Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus<i>Pleurotus ostreatus</i>

Qu, Jian; Zhao, Ming; Hsiang, Tom; Feng, Xiaoxing; Zhang, Jinxia; Huang, Chenyang

doi:10.1155/2016/2503023

Cited by 27 publications

(30 citation statements)

References 72 publications

(74 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…is genome assembly consisted of 36 contigs with an N50 of 1,826,870 base pairs (Table 3). e A. blazei genome is similar in size to the genomes of several other fruiting body formation fungi from the other Agaricales, including Schizophyllum commune (38.5 Mb) [44], V. volvacea (37.2 Mb) [17], and Coprinopsis cinerea (37 Mb) [45], but larger than that of Pleurotus ostreatus (34.9 Mb) [46] and A. bisporus (30.2 Mb) [16]. e completeness of genome was assessed using BUSCO software, and the result (Table 4) suggested a well-completed annotation set, with 93.7% of the Fungi BUSCOs within the RefSeq annotation set and 2.1% of fragmented.…”

Section: Resultsmentioning

confidence: 90%

Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei

JianHua

Guo

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

Agaricus blazei, a type of edible straw-rotting mushroom with somewhat sweet taste and fragrance of almonds, has attracted considerable scientific and practical attention. High-throughput Illumina PE150 and PacBio RSII platform were employed to generate a genomic sequence. De novo assembly generated 36 contigs with 38,686,133 bp in size, containing 10,119 putative predicted genes. Additionally, we also studied transcriptional regulation of the mycelia and the primordia for exploration of genes involved in fruiting body formation. Expression profiling analysis revealed that 2,164 genes were upregulated in mycelia and 1,557 in primordia. Functional enrichment showed that differentially expressed genes associated with response to stress, ribosome biogenesis, arginine biosynthesis, and steroid biosynthesis pathway were more active in fruiting body. The genome and transcriptome analysis of A. blazei provide valuable sequence resources and contribute to our understanding of genes related to the biosynthesis pathway of polysaccharide and benzaldehyde, as well as the fruiting body formation.

show abstract

Section: Resultsmentioning

confidence: 90%

Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei

JianHua

Guo

et al. 2020

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…The dikaryotic P. ostreatus strain CCMSSC00389 (China Center for Mushroom Spawn Standards and Control, Beijing, China) was used in this study and was maintained on potato dextrose agar (PDA) at 4 °C. The corresponding genome and protein sequences are available at DDBJ/EMBL/GenBank under the accession number MAYC00000000 [ 25 , 26 ]. Escherichia coli DH5α (Tiangen, Beijing, China) used for plasmid construction was grown in Luria-Bertani broth containing ampicillin (100 μg/mL) or kanamycin (50 μg/mL).…”

Section: Methodsmentioning

confidence: 99%

Differential Expression Patterns of Pleurotus ostreatus Catalase Genes during Developmental Stages and under Heat Stress

Wang

Gao

et al. 2017

Genes

Self Cite

View full text Add to dashboard Cite

Catalases are ubiquitous hydrogen peroxide-detoxifying enzymes. They participate in fungal growth and development, such as mycelial growth and cellular differentiation, and in protecting fungi from oxidative damage under stressful conditions. To investigate the potential functions of catalases in Pleurotus ostreatus, we obtained two catalase genes from a draft genome sequence of P. ostreatus, and cloned and characterized them (Po-cat1 and Po-cat2). Po-cat1 (group II) and Po-cat2 (group III) encoded putative peptides of 745 and 528 amino acids, respectively. Furthermore, the gene structures were variant between Po-cat1 and Po-cat2. Further research revealed that these two catalase genes have divergent expression patterns during different developmental stages. Po-cat1/Po-cat1 was at a barely detectable level in mycelia, accumulated gradually during reproductive growth, and was maximal in separated spores. But no catalase activity of Po-cat1 was detected by native-PAGE during any part of the developmental stages. In contrast, high Po-cat2/Po-cat2 expression and Po-cat2 activity found in mycelia were gradually lost during reproductive growth, and at a minimal level in separated spores. In addition, these two genes responded differentially under 32 °C and 40 °C heat stresses. Po-cat1 was up-regulated under both temperature conditions, while Po-cat2 was up-regulated at 32 °C but down-regulated at 40 °C. The accumulation of catalase proteins correlated with gene expression. These results indicate that the two divergent catalases in P. ostreatus may play different roles during development and under heat stress.

show abstract

“…Genome sequences are valuable resources for genetic or molecular-based analysis, which is beneficial to the decryption of genetic diversity and genes controlling important agronomic traits [ 4 ]. To date, two genomes of P. ostreatus , PC15 [ 5 ] and CCEF00389 [ 6 ], are available, and the PC15 genome has been widely used since its release [ 7 , 8 ]. Several commercial strains are used in production at present [ 9 ], and they are genetically diverse according to identification by using molecular markers [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Gao

et al. 2018

IJMS

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible FungusPleurotus ostreatus

Cited by 27 publications

References 72 publications

Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei

Genome Survey and Transcriptome Analysis on Mycelia and Primordia of Agaricus blazei

Differential Expression Patterns of Pleurotus ostreatus Catalase Genes during Developmental Stages and under Heat Stress

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

Contact Info

Product

Resources

About