Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage

Kiyama, Ryoiti; Furutani, Yoshiyuki; Kawaguchi, Keiko; Nakanishi, Toshio

doi:10.1038/s41598-018-34415-6

Cited by 26 publications

(23 citation statements)

References 72 publications

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“…Therefore, it is important to elucidate the mechanisms of fruiting body development in S. latifolia. Recently, several research groups have sequenced the whole genome sequence of Sparassis species [19,29], which will provide base information for further study. Previous study showed that light was an essential environmental factor for the primordia formation in S. latifolia [30], but the molecular mechanism of light-induced primordia formation in S. latifolia is still unclear.…”

Section: Discussionmentioning

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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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: Discussionmentioning

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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“…A. blazei also possessed two potential β-1,3-glucan synthase genes (A09123 and A09827, named AbFKS1 and AbFKS2, respectively) known to play an important role in β-1,3-glucan biosynthesis [52][53][54]. AbFKS1 and AbFKS2 shared high similarity to two A. bisporus β-1,3-glucan synthase genes EKM78523 and EKM82691.1 with the identity of 93% and 90%, respectively, and they were classified into two types (Figure 2).…”

Section: Identification Of Genes Involved In β-13-glucan and Udp-glumentioning

confidence: 99%

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

JianHua

Guo

et al. 2020

BioMed Research International

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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.

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“…The construction of a phylogenetic tree for A. cornea , A. heimuer , and other 19 published fungal species were conducted as previously described (Wang et al, 2019) including A. subglabra (AS) TFB-10046 SS5, Tremella mesenterica DSM 1558, Coniophora puteana RWD-64-598 SS2, Trametes versicolor FP-101664 SS1, Dacryopinax primogenitus DJM 731 (Floudas et al, 2012), Laccaria bicolor S238N-H28 (Martin et al, 2008), Serpula lacrymans S7.9 (Eastwood et al, 2011), C. cinerea okayama7#130 (Stajich et al, 2010), S. commune H4-8 (Ohm et al, 2010), Ganoderma sinense ZZ0214-1 (Zhu et al, 2015), Tremella fuciformis 7 , Exidia glandulosa HHB12029, Sistotremastrum niveocremeum HHB9708 (Nagy et al, 2015), Phellinus lamaoensis , Coniferiporia sulphurascens (Chung et al, 2017), Polyporus brumalis (Miyauchi et al, 2018), Lentinus tigrinus ALCF2SS1-7 (Wu et al, 2018), Trametes hirsute (Pavlov et al, 2015), Sparassis crispa (Kiyama et al, 2018). The common, unique, and single-copy gene families of these 21 species were identified with OrthoMCL (Li et al, 2003) and OrthoVenn (Wang et al, 2015).…”

Section: Methodsmentioning

confidence: 99%

Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species

et al. 2019

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Species in the genus Auricularia play important roles for people’s food and nutrition especially Auricularia cornea and A. heimuer. To understand their evolutionary history, genome structure, and population-level genetic variation, we performed a high-quality genome sequencing of Auricularia cornea and the corresponding comparative genomic analysis. The genome size of A. cornea was similar to Auricularia subglabra, but 1.5 times larger than that of A. heimuer. Several factors were responsible for genome size variation including gene numbers, repetitive elements, and gene lengths. Phylogenomic analysis revealed that the estimated divergence time between A. heimuer and other Auricularia is ∼79.1 million years ago (Mya), while the divergence between A. cornea and A. subglabra occurred in ∼54.8 Mya. Population genomic analysis also provided insight into the demographic history of A. cornea and A. heimuer, indicating that their populations fluctuated over time with global climate change during Marine Isotope Stage 5-2. Moreover, despite the highly similar external morphologies of A. cornea and A. heimuer, their genomic properties were remarkably different. The A. cornea genome only shared 14% homologous syntenic blocks with A. heimuer and possessed more genes encoding carbohydrate-active enzymes and secondary metabolite biosynthesis proteins. The cross-taxa transferability rates of simple sequence repeat (SSR) and insertion or deletion (InDel) markers within the genus Auricularia were also lower than that previously observed for species within the same genus. Taken together, these results indicate a high level of genetic differentiation between these two Auricularia species. Consequently, our study provides new insights into the genomic evolution and genetic differentiation of Auricularia species that will facilitate future genetic breeding.

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Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage

Cited by 26 publications

References 72 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

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

Genomic Analyses Provide Insights Into the Evolutionary History and Genetic Diversity of Auricularia Species

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