scholarly journals Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome

2018 ◽  
Vol 19 (7) ◽  
pp. 2052 ◽  
Author(s):  
Lining Wang ◽  
Wei Gao ◽  
Xiangli Wu ◽  
Mengran Zhao ◽  
Jibin Qu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Pleurotus Ostreatus ◽  
Developmental Stages ◽  
De Novo ◽  
Draft Genome ◽  
Myb Transcription Factor ◽  
Entire Genome ◽  
Mushroom Species ◽  
Genome Wide ◽  
Myb Genes

Pleurotus ostreatus is a commercially grown mushroom species in China. However, studies on the mechanisms of the fruiting body development and stress response of P. ostreatus are still at a primary stage. In this study, we report the entire genome sequence of P. ostreatus CCMSSC03989. Then, we performed comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during a series of developmental stages and under the condition of heat stress. A 34.76 Mb genome was obtained through next-generation sequencing (NGS) and Bionano optical mapping approaches. The genome has a scaffold N50 of 1.1 Mb and contains 10.11% repeats, and 10,936 gene models were predicted. A total of 20 MYB genes (PoMYB) were identified across the genome, and the full-length open reading frames were isolated. The PoMYBs were classified into 1 repeat (1R), 2R, and 3R-MYB groups according to their MYB domain repeat numbers, and 3R-MYBs possessed relatively more introns than 1R and 2R-MYBs. Based on phylogenetic analysis, the PoMYBs were divided into four groups and showed close relationships with the MYB genes of plants and fungi. RNA-sequencing (RNA-Seq) and quantitative PCR (qPCR) analyses revealed that PoMYB expression showed stage-specific patterns in reproductive stages and could be induced by heat stress. The P. ostreatus draft genome will promote genome-wide analysis, and our study of PoMYBs will promote further functional analysis of MYB genes in mushrooms.

scholarly journals Genome-wide characterization of the Zn(II)2Cys6 zinc cluster-encoding gene family in Pleurotus ostreatus and expression analyses of this family during developmental stages and under heat stress

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9336
Author(s):  
Zhihao Hou ◽  
Qiang Chen ◽  
Mengran Zhao ◽  
Chenyang Huang ◽  
Xiangli Wu
Keyword(s):  
Heat Stress ◽  
Pleurotus Ostreatus ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Mechanisms ◽  
Fruiting Body Formation ◽  
Zinc Cluster ◽  
Genome Wide ◽  
A Genome

Pleurotus ostreatus is one of the most widely cultivated mushrooms in China. The regulatory mechanisms of fruiting body formation and the response to heat stress in P. ostreatus are main research focuses. The Zn(II)2Cys6 family is one of the largest families of transcriptional factors and plays important roles in multiple biological processes in fungi. In this study, we identified 66 zinc cluster proteins in P. ostreatus (PoZCPs) through a genome-wide search. The PoZCPs were classified into 15 types according to their zinc cluster domain. Physical and chemical property analyses showed a huge diversity among the PoZCPs. Phylogenetic analysis of PoZCPs classified these proteins into six groups and conserved motif combinations and similar gene structures were observed in each group. The expression profiles of these PoZCP genes during different developmental stages and under heat stress were further investigated by RNA-sequencing (RNA-seq), revealing diverse expression patterns. A total of 13 PoZCPs that may participate in development or the heat stress response were selected for validation of their expression levels through real-time quantitative PCR (RT-qPCR) analysis, and some developmental stage-specific and heat stress-responsive candidates were identified. The findings contribute to our understanding of the roles and regulatory mechanisms of ZCPs in P. ostreatus.

scholarly journals Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

2018 ◽  
Vol 2018 ◽  
pp. 1-13
Author(s):  
Qing Chen ◽  
Xunju Liu ◽  
Yueyang Hu ◽  
Bo Sun ◽  
Yaodong Hu ◽  
...  
Keyword(s):  
Developmental Stages ◽  
De Novo ◽  
Developmental Regulation ◽  
Draft Genome ◽  
Pathogen Resistance ◽  
Flavonoid Biosynthesis ◽  
Great Promise ◽  
Protein Coding ◽  
Genome Wide ◽  
Phenylpropanoid Biosynthesis

