3300025302: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape MF_Cvi_mMS (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025302
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0061147 | Ga0207426
• Sample Name: Arabidopsis root microbial communities from the University of North Carolina, USA - plate scrape MF_Cvi_mMS (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 414835864
• Sequencing Scaffolds: 15
• Novel Protein Genes: 17
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	3
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium valentinum	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	2
All Organisms → cellular organisms → Bacteria → Acidobacteria	1
Not Available	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter	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?
F015610	Metagenome / Metatranscriptome	253	Y
F015908	Metagenome / Metatranscriptome	251	Y
F021809	Metagenome / Metatranscriptome	217	Y
F027664	Metagenome	194	Y
F030808	Metagenome / Metatranscriptome	184	Y
F039184	Metagenome / Metatranscriptome	164	Y
F039839	Metagenome / Metatranscriptome	163	Y
F042047	Metagenome / Metatranscriptome	159	Y
F053413	Metagenome / Metatranscriptome	141	Y
F060695	Metagenome	132	Y
F074001	Metagenome / Metatranscriptome	120	Y
F074960	Metagenome / Metatranscriptome	119	Y
F075003	Metagenome / Metatranscriptome	119	Y
F092690	Metagenome / Metatranscriptome	107	Y
F094368	Metagenome	106	Y
F103371	Metagenome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0207426_1013480	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	3028
Ga0207426_1013793	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	2981
Ga0207426_1019661	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	2357
Ga0207426_1045483	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1335
Ga0207426_1047866	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	1287
Ga0207426_1049282	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1261
Ga0207426_1057542	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1131
Ga0207426_1063184	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Rhodospirillales	1057
Ga0207426_1074678	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	935
Ga0207426_1092530	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium → Bradyrhizobium valentinum	797
Ga0207426_1097575	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	765
Ga0207426_1118833	All Organisms → cellular organisms → Bacteria → Acidobacteria	656
Ga0207426_1121829	Not Available	644
Ga0207426_1123951	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Ramlibacter	635
Ga0207426_1135909	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	590

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0207426_1000609	Ga0207426_100060926	F103371	MSYDDWKTHNPDDDRCEFCGAAPWECRGGWQPNNCTGECGKGWRDPDHEYEKMRDEA
Ga0207426_1000609	Ga0207426_100060932	F103371	MSYDDWKTHNPDDDRCEFCGAAPWECRGGWQPNKCSGECGTGWRDPDHEYEKMRDEA
Ga0207426_1013480	Ga0207426_10134804	F053413	MFLSPLGERLGEGAATDGARGTPSPNLSPKGERSKRRGRSC
Ga0207426_1013793	Ga0207426_10137933	F015908	MRYMMIAAVLGMLASQAQAESKKYRSVLIPEKSVQACSGWGQTYTVDVSNGVLTLGVNYARRLFSAPVDSDGKIAASYKDPSGGILKFIALGNGEYELSNPLVPCYYRLVPSASPPWNS
Ga0207426_1019661	Ga0207426_10196612	F039184	MDEDFSFMRACDLARTADENFKLAWIAEIEASWQVSDLDHGDFGFILVMADGRRLYWRYTSDDPGAGRVEDLVVSELAAGEVPEGDAPWSRPELLNKRLAVLRRLA
Ga0207426_1045483	Ga0207426_10454832	F042047	MPSAKQCRAFAAEYKKLAIDPNNSARRSSVLKSISNSWTALGHQLESLAMVAKEEQR
Ga0207426_1047866	Ga0207426_10478662	F074960	MRDVDDGGLEAQRVALRGDAVDELGRDDVDAGKAAIIEIVEVVQTARCAGASIA
Ga0207426_1049282	Ga0207426_10492823	F075003	MLRLSIACVLVLAVSLPASANWTRAQRAQFLGQCVESCQSTLNLPDSKRRVCDATCGCVADQAETLVTPADMYALDEAAAAGRTTETMQKIRGFFPACAKKSARMP
Ga0207426_1057542	Ga0207426_10575423	F030808	VEVDMNLNLSAFQSQEFIVGIAVAAILVSALIASSMFRNIALALAAGGVVLLYLQGGVPALLATSAMLEKEIRALPEFSNGLIVGFAVAAVFLFGMQKRST
Ga0207426_1063184	Ga0207426_10631842	F060695	MRASASLLWLGAAVTLSAFVSAYVVAMFVADRLADCTTPAVLPVAYCVMLGYAIMGAQIGINDLVNSGRPPPYLEELQWASFILIGLGIVWVGFAYSIWVVVGFLMLFFVPLGAVYLIVGMPVFAAVMRLYERAVPDLDAAAAWPATVLAVAPFVVFSLHDIEARCGVLQ
Ga0207426_1074678	Ga0207426_10746782	F015610	MPIIDIHTHCAPPRPPGDRFGVAEALRGVPVGRNMITNYRGLPAVSYYEMGDFELQQEACAKAGVTHRLISTPFAAEVMAAISKSPSLDICKAVNDGIAGIVAR
Ga0207426_1092530	Ga0207426_10925301	F039839	MRQTVLPTRIHGTIAPTRGESFARRTAPVGPRSARRQDLRFGLPLTPESGGPSRHRAAQFARAMHRARRRQEFQNAQQDVD
Ga0207426_1097575	Ga0207426_10975752	F094368	MEPIAYLDPEVRPPEYRVPRGRSGVGAQSALETLLRDLERIRRAKEAYGDLARTQENSQFLF
Ga0207426_1118833	Ga0207426_11188331	F027664	VCGLIVFTGSARAQYKIELQTCEDLKIAKKQYGVFTVETASCVNPTKIIQPKGSLRNVHILATFPAVPTGARITFLVNENNADGEQVQYVDYTASPQHTTAYAQLTINKPGKYFVRMVNYLDKSQVWATADFSVGEDQIGARSTGNTVAGKGKVSVCKEIDDNWTCVGESNQWAANKAFNILFENSTPVGVDFIGIVFFKRGPDGKDVEFIKEYQQNI
Ga0207426_1121829	Ga0207426_11218292	F021809	AALMLSLAQLALAQQALAQPASAQSNDCSREAASIRKAETQLPRLEVAPPADQQIVCITLETNILFAKRLGAHVAQCPRSPYAQKVSDWQRTGEQYAAQFNERRCKPAIKTFRG
Ga0207426_1123951	Ga0207426_11239512	F092690	MNTESEVDRNARLVRNLLALRMVLCMDQMQTGKWGDRIEEIDQELATLGHDMKSTAACATESLRRTFLLPRLVSRRSRAAHRPPARAVPRG
Ga0207426_1135909	Ga0207426_11359092	F074001	MNQLPSQPVIDQAKSKTDQVQRDLEVASAELGLTHGALERELPPGVKKGDVAWALHQNKVLEKKVQQAAEELEEVTELLDQAKDDPA