4.7 Article

Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Plant Sciences

Lineage-Specific Genes and Cryptic Sex: Parallels and Differences between Arbuscular Mycorrhizal Fungi and Fungal Pathogens

Didier Reinhardt et al.

Summary: Arbuscular mycorrhizal fungi have long been considered ancient asexuals, but recent genomic studies suggest they may have sexual features. Comparative genomics of conspecific isolates of AMF show unexpected interstrain diversity, indicating a high number of lineage-specific genes, similar to fungal pathogens of plants and humans. These genomic similarities may play a role in AMF adaptation to the environment and symbiotic functioning.

TRENDS IN PLANT SCIENCE (2021)

Article Plant Sciences

Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi

Lotus A. Lofgren et al.

Summary: This study conducted a comparative genomic analysis of ectomycorrhizal (ECM) fungi, particularly focusing on the specialist genus Suillus, and found that Suillus has highly dynamic genomes with many rapidly evolving gene families, indicating that host specificity is a dynamic process at the genome level which is mainly influenced by secondary metabolites.

NEW PHYTOLOGIST (2021)

Review Geosciences, Multidisciplinary

A review of Pangaea dispersal and Large Igneous Provinces - In search of a causative mechanism

Alexander L. Peace et al.

EARTH-SCIENCE REVIEWS (2020)

Article Biochemistry & Molecular Biology

A computational framework to explore large-scale biosynthetic diversity

Jorge C. Navarro-Munoz et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Ecology

Synergies Between Division of Labor and Gut Microbiomes of Social Insects

Veronica M. Sinotte et al.

FRONTIERS IN ECOLOGY AND EVOLUTION (2020)

Review Biotechnology & Applied Microbiology

The role of melanins in melanotic fungi for pathogenesis and environmental survival

Helene C. Eisenman et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2020)

Article Evolutionary Biology

Genome Size Versus Genome Assemblies: Are the Genomes Truly Expanded in Polyploid Fungal Symbionts?

Pepijn W. Kooij et al.

GENOME BIOLOGY AND EVOLUTION (2020)

Article Biochemistry & Molecular Biology

ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

Chao Zhang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Plant Sciences

Genome Mining Reveals Neurospora crassa Can Produce the Salicylaldehyde Sordarial

Zhiyue Zhao et al.

JOURNAL OF NATURAL PRODUCTS (2019)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Ivica Letunic et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Mycology

Notes, outline and divergence times of Basidiomycota

Mao-Qiang He et al.

FUNGAL DIVERSITY (2019)

Article Biochemistry & Molecular Biology

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

Alex L. Mitchell et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

Fungal Highly Reducing Polyketide Synthases Biosynthesize Salicylaldehydes That Are Precursors to Epoxycyclohexenol Natural Products

Ling Liu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Biotechnology & Applied Microbiology

OrthoFinder: phylogenetic orthology inference for comparative genomics

David M. Emms et al.

GENOME BIOLOGY (2019)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Dan Vanderpool et al.

MOLECULAR ECOLOGY (2018)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Multidisciplinary Sciences

Stingless Bee Larvae Require Fungal Steroid to Pupate

Camila R. Paludo et al.

SCIENTIFIC REPORTS (2018)

Review Biotechnology & Applied Microbiology

Fungal mitochondrial genomes and genetic polymorphisms

Sarah Sandor et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2018)

Article Multidisciplinary Sciences

Strobilurin biosynthesis in Basidiomycete fungi

Risa Nofiani et al.

NATURE COMMUNICATIONS (2018)

Article Evolutionary Biology

Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia

Taruna A. Schuelke et al.

GENOME BIOLOGY AND EVOLUTION (2017)

Article Biochemistry & Molecular Biology

STRIDE: Species Tree Root Inference from Gene Duplication Events

David M. Emms et al.

MOLECULAR BIOLOGY AND EVOLUTION (2017)

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Multidisciplinary Sciences

The evolution of host-symbiont dependence

Roberta M. Fisher et al.

NATURE COMMUNICATIONS (2017)

Review Microbiology

Inside Out: Archaeal Ectosymbionts Suggest a Second Model of Reduced-Genome Evolution

Trevor Nicks et al.

FRONTIERS IN MICROBIOLOGY (2017)

Article Ecology

Cooperation facilitates the colonization of harsh environments

Charlie K. Cornwallis et al.

NATURE ECOLOGY & EVOLUTION (2017)

Article Biochemical Research Methods

Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

Kosai Al-Nakeeb et al.

BMC BIOINFORMATICS (2017)

Review Microbiology

Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution

Grzegorz Janusz et al.

FEMS MICROBIOLOGY REVIEWS (2017)

Article Biochemical Research Methods

GenomeScope: fast reference-free genome profiling from short reads

Gregory W. Vurture et al.

BIOINFORMATICS (2017)

Article Chemistry, Multidisciplinary

Induced Chemical Defense of a Mushroom by a Double-Bond-Shifting Polyene Synthase

Philip Brandt et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Article Biochemical Research Methods

Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function

P. K. Busk et al.

BMC BIOINFORMATICS (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

MultiQC: summarize analysis results for multiple tools and samples in a single report

Philip Ewels et al.

