3300001430: Switchgrass rhizosphere bulk soil microbial communities from Kellogg Biological Station, Michigan, USA, with spike-in - S5

Overview

Basic Information

• IMG/M Taxon OID: 3300001430
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0090294 | Gp0057744 | Ga0003952
• Sample Name: Switchgrass rhizosphere bulk soil microbial communities from Kellogg Biological Station, Michigan, USA, with spike-in - S5
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 11154685
• Sequencing Scaffolds: 27
• Novel Protein Genes: 27
• Associated Families: 27

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	5
All Organisms → cellular organisms → Bacteria	2
Not Available	4
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	5
All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Solibacter → Candidatus Solibacter usitatus	1
All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	1
All Organisms → cellular organisms → Bacteria → Acidobacteria	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa
• Type: Environmental
• Taxonomy: Environmental → Terrestrial → Soil → Unclassified → Unclassified → Corn, Switchgrass And Miscanthus Rhizosphere → Corn, Switchgrass And Miscanthus Rhizosphere Microbial Communities From Kellogg Biological Station, Michigan, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): terrestrial biome → rhizosphere → bulk soil
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: Kellogg Biological Station, Michigan, USA
• Coordinates
  • Lat. (^o): 42.3948
  • Long. (^o): -85.3738
  • Alt. (m): N/A
  • Depth (m): 0

Associated Families

Family	Category	Number of Sequences	3D Structure?
F003139	Metagenome / Metatranscriptome	505	Y
F007622	Metagenome / Metatranscriptome	348	N
F009633	Metagenome / Metatranscriptome	315	N
F015371	Metagenome / Metatranscriptome	255	Y
F017759	Metagenome	239	N
F019351	Metagenome / Metatranscriptome	230	Y
F025757	Metagenome	200	N
F032294	Metagenome / Metatranscriptome	180	Y
F032686	Metagenome	179	Y
F033457	Metagenome / Metatranscriptome	177	Y
F033608	Metagenome / Metatranscriptome	177	Y
F040185	Metagenome	162	N
F042538	Metagenome / Metatranscriptome	158	Y
F049803	Metagenome / Metatranscriptome	146	Y
F058528	Metagenome / Metatranscriptome	135	N
F063749	Metagenome / Metatranscriptome	129	Y
F065229	Metagenome / Metatranscriptome	128	Y
F065246	Metagenome / Metatranscriptome	128	Y
F078898	Metagenome	116	N
F079360	Metagenome / Metatranscriptome	116	N
F081911	Metagenome	114	N
F083408	Metagenome / Metatranscriptome	113	Y
F084328	Metagenome	112	N
F087926	Metagenome / Metatranscriptome	110	N
F097858	Metagenome / Metatranscriptome	104	Y
F098258	Metagenome	104	Y
F099461	Metagenome	103	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
JGI24032J14994_100145	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	3376
JGI24032J14994_100158	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	3336
JGI24032J14994_100393	All Organisms → cellular organisms → Bacteria	2297
JGI24032J14994_100589	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1895
JGI24032J14994_100732	Not Available	1680
JGI24032J14994_100750	All Organisms → cellular organisms → Bacteria	1654
JGI24032J14994_101019	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → unclassified Alphaproteobacteria → Alphaproteobacteria bacterium	1312
JGI24032J14994_101130	All Organisms → cellular organisms → Bacteria → Proteobacteria	1214
JGI24032J14994_101369	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1035
JGI24032J14994_101504	All Organisms → cellular organisms → Bacteria → Proteobacteria	956
JGI24032J14994_101637	Not Available	890
JGI24032J14994_101709	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria	862
JGI24032J14994_101748	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	848
JGI24032J14994_101766	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae	837
JGI24032J14994_102299	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Hyphomicrobiaceae → Rhodoplanes → unclassified Rhodoplanes → Rhodoplanes sp. Z2-YC6860	687
JGI24032J14994_102327	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	683
JGI24032J14994_102567	All Organisms → cellular organisms → Bacteria → Acidobacteria → Acidobacteriia → Bryobacterales → Solibacteraceae → Candidatus Solibacter → Candidatus Solibacter usitatus	640
JGI24032J14994_102697	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Xanthobacteraceae → Pseudolabrys → Pseudolabrys taiwanensis	622
JGI24032J14994_102783	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	609
JGI24032J14994_103070	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	572
JGI24032J14994_103168	Not Available	559
JGI24032J14994_103239	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	553
JGI24032J14994_103247	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	552
JGI24032J14994_103382	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	539
JGI24032J14994_103443	All Organisms → cellular organisms → Bacteria → unclassified Bacteria → bacterium	534
JGI24032J14994_103492	All Organisms → cellular organisms → Bacteria → Acidobacteria	530
JGI24032J14994_103562	Not Available	523