The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.

scholarly journals Genome-Wide Analysis of the MYB Transcription Factor Superfamily in Physcomitrella patens

2020 ◽  
Vol 21 (3) ◽  
pp. 975 ◽  
Author(s):  
Xiaojun Pu ◽  
Lixin Yang ◽  
Lina Liu ◽  
Xiumei Dong ◽  
Silin Chen ◽  
...  
Keyword(s):  
Stress Responses ◽  
Physcomitrella Patens ◽  
Myb Transcription Factor ◽  
Rna Seq ◽  
Genome Wide ◽  
Terrestrial Environments ◽  
Gene Structures ◽  
Myb Genes ◽  
Myb Proteins ◽  
R2r3 Myb

MYB transcription factors (TFs) are one of the largest TF families in plants to regulate numerous biological processes. However, our knowledge of the MYB family in Physcomitrella patens is limited. We identified 116 MYB genes in the P. patens genome, which were classified into the R2R3-MYB, R1R2R3-MYB, 4R-MYB, and MYB-related subfamilies. Most R2R3 genes contain 3 exons and 2 introns, whereas R1R2R3 MYB genes contain 10 exons and 9 introns. N3R-MYB (novel 3RMYB) and NR-MYBs (novel RMYBs) with complicated gene structures appear to be novel MYB proteins. In addition, we found that the diversity of the MYB domain was mainly contributed by domain shuffling and gene duplication. RNA-seq analysis suggested that MYBs exhibited differential expression to heat and might play important roles in heat stress responses, whereas CCA1-like MYB genes might confer greater flexibility to the circadian clock. Some R2R3-MYB and CCA1-like MYB genes are preferentially expressed in the archegonium and during the transition from the chloronema to caulonema stage, suggesting their roles in development. Compared with that of algae, the numbers of MYBs have significantly increased, thus our study lays the foundation for further exploring the potential roles of MYBs in the transition from aquatic to terrestrial environments.

scholarly journals The draft genome sequence of Japanese rhinoceros beetle Trypoxylus dichotomus

2022 ◽  
Author(s):  
Shinichi Morita ◽  
Tomoko F. Shibata ◽  
Tomoaki Nishiyama ◽  
Yuuki Kobayashi ◽  
Katsushi Yamaguchi ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Genetic Regulation ◽  
Draft Genome ◽  
Evolutionary Developmental Biology ◽  
Rhinoceros Beetle ◽  
Insect Order ◽  
Trypoxylus Dichotomus

Beetles are the largest insect order and one of the most successful animal groups in terms of number of species. The Japanese rhinoceros beetle Trypoxylus dichotomus (Coleoptera, Scarabaeidae, Dynastini) is a giant beetle with distinctive exaggerated horns present on the head and prothoracic regions of the male. T. dichotomus has been used as research model in various fields such as evolutionary developmental biology, ecology, ethology, biomimetics, and drug discovery. In this study, de novo assembly of 615 Mb, representing 80% of the genome estimated by flow cytometry, was obtained using the 10x Chromium platform. The scaffold N50 length of the genome assembly was 8.02 Mb, with repetitive elements predicted to comprise 49.5% of the assembly. In total, 23,987 protein-coding genes were predicted in the genome. In addition, de novo assembly of the mitochondrial genome yielded a contig of 20,217 bp. We also analyzed the transcriptome by generating 16 RNA-seq libraries from a variety of tissues of both sexes and developmental stages, which allowed us to identify 13 co-expressed gene modules. The detailed genomic and transcriptomic information of T. dichotomus is the most comprehensive among those reported for any species of Dynastinae. This genomic information will be an excellent resource for further functional and evolutionary analyses, including the evolutionary origin and genetic regulation of beetle horns and the molecular mechanisms underlying sexual dimorphism.

