3300003215: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape MF_Col_mMF

Overview

Basic Information

• IMG/M Taxon OID: 3300003215
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0061140 | Ga0007020
• Sample Name: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape MF_Col_mMF
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 356584568
• Sequencing Scaffolds: 19
• Novel Protein Genes: 20
• Associated Families: 19

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium diazoefficiens	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium → Phenylobacterium zucineum	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	2
Not Available	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiales incertae sedis → Vineibacter → Vineibacter terrae	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Rhizosphere → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: University of North Carolina, USA
• Coordinates
  • Lat. (^o): 35.9082
  • Long. (^o): -79.0499
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001574	Metagenome / Metatranscriptome	669	Y
F002233	Metagenome / Metatranscriptome	580	Y
F002851	Metagenome / Metatranscriptome	526	Y
F003272	Metagenome / Metatranscriptome	496	Y
F012265	Metagenome / Metatranscriptome	282	Y
F013130	Metagenome / Metatranscriptome	274	Y
F013935	Metagenome / Metatranscriptome	267	Y
F019507	Metagenome / Metatranscriptome	229	Y
F020707	Metagenome / Metatranscriptome	222	Y
F027677	Metagenome / Metatranscriptome	194	Y
F030808	Metagenome / Metatranscriptome	184	Y
F033510	Metagenome / Metatranscriptome	177	Y
F034624	Metagenome / Metatranscriptome	174	Y
F042047	Metagenome / Metatranscriptome	159	Y
F043128	Metagenome / Metatranscriptome	157	Y
F044594	Metagenome / Metatranscriptome	154	Y
F070394	Metagenome	123	Y
F094085	Metagenome / Metatranscriptome	106	Y
F099471	Metagenome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI25153J46596_10000740	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	20002
JGI25153J46596_10001538	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	13684
JGI25153J46596_10001806	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	12687
JGI25153J46596_10002660	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	10206
JGI25153J46596_10004066	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	7965
JGI25153J46596_10004895	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	7119
JGI25153J46596_10005110	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium diazoefficiens	6927
JGI25153J46596_10005140	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii	6899
JGI25153J46596_10005736	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii	6471
JGI25153J46596_10007393	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	5411
JGI25153J46596_10014291	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Caulobacterales → Caulobacteraceae → Phenylobacterium → Phenylobacterium zucineum	3308
JGI25153J46596_10014327	All Organisms → cellular organisms → Bacteria	3302
JGI25153J46596_10019081	All Organisms → cellular organisms → Bacteria → Proteobacteria	2637
JGI25153J46596_10021657	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium elkanii	2390
JGI25153J46596_10055643	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1106
JGI25153J46596_10067716	Not Available	938
JGI25153J46596_10071279	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	898
JGI25153J46596_10076723	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiales incertae sedis → Vineibacter → Vineibacter terrae	845
JGI25153J46596_10145369	Not Available	514

