3300025272: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mCL_r2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025272
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101302 | Ga0209455
• Sample Name: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Col_mCL_r2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 201830048
• Sequencing Scaffolds: 13
• Novel Protein Genes: 13
• Associated Families: 13

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Bordetella → unclassified Bordetella → Bordetella sp. FB-8	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Aeromonadales → Aeromonadaceae → Aeromonas	1
Not Available	5
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → unclassified Methylovirgula → Methylovirgula sp. 4M-Z18	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
F027546	Metagenome / Metatranscriptome	194	Y
F031516	Metagenome / Metatranscriptome	182	Y
F035339	Metagenome / Metatranscriptome	172	Y
F040711	Metagenome / Metatranscriptome	161	Y
F044585	Metagenome / Metatranscriptome	154	Y
F052031	Metagenome / Metatranscriptome	143	Y
F055847	Metagenome / Metatranscriptome	138	Y
F070251	Metagenome	123	Y
F080227	Metagenome / Metatranscriptome	115	Y
F080539	Metagenome / Metatranscriptome	115	Y
F080973	Metagenome	114	Y
F095729	Metagenome	105	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209455_1003683	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	5310
Ga0209455_1004631	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Alcaligenaceae → Bordetella → unclassified Bordetella → Bordetella sp. FB-8	4441
Ga0209455_1019431	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae	1373
Ga0209455_1019456	All Organisms → cellular organisms → Bacteria	1371
Ga0209455_1021638	All Organisms → cellular organisms → Bacteria → Proteobacteria	1243
Ga0209455_1028704	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Aeromonadales → Aeromonadaceae → Aeromonas	969
Ga0209455_1030542	All Organisms → cellular organisms → Bacteria → Proteobacteria	917
Ga0209455_1033850	Not Available	836
Ga0209455_1035075	Not Available	811
Ga0209455_1038916	Not Available	738
Ga0209455_1045627	Not Available	640
Ga0209455_1048550	Not Available	606
Ga0209455_1059853	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Beijerinckiaceae → Methylovirgula → unclassified Methylovirgula → Methylovirgula sp. 4M-Z18	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209455_1003683	Ga0209455_10036835	F080973	MVLAAATISMAYPTQGDVREMIAGAIGELTGTPAAEVDLGNSRVLVLTDTRSGYNWSYPDAMVKARFRPFVHRAVSMVRQQYPILR
Ga0209455_1004631	Ga0209455_10046312	F070251	MSAPGRPKRSFPPWGEGAQRQGGAMSAPGRPKRSFPLGGKARSAKGAI
Ga0209455_1019431	Ga0209455_10194312	F055847	MNRRYAYRDYAILVSAHPAAGARGWRPEICVIAPDDRWEFVPTHHSLVANDPQYCLEIGRLCAESAIQSMDPAREKAAYAGLLH
Ga0209455_1019456	Ga0209455_10194561	F040711	MHRGHSRSGALDLPDPSLLVEQALMSSDSSRDRLAAALGDDAKNVLMERGYSLGFVGVHGQVRLVQFRLSKKGFALDAAADDSDFATMLDEFTTLVTRLLMERWGGIALRAAFDAEGELVERLYETGTLDRCDEMDPVSPAKKLVKDGEQVDARELLVRASARLVEN
Ga0209455_1021638	Ga0209455_10216381	F027546	MKVAGETEPERWRPLGERVAHTPPAKPEWQPLPHAPCIEVNRQGQL
Ga0209455_1028704	Ga0209455_10287041	F080227	SGAFAADDGCRTNANGVQTCDVATGHESSRAAVVAEIHAKADTSTGCRTVANGVQVCDLPTGRERTREAVVADLHGGAGYAIEGCRTVANGVQKCDVPTPFAARRETTTAAAR
Ga0209455_1030542	Ga0209455_10305422	F052031	MTIDPPATHPAATEHHEEMVQFVFRSAASSGLLEHARALLGAAPRELAESFEQAVRSAGLAS
Ga0209455_1033850	Ga0209455_10338501	F035339	ADRLASAPLTLRQLRADRVVLWCWLPLGGFAMFAVVAGWRHLAGEPPPWLYTTLDVLWIAVTFTLIARRSTARCPRCNHRWLRAFPWMSLGKVECGVCGHEMPEG
Ga0209455_1035075	Ga0209455_10350751	F095729	MKLSFRQFALVSTLLATAAFPLLSHAQDVRREDRVLHFLDSGHIDANKDGMVSKKEFMDAMSKTWDMHMDDAKKAEPMMQKDKMTLQQ
Ga0209455_1038916	Ga0209455_10389161	F044585	MTPAEIDHQALTALRLLPDEPERAMRVWDDAFARATAAGLDRTLLRLRIVKMHHQARFGDRHALGPKMLAATVEARAHGWRTESLLVDLLEVFLATLSANHADGMGDVEAIRAEAEAHLDPIELSWMELMAGHFRGYMLGWALEPERTYRALNRLIACPDSPPGLVANVQMNIGHSHLLVGNVDLA
Ga0209455_1045627	Ga0209455_10456271	F031516	MNDIRNPSDVDMLHFDTAQMAAITQAHFFSRVAEFIRDQTTVPAYRQAALDTALRTSLWAPHWSTLRDATEHDAALFMCFLLACATLGVDATRAAEAVRQTSDPETSMKLFLSERGLLRFSAF
Ga0209455_1048550	Ga0209455_10485502	F023377	MTHRPVRLPRAFRMAMAATFALAAVGVQAMTVSYQCTGRRVLTAELTPRQGQLHFEGHDWTVRRVPDGHEARYVNKKDAVSVVTRERTMTFTHGDETLQCFLYSDALPGDAPQQKAN
Ga0209455_1059853	Ga0209455_10598531	F080539	LEGFDIRITGVYTKPRPFGFDFDCKRPRDLLVLARSKAVLNEDKDDTLEGAVSAEQTHGTGFRQIGTGPRLHLEIAMDRKCNVHIDSHGYVVGPGQYDWNRALEHGYWDLLSDKAPGLFGAFGKQGQVGPMIRPMQGVDGRMRWVIGLTGHW