BIOINFORMATICS (2016)

Review Biochemistry & Molecular Biology

Mechanistic insights into class B radical-S-adenosylmethionine methylases: ubiquitous tailoring enzymes in natural product biosynthesis

Shanshan Zhou et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2016)

Article Genetics & Heredity

A detailed analysis of the recombination landscape of the button mushroom Agaricus bisporus var. bisporus

Anton S. M. Sonnenberg et al.

FUNGAL GENETICS AND BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Redundans: an assembly pipeline for highly heterozygous genomes

Leszek P. Pryszcz et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

Jana Trifinopoulos et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Small genome of the fungus Escovopsis weberi, a specialized disease agent of ant agriculture

Tom J. B. de Man et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Multidisciplinary Sciences

Reciprocal genomic evolution in the ant-fungus agricultural symbiosis

Sanne Nygaard et al.

NATURE COMMUNICATIONS (2016)

Review Biochemistry & Molecular Biology

Translating biosynthetic gene clusters into fungal armor and weaponry

Nancy P. Keller

NATURE CHEMICAL BIOLOGY (2015)

Article Multidisciplinary Sciences

Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole

Gordon M. Bennett et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Editorial Material Multidisciplinary Sciences

Evolving new organisms via symbiosis

E. Toby Kiers et al.

SCIENCE (2015)

Review Mycology

Mitochondrial inheritance in basidiomycete fungi

Jianping Xu et al.

FUNGAL BIOLOGY REVIEWS (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Multidisciplinary Sciences

Complementary symbiont contributions to plant decomposition in a fungus-farming termite

Michael Poulsen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Multidisciplinary Sciences

Symbiotic adaptations in the fungal cultivar of leaf-cutting ants

Henrik H. De Fine Licht et al.

NATURE COMMUNICATIONS (2014)

Article Biochemical Research Methods

QUAST: quality assessment tool for genome assemblies

Alexey Gurevich et al.

BIOINFORMATICS (2013)

Article Biochemical Research Methods

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

Gordon Gremme et al.

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS (2013)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

Hai Fang et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Multidisciplinary Sciences

Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts

Henrik H. De Fine Licht et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemical Research Methods

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich et al.

JOURNAL OF COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

NIH Image to ImageJ: 25 years of image analysis

Caroline A. Schneider et al.

NATURE METHODS (2012)

Review Microbiology

Extreme genome reduction in symbiotic bacteria

John P. McCutcheon et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Review Microbiology

Genome evolution in filamentous plant pathogens: why bigger can be better

Sylvain Raffaele et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Article Biochemistry & Molecular Biology

ExPASy: SIB bioinformatics resource portal

Panu Artimo et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Ecology

phytools: an R package for phylogenetic comparative biology (and other things)

Liam J. Revell

METHODS IN ECOLOGY AND EVOLUTION (2012)

Article Biochemical Research Methods

A novel hybrid gene prediction method employing protein multiple sequence alignments

Oliver Keller et al.

BIOINFORMATICS (2011)

Article Biochemical Research Methods

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

Guillaume Marcais et al.

BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Adaptive seeds tame genomic sequence comparison

Szymon M. Kielbasa et al.

GENOME RESEARCH (2011)

Review Entomology

Facultative Symbionts in Aphids and the Horizontal Transfer of Ecologically Important Traits

Kerry M. Oliver et al.

ANNUAL REVIEW OF ENTOMOLOGY (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Evolutionary Biology

Experimental evolution of specialization by a microsporidian parasite

Mathieu Legros et al.

BMC EVOLUTIONARY BIOLOGY (2010)

Review Entomology

Chemical warfare in termites

Jan Sobotnik et al.

JOURNAL OF INSECT PHYSIOLOGY (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)

Jason E. Stajich et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Biochemistry & Molecular Biology

Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus

Sean Agger et al.

MOLECULAR MICROBIOLOGY (2009)

Article Environmental Sciences

Monitoring mercury in two South African herbaria

Maria Kataeva et al.

SCIENCE OF THE TOTAL ENVIRONMENT (2009)

Article Biochemistry & Molecular Biology

An improved general amino acid replacement matrix

Si Quang Le et al.

MOLECULAR BIOLOGY AND EVOLUTION (2008)

Article Multidisciplinary Sciences

Australia's Oldest Marsupial Fossils and their Biogeographical Implications

Robin M. D. Beck et al.

PLOS ONE (2008)

Review Multidisciplinary Sciences

Mutation pressure and the evolution of organelle genomic architecture

M Lynch et al.

SCIENCE (2006)

Review Parasitology

Speciation in parasites:: a population genetics approach

T Huyse et al.

TRENDS IN PARASITOLOGY (2005)

Article Biochemical Research Methods

MUSCLE: a multiple sequence alignment method with reduced time and space complexity

RC Edgar

BMC BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

Mauve: Multiple alignment of conserved genomic sequence with rearrangements

ACE Darling et al.

GENOME RESEARCH (2004)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)