3300003399: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 PM

Overview

Basic Information

• IMG/M Taxon OID: 3300003399
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089075 | Ga0008477
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant M2 PM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 10787973
• Sequencing Scaffolds: 14
• Novel Protein Genes: 14
• Associated Families: 14

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	5
Not Available	4
All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. KM1	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Desulfomonile → Desulfomonile tiedjei	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Hahellaceae → Hahella → Hahella chejuensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Epiphytes → Unclassified → Arabidopsis Thaliana Rhizosphere → Arabidopsis Thaliana Rhizosphere Microbial Communities From The Joint Genome Institute, Usa, That Affect Carbon Cycling

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Joint Genome Institute, California, USA
• Coordinates
  • Lat. (^o): 37.931388
  • Long. (^o): -122.021761
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F005950	Metagenome / Metatranscriptome	385	Y
F006408	Metagenome / Metatranscriptome	374	Y
F010272	Metagenome / Metatranscriptome	306	Y
F020942	Metagenome / Metatranscriptome	221	N
F023901	Metagenome / Metatranscriptome	208	N
F045401	Metagenome	153	N
F057496	Metagenome / Metatranscriptome	136	N
F059733	Metagenome	133	N
F071574	Metagenome	122	Y
F076440	Metagenome / Metatranscriptome	118	N
F078854	Metagenome	116	Y
F086321	Metagenome	111	N
F087425	Metagenome	110	N
F087678	Metagenome / Metatranscriptome	110	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26136J50244_100514	All Organisms → cellular organisms → Archaea	1324
JGI26136J50244_101018	All Organisms → cellular organisms → Archaea	896
JGI26136J50244_101025	All Organisms → cellular organisms → Archaea	894
JGI26136J50244_101244	Not Available	802
JGI26136J50244_101355	All Organisms → cellular organisms → Archaea	765
JGI26136J50244_101673	Not Available	688
JGI26136J50244_102054	All Organisms → cellular organisms → Bacteria → Nitrospirae → Nitrospira → Nitrospirales → Nitrospiraceae → Nitrospira → unclassified Nitrospira → Nitrospira sp. KM1	634
JGI26136J50244_102491	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	582
JGI26136J50244_102531	All Organisms → cellular organisms → Bacteria → Proteobacteria → delta/epsilon subdivisions → Deltaproteobacteria → Syntrophobacterales → Syntrophaceae → Desulfomonile → Desulfomonile tiedjei	578
JGI26136J50244_102542	Not Available	576
JGI26136J50244_102584	Not Available	572
JGI26136J50244_102845	All Organisms → cellular organisms → Bacteria → Proteobacteria → Gammaproteobacteria → Oceanospirillales → Hahellaceae → Hahella → Hahella chejuensis	550
JGI26136J50244_103008	All Organisms → cellular organisms → Archaea	538
JGI26136J50244_103421	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Rokubacteria → unclassified Candidatus Rokubacteria → Candidatus Rokubacteria bacterium	510

