3300003762: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mMF_r2

Overview

Basic Information

• IMG/M Taxon OID: 3300003762
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101315 | Ga0055542
• Sample Name: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mMF_r2
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 153174510
• Sequencing Scaffolds: 10
• Novel Protein Genes: 10
• Associated Families: 9

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
Not Available	4
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae → Leifsonia	1
All Organisms → cellular organisms → Bacteria	2

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 → Roots → Endophytes → Unclassified → Arabidopsis Root → 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: USA: North Carolina
• Coordinates
  • Lat. (^o): 35.6667
  • Long. (^o): -78.5097
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F027546	Metagenome / Metatranscriptome	194	Y
F040130	Metagenome / Metatranscriptome	162	Y
F049749	Metagenome	146	Y
F053329	Metagenome / Metatranscriptome	141	Y
F059118	Metagenome	134	N
F079536	Metagenome / Metatranscriptome	115	Y
F080973	Metagenome	114	Y
F096514	Metagenome / Metatranscriptome	104	Y
F103112	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0055542_1002070	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	7506
Ga0055542_1004662	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae	3259
Ga0055542_1008016	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	2095
Ga0055542_1011511	Not Available	1566
Ga0055542_1018268	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae → Leifsonia	1067
Ga0055542_1025729	Not Available	798
Ga0055542_1030069	Not Available	703
Ga0055542_1032562	All Organisms → cellular organisms → Bacteria	658
Ga0055542_1038636	All Organisms → cellular organisms → Bacteria	572
Ga0055542_1041530	Not Available	540

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0055542_1002070	Ga0055542_10020701	F059118	MLLIALMGGLLANPPVHDPLVPPMRVTTSFACHGTQRSITVARGIGRDAVVAVTANGRPMVGAAMSAIRIGLAPLIAIEEVTPYCGDGPDRIRIKGWIDDRKRNLMIFFGTGGQAAVRDVG*
Ga0055542_1004662	Ga0055542_10046624	F096514	MDLIDLYHRRGIALVRSKLRGSAAARQGYGRLARMYSEQIERRRAMAPDSVDLTPAL*
Ga0055542_1008016	Ga0055542_10080162	F079536	MSIDSLSPAVGSGRANEVLLKQLGEVTVQASRLEHLAVEIAQNLKIDATVADAVPSLQDSKLTPPPWSTISAKDIKNWAASTGRLLEIRDSMFEASGAARFAGSRGDTIATESADGTVFPADEEYLGRYLKRLTRHLAAGSELLSRLDYHDENGQRWPLVTIYAQRAPGEGSEQTPLRLPEAWQRWLSA*
Ga0055542_1011511	Ga0055542_10115111	F080973	IARAICQLTGIPTCEIDLGPSRVLIHPDTRCGYNWSYPDAMVKARFRPFVHRAVSMVRDQYPILR*
Ga0055542_1018268	Ga0055542_10182681	F103112	SPRIRQLVQPEMSVADRNLSITNEVRTIMTTTALPASTARRAAQQQGVELLVSRVAMGMLRWSQHRAARRRVTHEEMMLLRQVQKDSANAVDLSRLNRLG*
Ga0055542_1025729	Ga0055542_10257291	F049749	AWCSPFGEDGPAGELLALVDQVLAAIAAKPLEGAINHGDVQPMSSLRRALAKMKPAQLDTLTVQDESGDVICSFGAEGASVGDRSRAFEIFALLPPAAEAQQDKLLRMLLGYGLHYGYARSLGPDFNPLSEVRVKRGFFDTAIQVDGGRADWLVPEMDVRAGAVRGVYPANVFSAIGLARLAGSGLRLPPSAPTLGETLWRPSAAERAEILRLNPTYRDYLHFGDA*
Ga0055542_1030069	Ga0055542_10300691	F080973	MAYPTQGDVREMIAGAIGELTGTPAAEVDLGNSRVLVLTDTRSGYNWSYPDAMVKARFRPFVHRAVSMVRQQYPFLR*
Ga0055542_1032562	Ga0055542_10325621	F027546	MRVAGESKPAPWQPLGERVVRPQPVQPEWKPLAHAPCIEVNRQGQLRTNLPLPK*
Ga0055542_1038636	Ga0055542_10386361	F040130	VLLGVVLGMAVVAGSSPWRELLKKPEPVPSAPIQRERAPDQRV*
Ga0055542_1041530	Ga0055542_10415301	F053329	CSSRWAAAGSPTRKPRPDGIRFALDERAVDGVPQDSAMPPDLENPSAHEPALSRNHAAGVPRETASPAERALAPDGDAPMQSASATADDGTYVGQAGGYMGGPLPAVESGHAEVDKANVRGDGAYGFPAGPGVGVPGGEHQPAAQKPDVVPNPYPER*