4.6 Article

Whole-genome sequence of a high-temperature edible mushroom Pleurotus giganteus (zhudugu)

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Chromosomal genome and population genetic analyses to reveal genetic architecture, breeding history and genes related to cadmium accumulation in Lentinula edodes

Hailong Yu et al.

Summary: This study constructed a high-quality chromosome-level genome for Lentinula edodes and performed population genetics analysis. The results revealed significant differences among Chinese wild strains and provided insights into the breeding history of L. edodes. Additionally, genes associated with Cd accumulation traits were identified. These findings provide genetic resources for functional genomic, evolutionary, and artificial breeding studies on L. edodes.

BMC GENOMICS (2022)

Article Microbiology

Whole Genome Sequence of an Edible Mushroom Stropharia rugosoannulata (Daqiugaigu)

Shuwen Li et al.

Summary: In this study, we obtained the genome sequence of Stropharia rugosoannulata and performed gene and proteomic analysis. The results revealed the evolutionary relationship of S. rugosoannulata with other mushrooms and the differential protein expression profiles in different parts of the fruiting body. These findings provide valuable genetic resources for comparative genomics and molecular breeding.

JOURNAL OF FUNGI (2022)

Review Multidisciplinary Sciences

Biodelignification of lignocellulose using ligninolytic enzymes from white-rot fungi

Herman Suryadi et al.

Summary: This review explores the applications of enzymes in lignocellulose research, including the preparation methods, factors affecting enzyme activity, and potential future prospects.

HELIYON (2022)

Article Multidisciplinary Sciences

Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Jingcheng Zhang et al.

Summary: This study analyzed the population structure and demographic history of 133 Lentinula edodes strains, uncovered the genetic basis of adaptive evolution, and determined the involvement of genes related to fruiting body development in adaptive evolution.

JOURNAL OF ADVANCED RESEARCH (2022)

Article Multidisciplinary Sciences

A genetic module at one locus in rice protects chloroplasts to enhance thermotolerance

Hai Zhang et al.

Summary: The study identified two genes, TT3.1 and TT3.2, that enhance rice thermotolerance by facilitating the communication between the plasma membrane and chloroplasts. They found that upon heat stress, TT3.1 translocates to endosomes where it ubiquitinates TT3.2 for degradation, implying its role as a potential thermosensor. The accumulation of mature TT3.2 proteins in chloroplasts is crucial for protecting thylakoids from heat stress.

SCIENCE (2022)

Article Microbiology

Label-Free Comparative Proteomics Analysis Revealed Heat Stress Responsive Mechanism in Hypsizygus marmoreus

Lili Xu et al.

Summary: Heat stress response in Hypsizygus marmoreus involves autolysis and apoptosis of mycelia, mediated by upregulation of cell wall degradation enzymes and inhibition of cell wall synthesis enzymes, and induction of ROS and caspases, respectively. Accumulation of ROS triggers antioxidant defense system activation and MAPK cascade involvement in signal transduction. Additionally, inducible expression of heat shock proteins and upregulation of trehalose synthesis enzymes were found, along with proteasome upregulation to prevent protein misfolding. Energy production enzymes were also upregulated to maintain cellular processes during heat response.

FRONTIERS IN MICROBIOLOGY (2021)

Letter Biochemistry & Molecular Biology

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

Mose Manni et al.

Summary: The BUSCO software provides essential methods for assessing the quality of genomic and metagenomic data, offering new functionalities and improvements to streamline the process. It is capable of evaluating both eukaryotic and prokaryotic species, and can be used across various data types including genome assemblies, metagenomic bins, transcriptomes, and gene sets.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biochemistry & Molecular Biology

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Carlos P. Cantalapiedra et al.

Summary: The article introduces a major upgrade of the eggNOG-mapper tool, optimized for functional annotation of vast genomic and metagenomic datasets, including database updates, efficiency enhancements, and new features such as de novo gene prediction and fast protein domain discovery.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Biotechnology & Applied Microbiology

Whole genome sequence of an edible and medicinal mushroom, Hericium erinaceus (Basidiomycota, Fungi)

Wenbing Gong et al.

GENOMICS (2020)

Article Multidisciplinary Sciences

A cullin-RING ubiquitin ligase promotes thermotolerance as part of the intracellular pathogen response in Caenorhabditis elegans

Johan Panek et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Multidisciplinary Sciences

RepeatModeler2 for automated genomic discovery of transposable element families

Jullien M. Flynn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Genetics & Heredity

Genome Assembly and Pathway Analysis of Edible Mushroom Agrocybe cylindracea

Yuan Liang et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2020)

Article Multidisciplinary Sciences

Whole-genome sequence of Phellinus gilvus (mulberry Sanghuang) reveals its unique medicinal values

Jinxi Huo et al.

JOURNAL OF ADVANCED RESEARCH (2020)

Article Biochemistry & Molecular Biology

Enzyme promiscuity of carbohydrate active enzymes and their applications in biocatalysis

Edward Pallister et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)

Review Biochemistry & Molecular Biology

The continuing expansion of CAZymes and their families

Marie-Line Garron et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2019)

Article Horticulture

Molecular analysis of B mating type diversity in Lentinula edodes

Byeongsuk Ha et al.

SCIENTIA HORTICULTURAE (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemistry & Molecular Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Han Zhang et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren et al.

GENOME RESEARCH (2017)

Article Genetics & Heredity

The draft genome of tropical fruit durian (Durio zibethinus)

Bin Tean Teh et al.

NATURE GENETICS (2017)

Article Integrative & Complementary Medicine

Pleurotus giganteus (Berk. Karun & Hyde), the giant oyster mushroom inhibits NO production in LPS/H2O2 stimulated RAW 264.7 cells via STAT 3 and COX-2 pathways

Asweni Baskaran et al.

BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE (2017)

Article Plant Sciences

Correct names of two cultivated mushrooms from the genus Pleurotus in China

Samantha C. Karunarathna et al.

PHYTOTAXA (2016)

Article Microbiology

Characterization of Lignocellulolytic Enzymes from White-Rot Fungi

Tamilvendan Manavalan et al.

CURRENT MICROBIOLOGY (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Article Agriculture, Multidisciplinary

Feruloyl Esterase from the Edible Mushroom Panus giganteus: A Potential Dietary Supplement

Li Wang et al.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

Helga Thorvaldsdottir et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Integrative & Complementary Medicine

Pleurotus giganteus (Berk.) Karunarathna & K.D. Hyde: Nutritional value and in vitro neurite outgrowth activity in rat pheochromocytoma cells

Chia-Wei Phan et al.

BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE (2012)

Article Biochemistry & Molecular Biology

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

Yupeng Wang et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Mycology

Lentinus giganteus revisited: new collections from Sri Lanka and Thailand

Samantha C. Karunarathna et al.

MYCOTAXON (2011)

Article Biochemistry & Molecular Biology

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Morgan N. Price et al.

MOLECULAR BIOLOGY AND EVOLUTION (2009)

Article Biochemistry & Molecular Biology

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

Brandi L. Cantarel et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

Vardges Ter-Hovhannisyan et al.

GENOME RESEARCH (2008)

Article Biochemistry & Molecular Biology

AUGUSTUS:: ab initio prediction of alternative transcripts

Mario Stanke et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

TigrScan and GlimmerHMM:: two open source ab initio eukaryotic gene-finders

WH Majoros et al.

BIOINFORMATICS (2004)

Review Biotechnology & Applied Microbiology

The F-box protein family

Edward T. Kipreos et al.

GENOME BIOLOGY (2000)