3300003379: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co S PM

Overview

Basic Information

• IMG/M Taxon OID: 3300003379
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0110179 | Gp0089081 | Ga0008483
• Sample Name: Arabidopsis thaliana rhizosphere microbial communities from the Joint Genome Institute, USA, that affect carbon cycling - Inoculated plant Co S PM
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 13561632
• Sequencing Scaffolds: 20
• Novel Protein Genes: 20
• Associated Families: 18

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Archaea	11
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1
All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	2
All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae	1
Not Available	3
All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → Kallotenuales → Kallotenuaceae → Kallotenue → Kallotenue papyrolyticum	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → malvids → Brassicales → Brassicaceae → Camelineae → Arabidopsis → Arabidopsis suecica	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?
F005683	Metagenome / Metatranscriptome	393	Y
F010126	Metagenome / Metatranscriptome	308	Y
F011965	Metagenome	285	Y
F019548	Metagenome / Metatranscriptome	229	N
F023901	Metagenome / Metatranscriptome	208	N
F027009	Metagenome / Metatranscriptome	196	Y
F033614	Metagenome / Metatranscriptome	177	Y
F041299	Metagenome	160	N
F041834	Metagenome	159	Y
F048397	Metagenome / Metatranscriptome	148	N
F057150	Metagenome	136	N
F068880	Metagenome / Metatranscriptome	124	Y
F081936	Metagenome / Metatranscriptome	114	N
F089980	Metagenome	108	N
F096280	Metagenome / Metatranscriptome	105	Y
F098876	Metagenome	103	N
F099772	Metagenome / Metatranscriptome	103	N
F100589	Metagenome / Metatranscriptome	102	N

