3300025254: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mMF_r2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025254
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101315 | Ga0209148
• Sample Name: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mMF_r2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 202483895
• Sequencing Scaffolds: 13
• Novel Protein Genes: 14
• Associated Families: 10

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	2
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	1
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1
Not Available	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	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 → 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?
F023377	Metagenome / Metatranscriptome	210	Y
F044564	Metagenome / Metatranscriptome	154	Y
F044585	Metagenome / Metatranscriptome	154	Y
F057616	Metagenome	136	Y
F059118	Metagenome	134	N
F062395	Metagenome / Metatranscriptome	130	Y
F079536	Metagenome / Metatranscriptome	115	Y
F080973	Metagenome	114	Y
F096514	Metagenome / Metatranscriptome	104	Y
F103112	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209148_1000059	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae	350224
Ga0209148_1000285	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	75960
Ga0209148_1000771	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia	24110
Ga0209148_1001539	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae → Sphingomonas	11206
Ga0209148_1001547	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Sphingomonadales → Sphingomonadaceae	11147
Ga0209148_1002390	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Actinobacteria → Actinomycetia → Micrococcales → Microbacteriaceae	6574
Ga0209148_1002541	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	6088
Ga0209148_1004131	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3665
Ga0209148_1004293	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3551
Ga0209148_1010166	Not Available	1797
Ga0209148_1010412	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1766
Ga0209148_1033548	Not Available	748
Ga0209148_1035592	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → unclassified Betaproteobacteria → Betaproteobacteria bacterium	716

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209148_1000059	Ga0209148_1000059268	F080973	MALPTQGDVRELIARAICQLTGIPTCEIDLGPSRVLIHPDTRCGYNWSYPDAMVKARFRPFVHRAVSMVRDQYPILR
Ga0209148_1000059	Ga0209148_1000059288	F059118	MLLIALMGGLLANPPVHDPLVPPMRVTTSFACHGTQRSITVARGIGRDAVVAVTANGRPMVGAAMSAIRIGLAPLIAIEEVTPYCGDGPDRIRIKGWIDDRKRNLMIFFGTGGQAAVRDV
Ga0209148_1000285	Ga0209148_100028565	F096514	MDLIDLYHRRGIALVRSKLRGSAAARQGYGRLARMYSEQIERRRAMAPDSVDLTPAL
Ga0209148_1000771	Ga0209148_100077114	F079536	MSIDSLSPAVGSGRANEVLLKQLGEVTVQASRLEHLAVEIAQNLKIDATVADAVPSLQDSKLTPPPWSTISAKDIKNWAASTGRLLEIRDSMFEASGAARFAGSRGDTIATESADGTVFPADEEYLGRYLKRLTRHLAAGSELLSRLDYHDENGQRWPLVTIYAQRAPGEGSEQTPLRLPEAWQRWLSA
Ga0209148_1001539	Ga0209148_10015395	F080973	MVLAAATISMAYPTQGDVREMIAGAIGELTGTPAAEVDLGNSRVLVLTDTRSGYNWSYPDAMVKARFRPFVHRAVSMVRQQYPFLR
Ga0209148_1001547	Ga0209148_10015479	F096514	MDLIDLYHRRGIALVRSKLRATPAARRGYGRLARIYSEQIERQRAMVVVKAPELKSAL
Ga0209148_1002390	Ga0209148_10023905	F103112	MNSPRIRQLVQPEMSVADRNLSITNEVRTIMTTTALPASTARRAAQQQGVELLVSRVAMGMLRWSQHRAARRRVTHEEMMLLRQVQKDSANAVDLSRLNRLG
Ga0209148_1002541	Ga0209148_10025416	F062395	GGRRRRGRLTRMKRVPAPAPAKRVVASSHVHSESRTSFRYEATWHIDGPLLTWKATVSLPGRRWCLAGGTPEWTGGNEAKAVRDDVARSIDGLET
Ga0209148_1004131	Ga0209148_10041312	F059118	MLPIALMLGGILDNPPAHDPLVPPTRVTTSFTCHGTQRTITVARGIGRDAVVALTANGKPVVGTAMSAIRSGLAPLTAIDEITPYCGDGPDRIRIKGWVDDKKSNLMIFFGPGGEAAVRDVG
Ga0209148_1004293	Ga0209148_10042931	F044564	MSTVPDTTPRALRIDGPLSARAVLDHFNEKGRGLLGPGQEDAAVRIAQLLAHEADLSAAWGGLPGTDHPRHWQPATGDEAPMSDARSEHRRLDVHLAQWWALPLAVRDRQPHSVILPMGTTREALAALVRRHMPGAWWNSTVRVTIDVET
Ga0209148_1010166	Ga0209148_10101662	F103112	MNSPRIRQLVQPEMSVADRNLSITNEVRTIMTTTAFPASTAHRTAQQQGVELLVSRVAMGMLRWSQHHAARRRVTHEEMQLLRQVQKDSANAIDLSRLSRLG
Ga0209148_1010412	Ga0209148_10104124	F057616	NDKAVPLLSGAPPQVRERDHDDSHAVDIDQTSKESKPT
Ga0209148_1033548	Ga0209148_10335481	F044585	EPDRAMRLWDNAFARASASGQDGMARSLLRLRIVRMHFQARFGDRDALEPPMLAASAEARVHGWRVESLLVDLLEVYLATLGGNHDEGLRDVEAIRAEAEAHLDPIELSAMELMAGHFRGYMLGWPHEPERTYRALSRLTASPQAPPGLIANVQMNIGHSHLLVGNVDLASTYLQEAVRLYEPLPLTPRKLAAARAWAQCLLARNEARRADAVLHPLLAARTELASTRFLADALLVAAEARVKLGDLAG
Ga0209148_1035592	Ga0209148_10355922	F023377	PRAIRMAMVAALALAGAAAQAMTVSYQCTGRRLLTAELAPRQGQLHFEGQDWTVSRVPGGHEAHYVNKKDGIDVVTRERNMTFTHGSETLQCFLYSDALPGDAPQKTN