA-editing sites merely alluded to potential polyA site-and/or read alignment inaccuracies leading us to conclude that RNA editing is not abundant in P. ostreatus.…”

Section: Discussionsupporting

confidence: 87%

Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi

Merényi

Virágh

Gluck‐Thaler

et al. 2021

Preprint

View full text Add to dashboard Cite

Multicellularity has been one of the most important innovations in the history of life. The role of regulatory evolution in driving transitions to multicellularity is being increasingly recognized; however, patterns and drivers of transcriptome evolution are poorly known in many clades. We here reveal that allele-specific expression, natural antisense transcripts and developmental gene expression, but not RNA editing or a developmental hourglass act in concert to shape the transcriptome of complex multicellular fruiting bodies of fungi. We find that transcriptional patterns of genes are strongly predicted by their evolutionary age. Young genes showed more expression variation both in time and space, possibly because of weaker evolutionary constraint, calling for partially non-adaptive interpretations of evolutionary changes in the transcriptome of multicellular fungi. Gene age also correlated with function, allowing us to separate fruiting body gene expression related to simple sexual development from that potentially underlying complex morphogenesis. Our study highlighted a transcriptional complexity that provides multiple speeds for transcriptome evolution, but also that constraints associated with gene age shape transcriptomic patterns during transitions to complex multicellularity in fungi.

show abstract

“…The development of high-throughput sequencing technology has led to the identification of milRNAs in Fusarium oxysporum , Rhizoctonia solani , Cordyceps guangdongensis , and Volvariella volvacea , while also considerably promoting the discovery of milRNAs with low expression and those that exhibit tissue-specific expression ( 29 – 31 ). In this study, the schizont phase of microsporidian infection was chosen for characterization, and a total of 11 mature milRNAs were identified and mapped, in addition to 1,063 sRNA types.…”

Section: Discussionmentioning

confidence: 99%

Nosema bombycis microRNA-like RNA 8 (Nb-milR8) Increases Fungal Pathogenicity by Modulating BmPEX16 Gene Expression in Its Host, Bombyx mori

Dong

Zheng

et al. 2021

Microbiol Spectr

View full text Add to dashboard Cite

show abstract

Genome-wide mRNA and miRNA analysis in the early stages of germ tube outgrowth in Coprinopsis cinerea

Cited by 13 publications

References 81 publications

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom-forming fungi (Agaricomycetes)

Gene age predicts the transcriptional landscape of sexual morphogenesis in multicellular fungi

Nosema bombycis microRNA-like RNA 8 (Nb-milR8) Increases Fungal Pathogenicity by Modulating BmPEX16 Gene Expression in Its Host, Bombyx mori

Contact Info

Product

Resources

About