Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Cao, Shuo; Yang, Yang; Bi, Guoan; Nelson, David R.; Hu, Sheng; Makunga, Nokwanda P.; Yu, Bin; Liu, Xin; Li, Xiaohua; Hu, Xuebo

doi:10.3389/fmicb.2021.746121

Cited by 11 publications

(20 citation statements)

References 66 publications

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“…Based on the comparison of OrthoMCL gene families and whole genomes, genetic differences were also found by Luo et al (2020) between North American (MD-104, see Floudas et al 2012) and Chinese (CGMCC5.78) strains. Similar result was obtained by Cao et al (2021), who sequenced a cultivated strain of Fuling mushroom (2018LT001), originated from Hubei, China.…”

Section: Differences Between "Fuling" and "Tuckahoe" Samplessupporting

confidence: 85%

“…Consequently, both traditional morphological examinations (Fries 1822;Merrill 1917), molecular phylogenetic studies based on barcoding sequences (Wu et al 2020), and genome-level comparisons (Luo et al 2020;Cao et al 2021) prove that Asian Fuling samples differs from the North Americans. So, it seems justified to treat "Fuling" (Pachyma hoelen) and Sclerotium cocos (syn.…”

Section: Differences Between "Fuling" and "Tuckahoe" Samplesmentioning

confidence: 99%

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Nomenclature of the Beeswax bracket (Ganoderma pfeifferi), a European wood decay fungus with medicinal properties

Papp¹,

Barina

Finy³

et al. 2022

TAXON

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In recent years, the scientific names of many cultivated and well-known medicinal fungal species have been changed. However, the results of taxonomic and nomenclature works on these economically important fungi are often overlooked or ignored in applied researches. The incorrect use of scientific names may cause uncertainty in research and in the global medicinal mushroom market. In this paper, we briefly review the current taxonomy and nomenclature of "Fuling" medicinal mushroom and make a proposal for biochemists, pharmacists and businessmen on the correct use of scientific names related to this species. Based on the recent taxonomic results and nomenclatural proposals, the use of the names Wolfiporia extensa, W. cocos and especially Poria cocos for the "Fuling" mushroom are incorrect and misleading; therefore, the acceptance of the names Pachyma hoelen or Wolfiporia hoelen is recommended.

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Section: Differences Between "Fuling" and "Tuckahoe" Samplessupporting

confidence: 85%

Section: Differences Between "Fuling" and "Tuckahoe" Samplesmentioning

confidence: 99%

Nomenclature of the Beeswax bracket (Ganoderma pfeifferi), a European wood decay fungus with medicinal properties

Papp¹,

Barina

Finy³

et al. 2022

TAXON

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show abstract

“…Notably, the genome of F. gymnauchen was large, possibly due to a higher repetitive sequence content. The repeat ratio of the genome affects not only genome size and recombination but also the chromosome’s structure [ 29 , 30 ]. If genomic heterozygosity is exorbitant, genome assembly will be difficult [ 16 ].…”

Section: Discussionmentioning

confidence: 99%

Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes

Ma,

Zhao,

Song

2024

IJMS

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As one of the most abundant groups in marine fish families, Gobiidae fish are important fishery resources in China, and some are also invasive species in certain regions worldwide. However, the phylogenetic relationships of Gobiidae fish remain ambiguous, and the study of their invasion-related genes is still scarce. This study used high-throughput sequencing technology to conduct a whole-genome survey of five Gobiidae fish species: Acanthogobius flavimanus, Acanthogobius stigmothonus, Favonigobius gymnauchen, Ctenotrypauchen microcephalus, and Tridentiger barbatus. De novo assembly of five fish genomes was performed, and genomic traits were compared through K-mer analysis. Among the five Gobiidae fish genomes, F. gymnauchen had the largest genome size (1601.98 Mb) and the highest heterozygosity (1.56%) and repeat rates (59.83%). Phylogenetic studies showed that A. flavimanus was most closely linked to A. stigmothonus, while Apogonidae and Gobiidae were closely related families. PSMC analysis revealed that C. microcephalus experienced a notable population expansion than the other four fish species in the Early Holocene. By using the KOG, GO, and KEGG databases to annotate single-copy genes, the annotated genes of the five fish were mainly classified as “signal transduction mechanisms”, “cellular process”, “cellular anatomical entity”, and “translation”. Acanthogobius flavimanus, A. stigmothonus, and T. barbatus had more genes classified as “response to stimulus” and “localization”, which may have played an important role in their invasive processes. Our study also provides valuable material about Gobiidae fish genomics and genetic evolution.

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“…However, the functions of SOAT in the synthesis of pharmacologically active compounds are still largely unknown in medicinal fungi. Furthermore, although the genome [ 25 , 35 ], transcriptome [ 26 ], secretome [ 36 ], and mitochondrial genome [ 37 ] of W. cocos have been investigated, the molecular mechanisms involved in the biosynthesis of secondary metabolites remained incompletely understood. The gene function study of WcSOAT has not been reported before.…”

Section: Discussionmentioning

confidence: 99%

Functional Analysis of Sterol O-Acyltransferase Involved in the Biosynthetic Pathway of Pachymic Acid in Wolfiporia cocos

et al. 2021

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Pachymic acid from Wolfiporia cocos possesses important medicinal values including anti-bacterial, anti-inflammatory, anti-viral, invigorating, anti-rejection, anti-tumor, and antioxidant activities. However, little is known about the biosynthetic pathway from lanostane to pachymic acid. In particular, the associated genes in the biosynthetic pathway have not been characterized, which limits the high-efficiency obtaining and application of pachymic acid. To characterize the synthetic pathway and genes involved in pachymic acid synthesis, in this study, we identified 11 triterpenoids in W. cocos using liquid chromatography tandem mass spectrometry (LC-MS/MS), and inferred the putative biosynthetic pathway from lanostane to pachymic acid based on analyzing the chemical structure of triterpenoids and the transcriptome data. In addition, we identified a key gene in the biosynthetic pathway encoding W. cocos sterol O-acyltransferase (WcSOAT), which catalyzes tumolusic acid to pachymic acid. The results show that silence of WcSOAT gene in W. cocos strain led to reduction of pachymic acid production, whereas overexpression of this gene increased pachymic acid production, indicating that WcSOAT is involved in pachymic acid synthesis in W. cocos and the biosynthesis of W. cocos pachymic acid is closely dependent on the expression of WcSOAT gene. In summary, the biosynthetic pathway of pachymic acid and the associated genes complement our knowledge on the biosynthesis of W. cocos pachymic acid and other triterpenoids, and also provides a reference for target genes modification for exploring high-efficiency obtaining of active components.

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Genomic and Transcriptomic Insight of Giant Sclerotium Formation of Wood-Decay Fungi

Cited by 11 publications

References 66 publications

Nomenclature of the Beeswax bracket (Ganoderma pfeifferi), a European wood decay fungus with medicinal properties

Nomenclature of the Beeswax bracket (Ganoderma pfeifferi), a European wood decay fungus with medicinal properties

Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes

Functional Analysis of Sterol O-Acyltransferase Involved in the Biosynthetic Pathway of Pachymic Acid in Wolfiporia cocos

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