Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species

Wen, Jiawei; Zhang, Zhibin; Gong, Lei; Xun, Hongwei; Li, Juzuo; Bao, Qiyu; Wang, Qi; Li, Yongming; Yu, Li; B, Liu

doi:10.3390/genes10060465

Cited by 8 publications

(10 citation statements)

References 49 publications

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“…Mutation of mod-E affects the sexual cycle and suppresses vegetative incompatibility in Podospora anserina (Loubradou, Bégueret & Turcq, 1997). More recently, CG methylation was found to primarily plays a repressive role on expression in two Pleurotus mushroom species (Wen et al, 2019). So differential splicing genes and transcriptional regulation might play significant roles in fruiting body development and require further investigation of transcriptional regulatory mechanisms during development in O. sinensis.…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis

Tong

Zhang

Wang

et al. 2020

PeerJ

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Ophiocordyceps sinensis is a highly valued fungus that has been used as traditional Asian medicine. This fungus is one of the most important sources of income for the nomadic populations of the Tibetan Plateau. With global warming and excessive collection, the wild O. sinensis resources declined dramatically. The cultivation of O. sinensis hasn’t been fully operational due to the unclear genetic basis of the fruiting body development. Here, our study conducted pairwise comparisons between transcriptomes acquired from different growth stages of O. sinensis including asexual mycelium (CM), developing fruiting body (DF) and mature fruiting body (FB). All RNA-Seq reads were aligned to the genome of O. sinensis CO18 prior to comparative analyses. Cluster analysis showed that the expression profiles of FB and DF were highly similar compared to CM. Alternative splicing analysis (AS) revealed that the stage-specific splicing genes may have important functions in the development of fruiting body. Functional enrichment analyses showed that differentially expressed genes (DEGs) were enriched in protein synthesis and baseline metabolism during fruiting body development, indicating that more protein and energy might be required for fruiting body development. In addition, some fruiting body development-associated genes impacted by ecological factors were up-regulated in FB samples, such as the nucleoside diphosphate kinase gene (ndk), β subunit of the fatty acid synthase gene (cel-2) and the superoxide dismutase gene (sod). Moreover, the expression levels of several cytoskeletons genes were significantly altered during all these growth stages, suggesting that these genes play crucial roles in both vegetative growth and the fruiting body development. Quantitative PCR (qPCR) was used to validate the gene expression profile and the results supported the accuracy of the RNA-Seq and DEGs analysis. Our study offers a novel perspective to understand the underlying growth stage-specific molecular differences and the biology of O. sinensis fruiting body development.

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Section: Discussionmentioning

confidence: 99%

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis

Tong

Zhang

Wang

et al. 2020

PeerJ

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“…Several cellular processes are emerging as important regulatory mechanisms underlying fruiting body morphogenesis, whereas some others that proved developmentally relevant in animals and plants seem to be of limited importance in fungi (e.g. gene body methylation (A et al 2018;Wen et al 2019)). This chapter summarizes the most important -mostly transcription related -processes described in fruiting bodies recently.…”

Section: Cellular and Regulatory Processes Involved In Fruiting Body Developmentmentioning

confidence: 99%

“…Kumm. (Wen et al 2019; Merényi et al 2021) , H. marmoreus (Zhang et al 2015b) , C. aegerita (Orban et al 2021) , Phanerochaete chrysosporium Burds. (Krizsán et al 2019) , Lentinus tigrinus (Bull.)…”

Section: Introductionmentioning

confidence: 99%

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Nagy

Vonk

Künzler

et al. 2021

Preprint

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Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates tissue differentiation, growth and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim to comprehensively identify conserved genes related to fruiting body morphogenesis and distill novel functional hypotheses for functionally poorly characterized genes. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide informed hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defense, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10% of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Key words: functional annotation; comparative genomics; cell wall remodeling; development; fruiting body morphogenesis; mushroom; transcriptome

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“…1). During the differentiation process, several developmental changes occur in the organism, including regulations on gene expression, redistribution of chemicals, and specification on morphology (10)(11)(12). Fruiting body is a highly differentiated multicellular structure which forms during the sexual reproductive process (9).…”

Section: Introductionmentioning

confidence: 99%

Carbon metabolism and transcriptome in developmental paths differentiation of a homokaryotic Coprinopsis cinerea strain

Xie¹,

Chang²,

Kwan³

2020

Fungal Genetics and Biology

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The balance and interplay between sexual and asexual reproduction is one of the most attractive mysteries in fungi. The choice of developmental strategy reflects the ability of fungi to adapt to the changing environment. However, the evolution of developmental paths and the metabolic regulation during differentiation and morphogenesis are poorly understood.Here, we monitor the carbohydrate metabolism and gene expression regulation during the early differentiation process from the "fungal stem cell", vegetative mycelium, to the highly differentiated tissue/cells, fruiting body, oidia or sclerotia, of a homokaryotic fruiting Coprinopsis cinerea strain A43mut B43mut pab1-1 #326, uncovering the systematic changes during morphogenesis and the evolutionary process of developmental strategies. Conversion between glucose and glycogen and conversion between glucose and beta-glucan are the main carbon flows in the differentiation processes. Genes related to carbohydrate transport and metabolism are significantly differentially expressed among paths. RNA editing, a novel layer of gene expression regulation, occurs in all four developmental paths and enriched in ImportanceFungi is a group of species with high diversity and plays essential roles to the ecosystem. The life cycle of fungi is complex in structure and delicate in function. Choice of developmental strategies and internal changes within the organism are both important for the fungus to fulfill their ecological functions, reflecting the relationship between environment and the population. This study put the developmental process of vegetative growth, sexual and asexual reproduction, resistant structure formation of a classical model basidiomycetes fungus, C. cinerea, together for the first time to view the developmental paths differentiation process with physiology, transcriptomics and evolutionary prospects. Carbohydrate assays and RNA-seq showed the changes of the fungus. Our results fill the gaps on gene expression regulation during the early stage of developmental paths differentiation, and expand our understanding of the evolutionary process of life history and reproductive strategy in fungi.

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Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species

Cited by 8 publications

References 49 publications

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis

Comparative transcriptome analysis revealed genes involved in the fruiting body development ofOphiocordyceps sinensis

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes

Carbon metabolism and transcriptome in developmental paths differentiation of a homokaryotic Coprinopsis cinerea strain

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