3300023100: Plant litter microbial communities from Arlington Agricultural Research Station in Wisconsin, United States - UWRJ-L013-104B-2

Overview

Basic Information

• IMG/M Taxon OID: 3300023100
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0095510 | Gp0290908 | Ga0247738
• Sample Name: Plant litter microbial communities from Arlington Agricultural Research Station in Wisconsin, United States - UWRJ-L013-104B-2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 593146743
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Soil Microbial Communities From Arlington Agricultural Research Station In Wisconsin And Kellogg Biological Station In Michigan, Replicating The Bioenergy Cropping Systems Trials (Bcsts)
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Plant Litter → Unclassified → Unclassified → Plant Litter → Soil Microbial Communities From Arlington Agricultural Research Station In Wisconsin And Kellogg Biological Station In Michigan, Replicating The Bioenergy Cropping Systems Trials (Bcsts)

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → agricultural field → plant litter
• Earth Microbiome Project Ontology (EMPO): Free-living → Non-saline → Soil (non-saline)

Location Information

• Location: USA: Wisconsin
• Coordinates
  • Lat. (^o): 43.3
  • Long. (^o): -89.38
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F012659	Metagenome / Metatranscriptome	278	Y
F013935	Metagenome / Metatranscriptome	267	Y
F031153	Metagenome / Metatranscriptome	183	Y
F069784	Metagenome	123	N
F082505	Metagenome / Metatranscriptome	113	Y
F086058	Metagenome / Metatranscriptome	111	Y
F090630	Metagenome	108	N
F091422	Metagenome / Metatranscriptome	107	Y
F099558	Metagenome / Metatranscriptome	103	Y
F100548	Metagenome / Metatranscriptome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0247738_10013753	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2753
Ga0247738_10057508	All Organisms → cellular organisms → Bacteria → Proteobacteria	1293
Ga0247738_10063689	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1222
Ga0247738_10071015	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1152
Ga0247738_10101213	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	947
Ga0247738_10197288	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae	652
Ga0247738_10283897	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	530
Ga0247738_10307687	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	506
Ga0247738_10310455	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	504
Ga0247738_10312876	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium	501

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0247738_10013753	Ga0247738_100137532	F091422	MLMVLDDARDALRRLGGERLHPRYMPGASELMMTSVKLHHATSEQDFEDVHALATSELGSGLASLAEIKRVDGLTDAAIWVVRRNDQVTGFLAPLALTSAGVAALTDGTFDAANIDQKWVARMGQPLAGFYCWCYAGKDQVSRGALVLALRTLIDKHFPDLPFFGKDTTEAGAKIMRHLGFFPFDGVQHLFWRCRSVMEAA
Ga0247738_10057508	Ga0247738_100575082	F082505	MWPFESRRKKAVVVFHIDQNGLAKGAYFRGEADVLIIDERDPKNRVYRMGQETADDELRRKIGKHPLGRILEEKASDDRHASPVLNLHWDGAGARAS
Ga0247738_10063689	Ga0247738_100636893	F012659	MQTQTEQKLLEVLVEMRNWLRVAVREPVKSALVAALPDTKSRAAYQMLDGNASFEQVRVTCKMSPNAVVALAARCTSMGLMEVTPDKKRVRLFNLQDFGLQSSIESSDLGSK
Ga0247738_10071015	Ga0247738_100710151	F069784	QPLTVRLDPESKKLFAEEAEKCGLEPGVAARQILELYVQRLRESGDYIQTLSDFSQALKKTA
Ga0247738_10101213	Ga0247738_101012132	F100548	MTEPEPPPETHFFQTSQPRELLACVEFAAERADKAAEDHGAWRWLCISMTLAVQNACLCALDTGDEYGTKGMTRTDAREVVRWTKAGRKGPTPLAVREPRIVSPLELLRRTGDPFFLRPPYQLPLNRQINDSFDALVDLRNTFLHFSVDGWTTDLREIPPLIITACNIVRHLAVTQPIYLKRAGRHHRERVAAALDRIAAAMEHYPDLPA
Ga0247738_10197288	Ga0247738_101972882	F013935	IVPEIGIFSELVQLGKARRGLIDVKDASSAARQTA
Ga0247738_10283897	Ga0247738_102838971	F099558	MSLSNTTYNSLVPSISRRDRNIVGRLMSAVLSQWPERTRGSPPTDAYLRRDIGLNPLESSRKYWDHQ
Ga0247738_10307687	Ga0247738_103076871	F090630	LLVMLPFATTEVRPLVVVPGMGLVLGVFAAIIILWSKSLRWSATTGEMMSAIRAEGGADSGAISWTLRENHEGENGSYWTREVSFSDFCSLNRPQIVRTWIVDGLIGILGWSVAFLLFSGPSFALTVTLAGLLAGHIARIAWLIRQRNLMLTLYQSTVTIVVGGVAGA
Ga0247738_10310455	Ga0247738_103104551	F031153	RTLEKKEQGLSPAPKIVSTLNFLENVDLILIVEATLLVRVRAPPETWTTKLEPLGQPELELVDHLFRLVTIFGNLCSKFQQSAK
Ga0247738_10312876	Ga0247738_103128761	F086058	MTTYRAYRVDSRRHIQSAAWLDAPNDDVAREKAAELCDEGTPAVELWQATRLVDEIECAEEDA