scholarly journals Expression patterns of two pal genes of Pleurotus ostreatus across developmental stages and under heat stress

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Ludan Hou ◽  
Lining Wang ◽  
Xiangli Wu ◽  
Wei Gao ◽  
Jinxia Zhang ◽  
...  
Keyword(s):  
Heat Stress ◽  
Pleurotus Ostreatus ◽  
Growth Stage ◽  
Developmental Stages ◽  
Expression Patterns ◽  
Phenylpropanoid Pathway ◽  
Regulatory Pathways ◽  
Defense Systems ◽  
Key Enzyme ◽  
Organismal Development

Abstract Background Phenylalanine ammonia-lyase (PAL, EC 4.3.1.24) is the first key enzyme in the phenylpropanoid pathway. The pal gene has been widely studied in plants and participates in plant growth, development and defense systems. However, in Pleurotus ostreatus, the biological functions of pal during organismal development and exposure to abiotic stress have not been reported. Results In this study, we cloned and characterized the pal1 (2232 bp) and pal2 (2244 bp) genes from the basidiomycete P. ostreatus CCMSSC 00389. The pal1 and pal2 genes are interrupted by 6 and 10 introns, respectively, and encode proteins of 743 and 747 amino acids, respectively. Furthermore, prokaryotic expression experiments showed that PAL enzymes catalyzed the conversion of L-phenylalanine to trans-cinnamic acid. The function of pal1 and pal2 was determined by constructing overexpression (OE) and RNA interference (RNAi) strains. The results showed that the two pal genes had similar expression patterns during different developmental stages. The expression of pal genes was higher in the reproductive growth stage than in the vegetative growth stage. And the interference of pal1 and pal2 delayed the formation of primordia. The results of heat stress assays showed that the RNAi-pal1 strains had enhanced mycelial tolerance to high temperature, while the RNAi-pal2 strains had enhanced mycelial resistance to H2O2. Conclusions These results indicate that two pal genes may play a similar role in the development of P. ostreatus fruiting bodies, but may alleviate stress through different regulatory pathways under heat stress.

scholarly journals Genome Wide Identification and Analysis of the R2R3-MYB Transcription Factor Gene Family in the Mangrove Avicennia marina

Agronomy ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 123
Author(s):  
Seema Pradhan ◽  
P Sushree Shyamli ◽  
Sandhya Suranjika ◽  
Ajay Parida
Keyword(s):  
Gene Family ◽  
Abiotic Stresses ◽  
High Salinity ◽  
Avicennia Marina ◽  
Myb Transcription Factor ◽  
Transcription Factor Gene ◽  
Genome Wide ◽  
Myb Genes ◽  
R2r3 Myb ◽  
Transcription Factor Gene Family

Drought and salinity stress have become the major factors for crop yield loss in recent years. Drastically changing climatic conditions will only add to the adverse effects of such abiotic stresses in the future. Hence, it is necessary to conduct extensive research to elucidate the molecular mechanisms that regulate plants’ response to abiotic stress. Halophytes are plants that can grow in conditions of high salinity and are naturally resistant to a number of abiotic stresses. Avicennia marina is one such halophyte, which grows in tropical regions of the world in areas of high salinity. In this study, we have analysed the role of R2R3-MYB transcription factor gene family in response abiotic stress, as a number of transcription factors have been reported to have a definite role in stress manifestation. We identified 185 R2R3 MYB genes at genome-wide level in A. marina and classified them based on the presence of conserved motifs in the protein sequences. Cis-regulatory elements (CREs) present in the promoter region of these genes were analysed to identify stress responsive elements. Comparative homology with genes from other plants provided an insight into the evolutionary changes in the A. marinaR2R3 MYB genes. In silico expression analysis revealed 34 AmR2R3 MYB genes that were differentially regulated in the leaves and root tissue of A. marina subjected to drought and salinity stress. This study is the first report of the R2R3 MYB gene family in the A. marina genome and will help in selecting candidates for further functional characterisation.

Sign in / Sign up

Export Citation Format

Share Document