Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes

Shim, Donghwan; Park, Sin‐Gi; Kim, Kang-Min; Bae, Wonsil; Lee, Gir-Won; Ha, Byeongsuk; Ro, Hyeon-Su; Kim, Myungkil; Ryoo, Rhim; Rhee, Sung‐Keun; Nou, Ill–Sup; Koo, Chang-Duck; Hong, Chang Pyo; Ryu, Hojin

doi:10.1016/j.jbiotec.2016.02.032

Cited by 48 publications

(50 citation statements)

References 7 publications

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“…Over 1000 SSR loci of the shiitake mushroom were found in whole genome sequencing performed by Shim et al [23] using L. edodes monokaryon strain B17 and comparing the resequencing data of 1 strain, Chamaram. We chose 205 SSR loci to test for polymorphism among the shiitake mushroom strains, and 44 SSR markers were finally selected for proper PCR conditions fixed in 23 strains (Supplementary Materials Figure S1).…”

Section: Methodsmentioning

confidence: 99%

“…In many recent studies, NGS-based transcriptome or genome sequencing is demonstrated to be efficient for the large-scale discovery of SSR loci in plants [21]. We have recently reported the genome sequence information of L. edodes [23], and have here developed higher polymorphic SSR markers based on the whole genome sequencing and determination of shiitake mushroom varieties. New SSR markers might be valuable tools to evaluate genetic variability and breeding in the shiitake mushroom.…”

Section: Introductionmentioning

confidence: 99%

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Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

Lee

Moon

Shim

et al. 2017

Genes

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The shiitake mushroom (Lentinula edodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivation of the shiitake mushroom has been greatly increased, especially in East Asia. Additionally, demand for the development of new cultivars with good agricultural traits has been greatly enhanced, but the development processes are complicated and more challenging than for other edible mushrooms. In this study, we developed 44 novel polymorphic simple sequence repeat (SSR) markers for the determination of shiitake mushroom cultivars based on a whole genome sequencing database of L. edodes. These markers were found to be polymorphic and reliable when screened in 23 shiitake mushroom cultivars. For the 44 SSR markers developed in this study, the major allele frequency ranged from 0.13 to 0.94; the number of genotypes and number of alleles were each 2–11; the observed and expected heterozygosity were 0.00–1.00 and 0.10–0.90, respectively; and the polymorphic information content value ranged from 0.10 to 0.89. These new markers can be used for molecular breeding, the determination of cultivars, and other applications.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

Lee

Moon

Shim

et al. 2017

Genes

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“…In the future, it will be necessary to determine whether the conclusion could be extended to other mushroom-forming basidiomycetes. However, the Protein BLAST search in the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/) explores ChiE1 and ChiIII homologs in many basidiomycete genomes, including the genomes of Agaricus bisporus (48) and Lentinula edodes (49). L. edodes chitinase Chi1 (50) and Chi3 (51) are the homologs of C. cinerea chitinase ChiE1 and ChiIII, respectively.…”

Section: Figmentioning

confidence: 99%

Chitinases Play a Key Role in Stipe Cell Wall Extension in the Mushroom Coprinopsis cinerea

Zhou

Kang

Liu

et al. 2019

Appl Environ Microbiol

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The elongation growth of the mushroom stipe is a characteristic but not well-understood morphogenetic event of basidiomycetes. We found that extending native stipe cell walls of Coprinopsis cinerea were associated with the release of N-acetylglucosamine and chitinbiose and with chitinase activity. Two chitinases among all detected chitinases from C. cinerea, ChiE1 and ChiIII, reconstituted heatinactivated stipe wall extension and released N-acetylglucosamine and chitinbiose. Interestingly, both ChiE1 and ChiIII hydrolyze insoluble crystalline chitin powder, while other C. cinerea chitinases do not, suggesting that crystalline chitin components of the stipe cell wall are the target of action for ChiE1 and ChiIII. ChiE1-or ChiIII-reconstituted heat-inactivated stipe walls showed maximal extension activity at pH 4.5, consistent with the optimal pH for native stipe wall extension in vitro; ChiE1or ChiIII-reconstituted heat-inactivated stipe wall extension activities were associated with stipe elongation growth regions; and the combination of ChiE1 and ChiIII showed a synergism to reconstitute heat-inactivated stipe wall extension at a low action concentration. Field emission scanning electron microscopy (FESEM) images showed that the inner surface of acid-induced extended native stipe cell walls and ChiE1-or ChiIII-reconstituted extended heat-inactivated stipe cell walls exhibited a partially broken parallel microfibril architecture; however, these broken transversely arranged microfibrils were not observed in the unextended stipe cell walls that were induced by neutral pH buffer or heat inactivation. Double knockdown of ChiE1 and ChiIII resulted in the reduction of stipe elongation, mycelium growth, and heatsensitive cell wall extension of native stipes. These results indicate a chitinasehydrolyzing mechanism for stipe cell wall extension. IMPORTANCE A remarkable feature in the development of basidiomycete fruiting bodies is stipe elongation growth that results primarily from manifold cell elongation. Some scientists have suggested that stipe elongation is the result of enzymatic hydrolysis of cell wall polysaccharides, while other scientists have proposed the possibility that stipe elongation results from nonhydrolytic disruption of the hydrogen bonds between cell wall polysaccharides. Here, we show direct evidence for a chitinase-hydrolyzing mechanism of stipe cell wall elongation in the model mushroom Coprinopsis cinerea that is different from the expansin nonhydrolysis mechanism of plant cell wall extension. We presumed that in the growing stipe cell walls, parallel chitin microfibrils are tethered by ␤-1,6-branched ␤-1,3-glucans, and that the breaking of the tether by chitinases leads to separation of these microfibrils to increase their spacing for insertion of new synthesized chitin and ␤-1,3-glucans under turgor pressure in vivo.O ne of the remarkable characteristics of the development of basidiomycete fruiting bodies is stipe elongation growth that results primarily from manifold cell elongation (1-5). The ...

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“…Because of the popularity of next-generation sequencing, many genome sequence drafts of basidiomycetous fungi are publicly available, especially from the 1,000 Fungal Genomes Project (14). More recently, the constructions of de novo draft genome sequences of Lentinula edodes were reported (15,16).…”

Section: Importancementioning

confidence: 99%

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

Sakamoto

Nakade

Sato

et al. 2017

Appl Environ Microbiol

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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 edodes. De 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 N 50 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 ␤-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 deathrelated 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 novo Lentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.

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Whole genome de novo sequencing and genome annotation of the world popular cultivated edible mushroom, Lentinula edodes

Cited by 48 publications

References 7 publications

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

Chitinases Play a Key Role in Stipe Cell Wall Extension in the Mushroom Coprinopsis cinerea

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

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