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The complete mitochondrial genome of the widely cultivated edible fungus Lentinula edodes.

ABSTRACT: The complete mitochondrial genome of the widely cultivated edible fungus Lentinula edodes was determined using the next-generation sequencing technology. The circular molecule is 116,819 bp in length with a GC content of 30.75%. Conserved genes including 13 putative protein-coding genes and 24 tRNAs were located on the same strand. We detected 14 introns invading 4 genes, including cob, cox1, nad1, and nad5. The phylogenetic analysis confirmed that L. edodes was a number of Agaricales. This mitochondrial genome may open new avenues for understanding the phylogeny and evolution of Omphalotaceae and Agaricales.

SUBMITTER: Yang R

PROVIDER: S-EPMC7800677 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of the widely cultivated edible fungus Lentinula edodes.

Yang Ruiheng R Li Yan Y Song Xiaoxia X Tang Lihua L Li Chuanhua C Tan Qi Q Bao Dapeng D

Mitochondrial DNA. Part B, Resources 20170111 1

The complete mitochondrial genome of the widely cultivated edible fungus Lentinula edodes was determined using the next-generation sequencing technology. The circular molecule is 116,819 bp in length with a GC content of 30.75%. Conserved genes including 13 putative protein-coding genes and 24 tRNAs were located on the same strand. We detected 14 introns invading 4 genes, including cob, cox1, nad1, and nad5. The phylogenetic analysis confirmed that L. edodes was a number of Agarica ...[more]

PMID: 33473699

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Project description:Lentinula edodes is one of the most popular edible mushrooms worldwide and contains important medicinal components such as lentinan, ergosterol, and eritadenine. Mushroom metabolism is regulated by the mycelia and fruit body using light; however, in mushrooms, the underlying molecular mechanisms controlling this process as well as light-induced gene expression remain unclear. Therefore, in this study, we compared morphological changes and gene expression in the fruit bodies of L. edodes cultivated under blue light and continuous darkness. Our results showed that blue light primarily induced pileus growth (diameter and thickness) compared to dark cultivation. Alternatively, stipe length development was promoted by dark cultivation. We also performed RNAseq on L. edodes under the blue light/dark cultivation conditions. A total of 12,051 genes were used for aligning the Illumina raw reads and 762 genes that showed fold change cut-offs of >|2| and significance p-values of <0.05 were selected under blue light condition. Among the genes which showed two-fold changed genes, 221 were upregulated and 541 were downregulated. In order to identify blue light induced candidate genes, differentially expressed genes (DEGs) were selected according to 4-fold changes and validated by RT-PCR. We identified 8 upregulated genes under blue light condition, such as DDR48-heat shock protein, Fasciclin-domain-containing protein and carbohydrate esterase family 4 protein, FAD NAD-binding domain-containing protein that are involved in morphological development of primordium and embryonic muscle development, cell adhesion and affect the structure of cellulosic and non-cellulosic cell walls of fruit body development, and photoreceptor of blue light signaling for fruit body and pigment development, respectively. This study provides valuable insights into the molecular mechanisms underlying the role of blue light in mushroom growth and development and can thus contribute to breeding programs to improve mushroom cultivation.

Project description:Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodesDe novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in the loss of quality of Lentinula edodes postharvest fruiting bodies, transcriptome analysis was carried out using serial analysis of gene expression (SuperSAGE). This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as β-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families GH5, GH16, GH30, GH55, and GH128, and thaumatin-like proteins. In addition, we found that several chitin-related genes are upregulated, such as putative chitinases in GH family 18, exochitinases in GH20, and a putative chitosanase in GH family 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high-mobility-group (HMG) domains and zinc finger domains. Several cell death-related proteins were also upregulated postharvest.IMPORTANCE Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes The genes for the loss of postharvest quality newly found in this research will be targets for the future breeding of strains that keep fresh longer than present strains. De novoLentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.

Dataset Information

The complete mitochondrial genome of the widely cultivated edible fungus Lentinula edodes.

Publications

The complete mitochondrial genome of the widely cultivated edible fungus <i>Lentinula edodes</i>.

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