Sequences

Scaffold ID	Protein ID	Family	Sequence
JGI24032J14994_100145	JGI24032J14994_1001454	F081911	NTGYIENPNQRAGSVIDNTSAGLLNTQSALPGPWTLPFKSNPWIGY*
JGI24032J14994_100158	JGI24032J14994_1001584	F033457	MRNXMSYVLASAFVVLLLAVVTPPGFGVAARPSIEGQRLAPQIVDRTRKSDQLPVPKATGRRLTPPAAPVLVGCDPVFSALSKDKQANYPGRCLA*
JGI24032J14994_100393	JGI24032J14994_1003933	F078898	MSAIGARQSGQISIPARTQNAVRRYRTMDLSKRQLLQEALAKAEAHHAYIAVSTPSGTRILLRPDFTCYETYVEGTGADGQLLTLTYEQIASVDVE*
JGI24032J14994_100589	JGI24032J14994_1005892	F040185	DNIGNSSPKAAQAVRRYRRVRLTALASIVAAVAWTSFCITTAFVRLDSANFGKWRDWLITADEPVMPLSDRLEAATAALREVSRGVPTPVVVVTDTIGAADSALPLSMKVTSYVPDTNIVLKGLAVGTTLTSGASVGDREWRINIEDLQNAYVIPPQGFVGPMAFVAELRDIDGHPLLRAPGQFTWTAVDPSSATAGKEPAEEEPPVTAVASAADAGNQQLIGQFVGQKEEVVLPKPRPIKHASLGGKATKPKKQIARAHGYKERMPRRDLGADTRWASNELPPHSLFSEPDRRRERRAIVDGIFRSLFYGGDANECEPATLERGTQKKSGDDCQWRR*
JGI24032J14994_100732	JGI24032J14994_1007321	F079360	GDLGTSWKEPLMRQTLTVAAIAVLVFAAIAELVAAPSRHAAGRDTSVQPTISTYDLHTGYRGMNTLPVAEIPQP*
JGI24032J14994_100750	JGI24032J14994_1007502	F097858	RTTMSTRYDISATERTAGNAGAAASLILGTLLLLIRP*
JGI24032J14994_101019	JGI24032J14994_1010191	F025757	RAPMSYSTSISLFWLEMAVLIGCVVLSIRMRSRAAMWVALAIVAHCAVWLAIHDEEILIRLVASALVYLGLLKFSPNAARVWLCAGGALAGAFLLGTMALSLLMSFPGRWSVFGLSMGATLLFLTSGLLIGFWVVYRWTDPTQLGDTQPRQEA*
JGI24032J14994_101130	JGI24032J14994_1011303	F084328	MRPKNAAPSVSDACPDWEAPAFTKLPIASRTGSGANVANDAPRAIEPEAPGQPLSKLGFSFEMSFPMSSRSE
JGI24032J14994_101369	JGI24032J14994_1013691	F063749	LLLERGDRPMKSLLVLVLALAATTAAAKPSPFEPARSANPIALARTSAGFNTGPAGATRERNYFRVPEADAHSGVFLCRFEPSMFAKVRLTQSCR*
JGI24032J14994_101504	JGI24032J14994_1015041	F009633	AAVADTRLKQALQVMATSNGVDATINKIETAFEGFEKDSLVIEEQDEFLQRREDLRHRVYELYAEFDSTAWWWARNIYDQARILHLISPARLDKLNQQIEQYNNNLVETAHAIDIPWHAYLGTNAVTHGSGAKEIMPSLTKQLRNLQQQRSEIAGNMAAXFQ*
JGI24032J14994_101637	JGI24032J14994_1016372	F017759	LFGVVVGLLNSECPQQDRAYESKYGADSQHIELQGKVHGSASLVDARRLARNQRRPKVPAIGPVLFAGEIAYRICAMDNRLIVRLKKSEEPKILTVQNSRGT
JGI24032J14994_101709	JGI24032J14994_1017092	F058528	FKRIGWKAKRDTSVNDVPDGLTVWPEDDVARAICNALTMATGALVAVREDQHLKDQGTYAIGVGYKLI*
JGI24032J14994_101748	JGI24032J14994_1017481	F032686	PVSEQGKGSLNGQDIELQGSWKAGNRQYEAKYSGAFVRRHADLKGTQTWTDGGKSFTRACTGTIKRPFRVFLPGEKK*
