The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<

<i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Yichun Xie [verfasserIn] Po-Lam Chan [verfasserIn] Hoi-Shan Kwan [verfasserIn] Jinhui Chang [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2023

Schlagwörter:	life history RNA editing alternative splicing transcriptomic divergence adaptation

Übergeordnetes Werk:	In: Journal of Fungi - MDPI AG, 2015, 9(2023), 915, p 915
Übergeordnetes Werk:	volume:9 ; year:2023 ; number:915, p 915

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc

DOI / URN:	10.3390/jof9090915

Katalog-ID:	DOAJ093373082

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allfields	10.3390/jof9090915 doi (DE-627)DOAJ093373082 (DE-599)DOAJf91b86c675c846fbb5825803544912d8 DE-627 ger DE-627 rakwb eng QH301-705.5 Yichun Xie verfasserin aut The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation Biology (General) Po-Lam Chan verfasserin aut Hoi-Shan Kwan verfasserin aut Jinhui Chang verfasserin aut In Journal of Fungi MDPI AG, 2015 9(2023), 915, p 915 (DE-627)796588538 (DE-600)2784229-0 2309608X nnns volume:9 year:2023 number:915, p 915 https://doi.org/10.3390/jof9090915 kostenfrei https://doaj.org/article/f91b86c675c846fbb5825803544912d8 kostenfrei https://www.mdpi.com/2309-608X/9/9/915 kostenfrei https://doaj.org/toc/2309-608X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2023 915, p 915
spelling	10.3390/jof9090915 doi (DE-627)DOAJ093373082 (DE-599)DOAJf91b86c675c846fbb5825803544912d8 DE-627 ger DE-627 rakwb eng QH301-705.5 Yichun Xie verfasserin aut The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation Biology (General) Po-Lam Chan verfasserin aut Hoi-Shan Kwan verfasserin aut Jinhui Chang verfasserin aut In Journal of Fungi MDPI AG, 2015 9(2023), 915, p 915 (DE-627)796588538 (DE-600)2784229-0 2309608X nnns volume:9 year:2023 number:915, p 915 https://doi.org/10.3390/jof9090915 kostenfrei https://doaj.org/article/f91b86c675c846fbb5825803544912d8 kostenfrei https://www.mdpi.com/2309-608X/9/9/915 kostenfrei https://doaj.org/toc/2309-608X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2023 915, p 915
allfields_unstemmed	10.3390/jof9090915 doi (DE-627)DOAJ093373082 (DE-599)DOAJf91b86c675c846fbb5825803544912d8 DE-627 ger DE-627 rakwb eng QH301-705.5 Yichun Xie verfasserin aut The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation Biology (General) Po-Lam Chan verfasserin aut Hoi-Shan Kwan verfasserin aut Jinhui Chang verfasserin aut In Journal of Fungi MDPI AG, 2015 9(2023), 915, p 915 (DE-627)796588538 (DE-600)2784229-0 2309608X nnns volume:9 year:2023 number:915, p 915 https://doi.org/10.3390/jof9090915 kostenfrei https://doaj.org/article/f91b86c675c846fbb5825803544912d8 kostenfrei https://www.mdpi.com/2309-608X/9/9/915 kostenfrei https://doaj.org/toc/2309-608X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2023 915, p 915
allfieldsGer	10.3390/jof9090915 doi (DE-627)DOAJ093373082 (DE-599)DOAJf91b86c675c846fbb5825803544912d8 DE-627 ger DE-627 rakwb eng QH301-705.5 Yichun Xie verfasserin aut The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation Biology (General) Po-Lam Chan verfasserin aut Hoi-Shan Kwan verfasserin aut Jinhui Chang verfasserin aut In Journal of Fungi MDPI AG, 2015 9(2023), 915, p 915 (DE-627)796588538 (DE-600)2784229-0 2309608X nnns volume:9 year:2023 number:915, p 915 https://doi.org/10.3390/jof9090915 kostenfrei https://doaj.org/article/f91b86c675c846fbb5825803544912d8 kostenfrei https://www.mdpi.com/2309-608X/9/9/915 kostenfrei https://doaj.org/toc/2309-608X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2023 915, p 915
allfieldsSound	10.3390/jof9090915 doi (DE-627)DOAJ093373082 (DE-599)DOAJf91b86c675c846fbb5825803544912d8 DE-627 ger DE-627 rakwb eng QH301-705.5 Yichun Xie verfasserin aut The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< 2023 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier <i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation. <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation Biology (General) Po-Lam Chan verfasserin aut Hoi-Shan Kwan verfasserin aut Jinhui Chang verfasserin aut In Journal of Fungi MDPI AG, 2015 9(2023), 915, p 915 (DE-627)796588538 (DE-600)2784229-0 2309608X nnns volume:9 year:2023 number:915, p 915 https://doi.org/10.3390/jof9090915 kostenfrei https://doaj.org/article/f91b86c675c846fbb5825803544912d8 kostenfrei https://www.mdpi.com/2309-608X/9/9/915 kostenfrei https://doaj.org/toc/2309-608X Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 9 2023 915, p 915
