PROJECT INFORMATION
GOLD Project ID
Gp0145125  
Project Name
Baeospora myosura KM189292  
Other Names
  
Legacy GOLD ID
  
NCBI BioProject Name Fungarium phylogenomics
NCBI BioProject ID 287237
NCBI BioProject Accession PRJEB8570
NCBI Locus Tag
  
NCBI BioSample Accession SAMEA3267761
PI
Added By JGI automated process on 2016-05-18
Last Modified By Supratim Mukherjee on 2017-03-29
Project Comments
  
Project Status
Permanent Draft  
Project Relevance
  
Sequencing Center Royal Botanic Gardens, Kew
Collaborating Institute
  
Funding Agency
  
Project Description
The enormous breadth and depth of specimens held within the world's biological collections offer an unparalleled opportunity to capture genomic data from across the entire range of known biological diversitya task that would take many lifetimes to complete if we could rely only on fresh samples. High-throughput sequencing provides a technical solution to the long-term problems of recalcitrant and degraded DNA typical of museum specimens, suggesting that we may be on the verge of a major collections-based revolution. Although the potential is great, the feasibility of using preserved collections for large-scale, taxonomically comprehensive phylogenomic studies remains unknown. Here we demonstrate the continued relevance of fungarium collections in the genomic era by analysing a genomic dataset composed of 39 genomes, including 14 newly generated draft genomes derived from short-read shotgun sequencing of preserved specimens, frozen and freeze-dried material, representing most of the known families of Agaricales. We predicted homologs of 210 putative single copy genes in the newly generated draft genome assemblies, of which 208 were used for phylogenetic reconstruction. Our analyses resulted in a robust and, for the first time, fully supported phylogeny of the Agaricales, supporting the recognition of eight new suborders and providing a resource for testing hypotheses of the evolution of mushrooms. Our analysis of optimal combinations of ranked genes using an information theory-based method provides guidance on gene selection for future studies, enabling efficient application of high-throughput sequencing techniques toward unlocking the potential of collections-based research in the genomic era.  
Is JGI Project
No  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
SRA Experiment
 
SRA Experiment Id ERX991752  (Link to NCBI )
Experiment Title Illumina MiSeq paired end sequencing
SRA Submission ID 1541966
Exp Library Strategy WGS
Library Source METAGENOMIC
Library Selection size fractionation
Library Name unspecified
Library Layout PAIRED
Library Instrument Illumina MiSeq
PROJECT COMPOSITION
Study Tales from the crypt: Genome mining from fungarium specimens improves resolution of the mushroom tree of life
Organism Baeospora myosura KM189292
Analysis Projects Baeospora myosura KM189292
Number of Analysis Projects (AP)
1  
Number of Derived Analyis Projects (DAP)
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 2: High-Quality Draft
Finishing Goal
  
Contamination Screening Input
  
DNA Amplification Method
  
Sequencing Comments
  
DNA Amplification Kit
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Library Layout
  
Library Screening Method
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0140031
Organism Name
Baeospora myosura KM189292  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
EUKARYAL  
Phylogeny
FUNGI-BASIDIOMYCOTA  
Genus
Baeospora  
Genus Synonyms
  
Species
Baeospora myosura  
Subspecies
  
Species Synonyms
  
Strain
KM189292  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
  
Type Strain
  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 139080
NCBI Superkingdom
Eukaryota  
NCBI Kingdom
Fungi  
NCBI Phylum
Basidiomycota  
NCBI Class
Agaricomycetes  
NCBI Order
Agaricales  
NCBI Family
Tricholomataceae  
NCBI Genus
Baeospora  
NCBI Species
Baeospora myosura  
ISOLATION CLASSIFICATION
Ecosystem
  
Ecosystem Category
  
Ecosystem Type
  
Ecosystem Subtype
  
Specific Ecosystem
  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

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