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI26142J50222_100183	All Organisms → cellular organisms → Archaea	2488
JGI26142J50222_100452	All Organisms → cellular organisms → Archaea	1436
JGI26142J50222_100591	All Organisms → cellular organisms → Archaea	1181
JGI26142J50222_100686	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrosopumilales → unclassified Nitrosopumilales → Nitrosopumilales archaeon	1085
JGI26142J50222_100764	All Organisms → cellular organisms → Archaea	1025
JGI26142J50222_100922	All Organisms → cellular organisms → Archaea	905
JGI26142J50222_101095	All Organisms → cellular organisms → Archaea	818
JGI26142J50222_101235	All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	759
JGI26142J50222_101386	All Organisms → cellular organisms → Archaea	714
JGI26142J50222_101480	All Organisms → cellular organisms → Archaea → TACK group → Thaumarchaeota → Nitrososphaeria → Nitrososphaerales → Nitrososphaeraceae	687
JGI26142J50222_101664	Not Available	652
JGI26142J50222_101848	All Organisms → cellular organisms → Bacteria → Nitrospirae → unclassified Nitrospirae → Nitrospirae bacterium	615
JGI26142J50222_101996	All Organisms → cellular organisms → Archaea	592
JGI26142J50222_102062	All Organisms → cellular organisms → Archaea	583
JGI26142J50222_102258	Not Available	563
JGI26142J50222_102262	All Organisms → cellular organisms → Bacteria → Terrabacteria group → Chloroflexi → Chloroflexia → Kallotenuales → Kallotenuaceae → Kallotenue → Kallotenue papyrolyticum	563
JGI26142J50222_102664	All Organisms → cellular organisms → Archaea	526
JGI26142J50222_102839	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → malvids → Brassicales → Brassicaceae → Camelineae → Arabidopsis → Arabidopsis suecica	514
JGI26142J50222_102863	Not Available	513
JGI26142J50222_103045	All Organisms → cellular organisms → Archaea	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI26142J50222_100183	JGI26142J50222_1001835	F081936	LLDRKLNAKKPSPPNVEASVNPKVEQLAHVLEITLIVVPDSADLLNFNFRFLIIYRLKFTKIAIRTELIQVKINASIISLGT*
JGI26142J50222_100452	JGI26142J50222_1004523	F005683	MEKSNGTKIMGILLVFXLVVYSIYFGQISFAEGVELKTVGKGAISCGNGEEVKGVRINFFVSYDEETPFAEWNMDHKELGSAGGMITNVKTSSDSFVLKGFEAFDSICDVETPSDVKLSGNCGEGTVRLVSDNGNKGTFASNVKCG*
JGI26142J50222_100591	JGI26142J50222_1005913	F048397	RTILEKNKCDKCNLTIHPNFIGNHKCDHQNCPICKNPITPSQYWPHIRSHPGHENDSPPLPKRNMYENRKNENHSGYGNYQRN*
JGI26142J50222_100686	JGI26142J50222_1006861	F041299	MQKFKPLILGIVCFLIGETFYFYQQYFLQIDIPYPSVADVPYLLASFFFSYFLISCVFSLLDRKNLSPLPIILGSPIAIFPIYVTLSSAYDLAINESTELEFIVNALYYIFDGLMLVTAVIIILNLKKYDPFIFHWICITVGLILLVIGDVGYTYFSIISESLIEEYEWLWSILYAIGYLFLGIGIYWFDRIKNTLEDKKINVFLEKDEMDRLKNSSKNELIADTGTEFSEHIIGYEKFVDKLKDYLERSKEIKILFYDKYWLSDEEVNLILEKIQQGAFFTQIQVNILLPSSETIFKNLVSHNDNRHILVSFFDRTFSSDSLVFIFEEKYVAIIDRKPTSESVDSDTVFYGLITNXDTI
JGI26142J50222_100764	JGI26142J50222_1007641	F010126	MNLFTSRLLTICGLISTALLFQIMISSNLVVAIESSESNTNKISSGSELESIVTNGSSTNQLAYRNSQHGIFMLFPSNWTFSNSGLPEYTQVAAFYGPLQNLSDPIPPRLTITVMNYQQNVSLKDFTNMTLSSLNQTNQVKILSSEPTTLAGQPGYQVVFSTLPNIGNPVSFEIMHSWISMGKKIYVLQYSAESSKFDTYLPTIKQILQSLRIDTTR*
JGI26142J50222_100922	JGI26142J50222_1009221	F089980	MDLESIIELIVMNWLGIFSLIATIIIGFTTIRYRNKQHQINGLLDAFRILNTREHRTSRRKVYDLYIEYEKNKDVRTFDNSPEVVDVRADFDVIGTLVKSGNINEKLFLIEYGPLAYRCWKYLKNHIEAERKKRNFDPFMMNFESLA
JGI26142J50222_101095	JGI26142J50222_1010951	F027009	SKMEADIIAEYFKKSKQNLQSEHDSMIQDVKQDISSYKKKALSNA*
JGI26142J50222_101235	JGI26142J50222_1012351	F033614	STALKLHGPWGTSYWLEFNPSTFKVGDGSSRPTLHPLSFDVKWEWSAVDPNIIYFINGTQLAKYNKSTHVVTNLGGRGVSLKYHVVVVGLDAWVCAAGPGTQNTYRQIFCLNPRNPSQTKFIDILKRTINGVYQSDPNWPTSAPYQTIGIHAMYGSATGTWLDVGFHRASWGAGGDSVFNLSTNKWSLLKANRYSSGHSSIGTRFVNGSGSINGMYSGGACVRNPSNLMDATRYTFIMQPPSAATGWHDGEH
JGI26142J50222_101386	JGI26142J50222_1013862	F023901	SCEGGLPLDPNKFGGYEFAINTKGWDAKREPTHNCHDQHKSGLIPTNLENDKAVRLRQTVKDESGKVHQIGEIDYMDGNGFHKVMDIFDSSPNPWMVDRNLYETKSYFWIRNNGSGYITVRDVSLEILS*
JGI26142J50222_101480	JGI26142J50222_1014802	F048397	VKDSTIFRTILEKNKCDKCNLTIHPNFIGNHKCDHQNCPICKNPITPSQYWPHIRSHPGHENDSPPLPKRNMYENRKNENHSGYGNYQRN*
JGI26142J50222_101664	JGI26142J50222_1016641	F019548	MNPSKKEIYKILERFTSQKGGILIILHNSFSSDSKPPQEQTSVVRDDERKSAIFEINFGTVAGLSMLCECEKALADQVMSLDFLDSGIEGDVIWFGGMLDKSGSEFIGSTYDDGLKSAPVEQSELVHRVNQAIDKCLEYMLNSVELDKKVYVDASDRMSGYVKLTRIGEHILEKYPDLFRDNTKSE
JGI26142J50222_101848	JGI26142J50222_1018481	F011965	NPSQTKFIDVLNKTINGIVQSDPKWPTSAAGQTIGIHSMYGSAAGTWLDVVFLQQSWGANGDSVFNLATNTWSLVTNSDTRWSGHSSMGNGKYVNGSGSINGMDSRGALLRDPNNLMDTTKYSFIMQPPSTAGWYDAEHSSWFNSSTNPQAPVLFSRYNCTAPPGPLTWYGEIIAAATDGSNTVWRFAHNHNGGLVGFAGQSFAQ
JGI26142J50222_101996	JGI26142J50222_1019963	F068880	KGVLESADRLTFGNSNYGYRYFLNLSFPSKLLDSSSGLIPKNEFLSKIPEGYDVPFKGMLIITQKHKELYAIIFLNPKEKFDSMLNQIQPTLDSIQLSG*
JGI26142J50222_102062	JGI26142J50222_1020621	F057150	MFKMKHMKIAIFVLAVSILGTSALIVNSGNMAYAQGNNTQGNVTTTIDADSLIKDLKARHPILAQLVTNEDKDLVVKFKDLDTKEAVKTAL
JGI26142J50222_102258	JGI26142J50222_1022581	F027009	MVASKMEADIIAEYFKKSKQNLQSEHDSMIQDVKQDISSYKK
JGI26142J50222_102262	JGI26142J50222_1022621	F041834	VNDYLIKPGSRSGFDIFLDETLPSKSKYALTTSFEKSEDDKPEVLQLSVGKNSKSSNTFRVLGEVMNQGKNDANAVKVSAIFYDEKHKVMDTDYVFTNPDIISPNKKAPFEFSFYVDNPEKIKSMAFNVQSDEXSXITDNGQNNTISQQ*
JGI26142J50222_102664	JGI26142J50222_1026641	F100589	WKLGELSPVEASKYLVNRKQDECRVSYDHNNVEYILRVMALMFMSWSVTNLKRKTQNGHCQNIDHPHGDTNPRLCKEGTIFHQDLYNECVKTFKDLLIHSDAQHH*
JGI26142J50222_102839	JGI26142J50222_1028391	F096280	VRRHKAKDSYRLWLQHEIFETQEEGWLVFWSRIXLDVMCMIVYKNLNRNPIL*
JGI26142J50222_102863	JGI26142J50222_1028631	F099772	MFRTFGQSFFLLLLTVCAVQLMGTACADDCLRQWSTSPVHAHDQLPGSPDGQTETDPGEGEFEELALAQGEAFRIIHLARACVLDNASCPRT
JGI26142J50222_103045	JGI26142J50222_1030451	F098876	LSKDVIEPVMRKFESYLESKDVNSSVHIQSQIVAGKNPSIEFSLHLKLTHESRYPNIKFSSSGEKISVQEDRLMTKDEVSQDMIPEYYDKELITEEFVKERLIRXIKSCFDKDWQSFYS*