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callnumber-first	Q - Science
author	Yichun Xie
spellingShingle	Yichun Xie misc QH301-705.5 misc <i<Coprinopsis cinerea</i< misc life history misc RNA editing misc alternative splicing misc transcriptomic divergence misc adaptation misc Biology (General) The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<
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topic_title	QH301-705.5 The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i< <i<Coprinopsis cinerea</i< life history RNA editing alternative splicing transcriptomic divergence adaptation
topic	misc QH301-705.5 misc <i<Coprinopsis cinerea</i< misc life history misc RNA editing misc alternative splicing misc transcriptomic divergence misc adaptation misc Biology (General)
topic_unstemmed	misc QH301-705.5 misc <i<Coprinopsis cinerea</i< misc life history misc RNA editing misc alternative splicing misc transcriptomic divergence misc adaptation misc Biology (General)
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title	The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<
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title_full	The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<
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title_sort	genome-wide characterization of alternative splicing and rna editing in the development of <i<coprinopsis cinerea</i<
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title_auth	The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<
abstract	<i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation.
abstractGer	<i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation.
abstract_unstemmed	<i<Coprinopsis cinerea</i< is one of the model species used in fungal developmental studies. This mushroom-forming <i<Basidiomycetes</i< fungus has several developmental destinies in response to changing environments, with dynamic developmental regulations of the organism. Although the gene expression in <i<C. cinerea</i< development has already been profiled broadly, previous studies have only focused on a specific stage or process of fungal development. A comprehensive perspective across different developmental paths is lacking, and a global view on the dynamic transcriptional regulations in the life cycle and the developmental paths is far from complete. In addition, knowledge on co- and post-transcriptional modifications in this fungus remains rare. In this study, we investigated the transcriptional changes and modifications in <i<C. cinerea</i< during the processes of spore germination, vegetative growth, oidiation, sclerotia formation, and fruiting body formation by inducing different developmental paths of the organism and profiling the transcriptomes using the high-throughput sequencing method. Transition in the identity and abundance of expressed genes drive the physiological and morphological alterations of the organism, including metabolism and multicellularity construction. Moreover, stage- and tissue-specific alternative splicing and RNA editing took place and functioned in <i<C. cinerea</i<. These modifications were negatively correlated to the conservation features of genes and could provide extra plasticity to the transcriptome during fungal development. We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. The multi-layer regulatory network of gene expression serves as the molecular basis of the functioning of developmental regulation.
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We suggest that <i<C. cinerea</i< applies different molecular strategies in its developmental regulation, including shifts in expressed gene sets, diversifications of genetic information, and reversible diversifications of RNA molecules. Such features would increase the fungal adaptability in the rapidly changing environment, especially in the transition of developmental programs and the maintenance and balance of genetic and transcriptomic divergence. 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The Genome-Wide Characterization of Alternative Splicing and RNA Editing in the Development of <i<Coprinopsis cinerea</i<

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