De novo transcriptomic analysis during Lentinula edodes fruiting body growth

Wang, Yingzhu; Zeng, Xianlu; Liu, Wenguang

doi:10.1016/j.gene.2017.10.061

Cited by 48 publications

(47 citation statements)

References 24 publications

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“…The ATAC-seq results were combined with expression data from RNA-seq analysis in order to accurately determine the transcription factors that play a regulatory role based on the chromatin open region and to further study how transcription factors regulated downstream genes. RNA-seq was performed as previously described [5]. Three biological replicates were used for RNA-seq.…”

Section: Integration Analysis Of Atac-seq and Rna-seqmentioning

confidence: 99%

“…Recently, the mechanisms of this process have been extensively studied. For instance, the studies on Pleurotus tuoliensis [3], Priurotus eryngii [4], Lentinula edodes [5], Schizophyllum commune [6], Flammulina velutipes [7], Ganoderma lucidum [8], Cordyceps militaris [9], Hypsizygus marmoreus [10,11], Termitomyces heimii [12], Coprinopsis cinerea [2,13], and Pleurotus ostreatus [14], found some key genes that regulated mushroom development, and demonstrated the underlying molecular mechanisms in this process. However, studies on the mechanisms of fruiting body development in Sparassis latifolia are still at a primary stage.…”

Section: Introductionmentioning

confidence: 99%

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Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Yang

Xiao

et al. 2019

IJMS

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Light is an essential environmental factor for Sparassis latifolia primordia formation, but the molecular mechanism is still unclear. In this study, differential expression profiling of light-induced primordia formation (LIPF) was established by integrating the assay for transposase accessible chromatin by sequencing (ATAC-seq) and RNA-seq technology. The integrated results from the ATAC-seq and RNA-seq showed 13 down-regulated genes and 17 up-regulated genes in both the L vs. D and P vs. D groups, for both methods. According to the gene ontology (GO) annotation of these differentially expressed genes (DEGs), the top three biological process categories were cysteine biosynthetic process via cystathionine, vitamin B6 catabolic, and glycine metabolic; the top three molecular function categories were 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, glycine binding, and pyridoxal phosphate binding; cellular component categories were significantly enriched in the glycine cleavage complex. The KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed that these genes were associated with vitamin B6 metabolism; selenocompound metabolism; cysteine and methionine metabolism; glycine, serine, and threonine metabolism; and glyoxylate and dicarboxylate metabolism pathways. The expression of most of the DEGs was validated by qRT-PCR. To the best of our knowledge, this study is the first integrative analysis of ATAC-seq and RNA-seq for macro-fungi. These results provided a new perspective on the understanding of key pathways and hub genes in LIPF in S. latifolia. It will be helpful in understanding the primary environmental response, and provides new information to the existing models of primordia formation in edible and medicinal fungi.

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Section: Integration Analysis Of Atac-seq and Rna-seqmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Yang

Xiao

et al. 2019

IJMS

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“…Hence, an effective genetic approach is essential for the development of new breeding methods 4 , 17 . In addition, gene expression of a target gene related to a specific beneficial property must be performed at different stages, e.g., mycelia, brown mycelial film, primordium, and the fruiting body 18 , 19 , to determine the stage at which optimum activity or the maximum yield of the desired substance occurs. Therefore, determining genetic changes compared with the parental strains at different developmental stages using high-throughput sequencing technology (next-generation sequencing technology) 20 will be necessary to generate improved strains and varieties of mushrooms by genetic modification.…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes

Song

Kim

2018

Sci Rep

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Lentinula edodes is a popular cultivated edible mushroom with high nutritional and medicinal value. To understand the regulation of gene expression in the dikaryotic mycelium and mature fruiting body in the commercially important Korean L. edodes strain, we first performed comparative transcriptomic analysis, using Illumina HiSeq platform. De novo assembly of these sequences revealed 11,675 representative transcripts in two different stages of L. edodes. A total of 9,092 unigenes were annotated and subjected to Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Gene expression analysis revealed that 2,080 genes were differentially expressed, with 1,503 and 577 upregulated in the mycelium and a mature fruiting body, respectively. Analysis of 18 KEGG categories indicated that fruiting body-specific transcripts were significantly enriched in ‘replication and repair’ and ‘transcription’ pathways, which are important for premeiotic replication, karyogamy, and meiosis during maturation. We also searched for fruiting body-specific proteins such as aspartic protease, gamma-glutamyl transpeptidase, and cyclohexanone monooxygenase, which are involved in fruiting body maturation and isolation of functional substances. These transcriptomes will be useful in elucidating the molecular mechanisms of mature fruiting body development and beneficial properties, and contribute to the characterization of novel genes in L. edodes.

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“…The quality and quantity of total RNA were assessed using NanoDrop 2000 analysis and gel electrophoresis. As described by [24], the cDNA libraries were prepared using a TruseqTM RNA sample prep Kit (Illumina), and RNA-sequencing was performed on an Illumina Hiseq 4000 (Version 2 × 150 bp) at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China). The raw sequence reads were deposited in the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra, accession number PRJNA622603).…”

Section: Alfalfa Treatementmentioning

confidence: 99%

Comparative transcriptome analysis between thrips-resistant and thrips-susceptible alfalfa (Medicago sativa L.)

Zhang¹,

Buhe²,

Wang³

et al. 2020

Preprint

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Background: Thrips (Thysanoptera: Thripidae) are major insect pests on alfalfa and result in decreased plant nutrients and growth, low yields and even plant death. In our previous studies, an alfalfa variety (Caoyuan No.4) with high thrips resistance was bred through consecutive field recurrent selection. In order to better understand the genetic and molecular mechanisms of thrips resistance in Caoyuan No.4, RNA-Sequencing was employed using the thrips-resistant alfalfa accession (Caoyuan No.4) and a thrips-susceptible alfalfa accession (Caoyuan No.2), each with and without thrips infestation.Results: There were 851 genes constitutively upregulated and 434 genes downregulated in Caoyuan No.4 compared to Caoyuan No.2 without thrips infestation. The upregulated genes were mainly involved in primary metabolism such as energy metabolism and carbohydrate metabolism, lipid metabolism and certain secondary metabolites, while the downregulated genes were mainly related to plant-pathogen interaction. In addition, very few DEGs (only 13) were detected in Caoyuan No.4 after thrips stress, but a total of 3326 contigs DEGs were detected in Caoyuan No.2 after thrips stress. The upregulated genes in Caoyuan No.2 after stress were mainly involved in isoflavonoid biosynthesis, proteasome, amino sugar and nucleotide sugar metabolism, flavonoid biosynthesis as well as plant-pathogen interaction. Moreover, 117 genes that were shared in both the S_CK vs S_T group and S_CK vs R_CK group were divided into 6 clusters, which are mainly involved in secondary metabolism, fatty acid metabolism, amino acid metabolism, rust resistance kinase, WRKY transcription factor and nodule lectin.Conclusion: Both constitutive defensive genes and potential induced defensive genes were detected in the defense of Caoyuan No.4. That two distinct kinds of defensive genes — constitutive defensive genes and induced defensive genes — can be simultaneously activated and thus potentially enhance plant protection against insects attacks is a signiﬁcant finding for plant resistance breeders.

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De novo transcriptomic analysis during Lentinula edodes fruiting body growth

Cited by 48 publications

References 24 publications

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Integration of ATAC-Seq and RNA-Seq Identifies Key Genes in Light-Induced Primordia Formation of Sparassis latifolia

Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes

Comparative transcriptome analysis between thrips-resistant and thrips-susceptible alfalfa (Medicago sativa L.)

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