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26136J50244_100514	JGI26136J50244_1005142	F023901	MRSRHNEQGQSCEGGVPLDPXKFGGYEFAIXTKGWDAKREPTHNCHDQHKSGLIPTNLENDKAVRLRQTVKDESGKVHQIGEIDYMDGNGFHKVMDIFDSSPNPWMVDRNLYETKSYFWIRNNGSGYITVRDVSLEILS*
JGI26136J50244_101018	JGI26136J50244_1010181	F005950	MTNGKNRIKVKIHRTSDYDDKYTGIRDFPDEKAMLQYGLSKVHKVIIRKYTEDDEFIARAQKTRGIK
JGI26136J50244_101025	JGI26136J50244_1010251	F057496	MAGVYRNHTKVAEDHSSAYCKDEYVFGDKGEPLRLSHLIAFNVIEDAEHISGILTVEFDYYSDDDSIKYRDMHYSNPRLIKHIEGNPTVMK
JGI26136J50244_101244	JGI26136J50244_1012442	F078854	LSPRFGFFKRKTSDNIQDKESEANSVYSVSNKELLEIVEKKKKVLEKDLIDNLEPTRNLVLECLDRLRKNADELEEQEIKAESPQFESLINTSKKILITSIKKESLIESYQIKSYEDAIKFKNNLELLI
JGI26136J50244_101355	JGI26136J50244_1013552	F010272	MNHERKLILIAIGAFVTLSLFVFPSTNMIAYSQSENKTQGKEQAQEKLFELAQKFNKILKDSNVNLTLPQNGDLSSKLQELKDSGAFKELSEKFSQAVQELGQGNKTEELKQEAGADLSKLMQKLQSLRNNSTQ*
JGI26136J50244_101673	JGI26136J50244_1016732	F071574	MPKMRTNYHYRGRIITLLPRMEGYMWTCQYVILKAGKTEIDGSPAKTYFSREEAESAAFTMAKTFIDQCQ
JGI26136J50244_102054	JGI26136J50244_1020541	F045401	MMPLPARVWTSGSVLLPAFAALLVTLSCSQLVYQPGAVVPTASPLPYSAMVRLTEIEAYQVEPGATMVADPRIENKVTGIAQPVSKAKKDWERSIADYLAARKTFTYLSTDSQTDLDLTMRLHIYIDPSVDSDFHHVYVARIDATLAEASGKRALSKYIGF
JGI26136J50244_102491	JGI26136J50244_1024911	F020942	PEVHIRKVDALGDRAHAAWRFGEVFLHNFVPRYLVSELFQPYPRGPYMGSLTAFGPGGNAWLSLWDDRARRGLDPGSVRAVKAYDVTLKGRGGFRAFSAIAATLHEAGLDHLLMPIPHDVNARALIDPFVSDLVEFNFCVKRLNGAAPVPSGPIYFDIRH*
JGI26136J50244_102531	JGI26136J50244_1025311	F087425	MTCAIYAKNATKQQRIGNVMRYVLILALMVLSHVDTAARAGRVEDRESLRRLPGVEVIVETFLSEEEAAGFSREAIRTGVELVLQSNGIRILSASERLQTSSAPFLYVKVNPLKHSSADTFCLAIEVELHQAVSLLNRPEQKMSARTWNRVQVAMIGDQITGRVTEVVEPLIKQFANDFLTVN*
JGI26136J50244_102542	JGI26136J50244_1025421	F086321	MNPSKKEIYKILERFTSQKGGILIILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSGIEGDVIWFGGMLEKSGSEFIGSTYDNGLKSAPV
JGI26136J50244_102584	JGI26136J50244_1025841	F087678	LATPPPDQAGFYWFRYDNLSSHVHFKVLLQVIQMQPKATEIGGKFVVRWFNQLVPLEQVPEGLWRGPVRDLR*
JGI26136J50244_102845	JGI26136J50244_1028451	F076440	MEKRMQISPGRNWSEGAGDRADQHFEIWYGEEERKDTLVARVWATKDGPHSVELYRKSSLIEPVRVRVLEGLMRELDFYLMKDERDVPRYLMHHCSMASHVYSPYGW
JGI26136J50244_103008	JGI26136J50244_1030082	F059733	DDLLEGFGSTDLEFAFSDFYKHRITDDLKFEYKTIQPPSLLEIDGHKTGSFHIMFSQKDEIDPISGEVQYWITFVGENGYMIEFLSIPENFDTPDNTEMRDRFISSINFLGLSNTTDTSGRISSVAMSY*
JGI26136J50244_103421	JGI26136J50244_1034212	F006408	GTRRTGGNMAAECLTLHHGGLRGGGRGWRAERCATPESCELHLCIADGDGGFWHPDDPLAFAKWRIRADLDAVPAHVMVNVSRSWDMLRRAAVVTAVGLGGTVAVLGVLWGRQRRFSMKTLSGSGA*