3300025261: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape CL_Cvi_mCL (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025261
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0061152 | Ga0209233
• Sample Name: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape CL_Cvi_mCL (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 273030715
• Sequencing Scaffolds: 8
• Novel Protein Genes: 10
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	2
Not Available	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae	1
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Granulicella	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium canariense	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?
F002233	Metagenome / Metatranscriptome	580	Y
F008001	Metagenome / Metatranscriptome	341	Y
F013935	Metagenome / Metatranscriptome	267	Y
F014055	Metagenome / Metatranscriptome	266	Y
F016724	Metagenome / Metatranscriptome	245	Y
F042042	Metagenome / Metatranscriptome	159	Y
F042926	Metagenome	157	Y
F057616	Metagenome	136	Y
F084292	Metagenome	112	Y
F084878	Metagenome	112	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209233_1007919	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	3329
Ga0209233_1014053	Not Available	2268
Ga0209233_1022744	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1599
Ga0209233_1035618	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae	1123
Ga0209233_1041022	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Acidobacteriales → Acidobacteriaceae → Granulicella	1002
Ga0209233_1050875	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium retamae	843
Ga0209233_1067658	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria	670
Ga0209233_1087917	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium canariense	538

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209233_1007919	Ga0209233_10079192	F008001	VSEPSIDEIIERLQFCIVDARALQLKMLERILSISLLEAHELKEKSGHVRLSRPH
Ga0209233_1014053	Ga0209233_10140533	F014055	MSREKTLENVSQGRRGFFRTLMIGAGATAVALPLMTTQSLAQKDGEDPKDGKCDDGLIVSKKTGKCKAIKKAPAQ
Ga0209233_1022744	Ga0209233_10227442	F002233	MRQVQSLLRNAPARIGRRIAQIVAIAAASLPQAGA
Ga0209233_1031957	Ga0209233_10319572	F084292	MTLHATLAEKIAEVPELYERGDESTARLLLGSGYLDAPQALTVEDVEAALQRHPELADRWLERGHDQRLAGGWGIECDHGRYKVQSYADG
Ga0209233_1035618	Ga0209233_10356183	F084878	MSDDNSHLAPRKLTHEQARMEQRLYWSRKSMPERLAAMTALTKRMNEMRGIFIDEQNPDLTPRRVRRRKS
Ga0209233_1041022	Ga0209233_10410221	F042926	MVGVFTCLIVLQFVVVVSHDLVDVSDWVRGSQVQAVIGKRKIWLATLANAVFPGIAVGFALYFWDRPKPLYVPTYWVVYYAIAVLSAVGMWYVPYFFGASEKQKREYSSMYDGTRHILPARGDNPR
Ga0209233_1050875	Ga0209233_10508751	F013935	LDLADARERILQRGALLHQLLGLLGVVPEIGIFCELVQLSEACRRFLDVKDASSAARLTA
Ga0209233_1057209	Ga0209233_10572091	F016724	MRTKQSILGLVYPGSEERRAPLVGMQFLHEGFVRPADVVAPRSRLQAKDLI
Ga0209233_1067658	Ga0209233_10676581	F042042	MLTTTRISAVLTSTDLVRSQEFYERQVGLTLSPETIPNHLLFESPDGSTLLVYGRPGGNKADHTQVRLWSHDIDSDVR
Ga0209233_1087917	Ga0209233_10879171	F057616	MNGGDGWVNDKAVPLLSGAPPQVRERDHDDSHAVDIDQTSKESKPT