JGI24032J14994_101766	JGI24032J14994_1017662	F083408	PRPALLTKRGADVLVRVEKMMDDANRALGPVAPARPTVSSGKDKQAQVPDKGEALAASLEGRAFGSHD*
JGI24032J14994_102299	JGI24032J14994_1022991	F087926	AERREAEGPPIPIRFGDASEAVNYAQDHKFALYWKGTHAFAKRQRELGDRFVARPVFTRKGSTYVGLVPLDRQKKKA*
JGI24032J14994_102327	JGI24032J14994_1023272	F098258	LGAKTFLSYWDFKRLNRQAKRELGKALNNWPKKTPWNVAPRFHLSPPTARENKTNTLSQWYFLRSQPYYYIVLLSPFVCVGLLFFLAEGYVFLLCLHSWILFGTITILSKDASVRYLQPMSLLTILIFAAFVKALIDRRFQPTSIGIHERLDFERRRSDRQPFDSPPMQEKEA*
JGI24032J14994_102567	JGI24032J14994_1025671	F015371	QIPGDVPGPGTAGWTQYQTCLQQNLNVSPQQSAQIAPILASEGQKVIAIRKNNSLSNVQKTQEVKTLQNESDPQLKAILSSAQYDKLKAVRYQALRWITQKRLGWQ*
JGI24032J14994_102697	JGI24032J14994_1026972	F042538	MQFVSDYMKAIDFIALAALVVIGVVSFYRQGSILLLVAAIVVAIWGA
JGI24032J14994_102783	JGI24032J14994_1027831	F065229	LVQWLSGLSAIILSDAIPAMLLIRFAISVFALMLLGLAVSLSVAQSEDETNAAQAATFIHQ*
JGI24032J14994_103070	JGI24032J14994_1030702	F003139	KAKEAQARIHXNEXDRDQLKRAVKLNEVDSAKEVLLRNGFTAADLESAKITLRTGGGKGGEDELEISATCCDPKEITIQRSLEYFTK*
JGI24032J14994_103168	JGI24032J14994_1031682	F049803	MNSMKISNAARLIFWLAAILAIGILVRAECSEKRANMANTTSAPLRIVDQNGRPAINGVPSATSQIVDVMVGPGFTFSP
JGI24032J14994_103239	JGI24032J14994_1032391	F019351	HLLIFLVLGLLALPIYFLDRALLGPTGGNWITLDFRGLIFWSYITLVVVHVASSSTAIFLFPNAGPLRIQLGSMVLSVVLLIAGVAVYGKVRRLVMSNEYQALMESRRRLINVIELKEWSYFPDESHPTEIRVNVIVHQSGRFAGNVTGKQTDSSGSSKTIFESINGPESQRQVGSGEVFTYA
JGI24032J14994_103247	JGI24032J14994_1032472	F033608	MKKKSTSQSAFFNLRVLIAAVFCLAGVAVGLLAMGAVSSVFAQAKAAKTNQDAPGTQTPDVVRMVG
JGI24032J14994_103382	JGI24032J14994_1033821	F007622	QGARDEPLAKWNGNSIVAIWVAARWGMKDLAIYEIEADQIKRVQPVWRRVWLLFDQDFRERFLSKYPDEKGSGVIFVSKGGPDSKPEFEFKGHKMLLNLFADNKPDLSVTPHWTASLHAVWNLDTAELEHVHFQPGPIELRPNY*
JGI24032J14994_103443	JGI24032J14994_1034431	F099461	MTLLSVTKDVCAAVGVLIPPTSVFISITGNRTMQEMLSLAN
JGI24032J14994_103492	JGI24032J14994_1034922	F032294	GGRGGGGQLVEANVYINPRGGVEEDYPLHAHTRDFLDKMKAKNRKTNAPMEVGYNSALPALLALEAMKDNKVLGWDATARKSKAI*
JGI24032J14994_103562	JGI24032J14994_1035621	F065246	ERXFAIRPTPVVQQSADAGGLIDRQGCKSDKSVPRNANVRILVQSGAWSSVDIDEDGNADGQVKTADLTSNLATMPPWG*