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI25153J46596_10000740	JGI25153J46596_1000074022	F002851	MRSLIETAAVIAACGSAIFWFMSAMCRLPDAKPGFDEEQVAELSKALRKMNRRNFWAAGLMGVTALLSASGRFIGFFGL*
JGI25153J46596_10001538	JGI25153J46596_100015382	F012265	MDNRRIERTQLDRPDQHAPDGVGGPARDRAVDPPEFARQIAAAXHERKGTVGKAILRELVSEFVKPTLXDPQILSTDRAIAILEXLLTTVLPQLKESEEFNRLAKTVLGEEIEQRRNLRARRLEDTAT*
JGI25153J46596_10001806	JGI25153J46596_1000180611	F099471	VAHGDAFSETFIEGLRRDLARWRTELAMLDVDQVPRGLFFQTSELRAWIDAGEDILARYEEHRA*
JGI25153J46596_10002660	JGI25153J46596_100026609	F044594	MSVLTHTSHIAYSAAPRAARQPGQFRRLLDRFLEWRQRRVEEDIAIHLGVTGGHITDEIERRIFERLMSRGGFRG*
JGI25153J46596_10004066	JGI25153J46596_100040667	F030808	MNLNLSAFQSQEFIVGIAVAAILVSALIASSMFRNIALALAAGGVVLLYLQGGVPALLATSAMVEKEIRALPEFSNGLIVGFAVAAVFLFGMQKRSA*
JGI25153J46596_10004895	JGI25153J46596_100048957	F027677	MKNLIYCGAAIALLLAVPAAAQNATPTINPNKMTDQMREKPPLQLSEQQRIAIQEALVTANSDQKTPDKFEPKVGERIPTVLKLDPMPAPLINHEPVLKQYDFVKLEKELLVVDPMNNTIVAVIERKFPQVNETQGSAPSGQTHDPASHGDEAETNKKD*
JGI25153J46596_10005110	JGI25153J46596_100051104	F042047	MPSIEQCRAYAAEYKMLGADPKNSARRSALLINISRSWIALGHQLESLADTVKSEGE*
JGI25153J46596_10005140	JGI25153J46596_100051404	F003272	MVRGGRAALVAAMMAATGTPVAGQVLDATYRGTMVCEKLPFTSGQMREAIEVTISGGAARYSHVVRLRNAAVEAAAEQGTGTVSGTKIDLQGSWKGGSWQYEAKYSGSFVRRSATLEGTQSWTDGGKTVTRACTGAIKRPFKPFLPRAKKSAQLQ*
JGI25153J46596_10005736	JGI25153J46596_100057362	F020707	MCLIHRDFKHFAPPNAKQFRHLRKVSSIMRAKVLSIMRGDQGQVTSP*
JGI25153J46596_10007393	JGI25153J46596_100073933	F001574	MTSLRLSSGGLDFLNPNGLARPALEKFSGAWLACFVVMAHGDFANALSLDHARIASVCGTIGALVAVVLLSQMDRTSVSLPKQMTVSAFATFIGDVFAHPSHFPPQWGEPLVTAGVSAVIAVALWQARRLLKSL*
JGI25153J46596_10014291	JGI25153J46596_100142912	F019507	MDARQLVDIACEDDPRAPCLWLPSDLFPEFCDAIRQRPNLVGAVIYRNKTIRDGGPYSDITTRRP*
JGI25153J46596_10014327	JGI25153J46596_100143273	F034624	MQLPEPPKIAAVEIVAAQPSEVDRAAVAHMGATAPKAVYVVKVKLQAKPPVTSMAWALYIDDERIPKYWEYTDGIYFTVPDSQFFSRHKGKQLRFSRNGTDFFDTGVKLAPAPSVAHGSAARLPLQADVLK*
JGI25153J46596_10019081	JGI25153J46596_100190813	F033510	MSVRITHEQLAAHDDKGERHVVMVTRAPVPSAPHLRGMPHYTWHDGQVLHLVDAKAGVLECAVTGQRLTIERWRG*
JGI25153J46596_10021657	JGI25153J46596_100216573	F002233	MEDEEMRQVRSLLSSASSRIGRRLSEIVAIAAASLPLAGA*
JGI25153J46596_10055643	JGI25153J46596_100556431	F020707	QMCLIHRDFKHFAPPNAKQFRHLRKVSSIMRAKVLSIMRGDQGQVTSP*
JGI25153J46596_10067716	JGI25153J46596_100677162	F094085	MRAFRTAAIALVLAAVATAPAFGVASVSVFGLKAPEEISGFTLNDSTNFEKLKPGDGYGLDYSQSGWKLDV
JGI25153J46596_10071279	JGI25153J46596_100712792	F013935	LGLLGIVPEIGIFGELVQLGEASRGLFDVKDASSAARLTA*
JGI25153J46596_10076723	JGI25153J46596_100767231	F070394	MLYRVRIDPIAQRLIDEFAVYLRHYDEDFAIEQLERLDRIIALNLGETPLTWNYFAFTGAPYRAYLFRVGRRTQYWLIYTVDEETRTVDLLHFWNASRDPDALDL*
JGI25153J46596_10076723	JGI25153J46596_100767232	F013130	MTAKIDTKDKRRRTTTVPVTTMEEIPVLSDLEREDLQRSLKDAEARIRAGQGADYDPKTFKSRLIDIYRGTKR*
JGI25153J46596_10145369	JGI25153J46596_101453692	F043128	PRQMTISAFATFIGDVFAHPSHFPPQWAEPLVTAGVSAAIAVALWQARRLIKSL*