genes MDPI Article Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species Jiawei Wen 1.2.t,Zhibin Zhang 1.*Lei Gong 1t,Hongwei Xun2,Juzuo Li1,Bao Qi3 Qi Wang3,Xiaomeng Li 1,Yu Li 3,*and Bao Liu 1 1 Key Laborat catio Normal University, nu.edu.cn (L):lixm441ner ducn (X.L):b nu.edu.cn(B.L) Of Ag the Min un 13 dible andMed Fungi Jilin Agricultural Univer .Changchun 130118,China:qibao3712@163.com(B.Q.); qwang2006@126.com(QW 4@nenu.edu.cn(ZZ):yuli966@126.com(Y.L):Tel:+8-431-8509-9367(Z.Z) 486.431-8453-33090YL5 t These authors contributed equally to this work updates Abstract:Pleurotus tuoliensis(Pt)and P.eryngii var.eryngii(Pe)are important edible mushrooms.The epigene tic and gene expression signature haracterizing major developmental transitions in thes in largely unk e,we rep ort global analyses of DNA methylation an um t t in hot h Pt and Pe th largely stable nes and trans elements (tes)across the developmental transitions.The repressive impact of dna methylation on expression of a small subset of genes is likely due to TE-associated effects rather than their own developmental dynamics.Global expression of gene orthologs was also broadly conserved between Pt and Pe,but discernible interspecific differences exist especially at the fruit body formation stage, s in trans-acting factors. The me hylome and transcriptom ones w or the litate furth rpinning gene expres d evelopmer tus and rolated a Keywords:Pleurotus tuoliensis;P.eryngii;DNA methylation;epigenetics;gene expression; development;interspecific divergence 1.Introduction nd Pleurotus eryngii (Pe)are two famous species of the Pleurotus complex tha ar encomp s the e oys genu e in East 5.D dra al chan driv h ental factors such as ter eriod and culture suhstrates 161 An study identified candidate genes related to mushroom formation in Pt,which was associated with reproductive growth,activation of specific transcription factors,upregulation of genes involved in the Gms2019,10,465doi10.390 Vgenes1006046 genes G C A T T A C G G C A T Article Transcriptome Changes during Major Developmental Transitions Accompanied with Little Alteration of DNA Methylome in Two Pleurotus Species Jiawei Wen 1,2,† , Zhibin Zhang 1,* ,† , Lei Gong 1,† , Hongwei Xun 2 , Juzuo Li 1 , Bao Qi 3 , Qi Wang 3 , Xiaomeng Li 1 , Yu Li 3,* and Bao Liu 1 1 Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China; wjw913@sina.com (J.W.); gongl100@nenu.edu.cn (L.G.); lijz346@nenu.edu.cn (J.L.); lixm441@nenu.edu.cn (X.L.); baoliu@nenu.edu.cn (B.L.) 2 Jilin Academy of Agricultural Sciences, Changchun 130033, China; xunhw334@nenu.edu.cn 3 Engineering Research Center of the Ministry of Education (MOE) for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China; qibao3712@163.com (B.Q.); q_wang2006@126.com (Q.W.) * Correspondence: zhangzb554@nenu.edu.cn (Z.Z.); yuli966@126.com (Y.L.); Tel.: +86-431-8509-9367 (Z.Z.); +86-431-8453-3309 (Y.L.) † These authors contributed equally to this work. Received: 17 April 2019; Accepted: 12 June 2019; Published: 17 June 2019


 Abstract: Pleurotus tuoliensis (Pt) and P. eryngii var. eryngii (Pe) are important edible mushrooms. The epigenetic and gene expression signatures characterizing major developmental transitions in these two mushrooms remain largely unknown. Here, we report global analyses of DNA methylation and gene expression in both mushrooms across three major developmental transitions, from mycelium to primordium and to fruit body, by whole-genome bisulfite sequencing (WGBS) and RNA-seq-based transcriptome profiling. Our results revealed that in both Pt and Pe the landscapes of methylome are largely stable irrespective of genomic features, e.g., in both protein-coding genes and transposable elements (TEs), across the developmental transitions. The repressive impact of DNA methylation on expression of a small subset of genes is likely due to TE-associated effects rather than their own developmental dynamics. Global expression of gene orthologs was also broadly conserved between Pt and Pe, but discernible interspecific differences exist especially at the fruit body formation stage, and which are primarily due to differences in trans-acting factors. The methylome and transcriptome repertories we established for the two mushroom species may facilitate further studies of the epigenetic and transcriptional regulatory mechanisms underpinning gene expression during development in Pleurotus and related genera. Keywords: Pleurotus tuoliensis; P. eryngii; DNA methylation; epigenetics; gene expression; development; interspecific divergence 1. Introduction Pleurotus tuoliensis (Pt) and Pleurotus eryngii (Pe) are two famous species of the Pleurotus eryngii complex that encompass the largest number of species in the oyster mushroom genus [1–3]. Both species are commercially important and widely cultivated especially in East Asia [4,5]. During sexual reproduction, basidiomycetes species undergo dramatic morphological changes driven by environmental factors such as temperature, photoperiod and culture substrates [6]. A previous study identified candidate genes related to mushroom formation in Pt, which was associated with reproductive growth, activation of specific transcription factors, upregulation of genes involved in the Genes 2019, 10, 465; doi:10.3390/genes10060465 www.mdpi.com/journal/genes