2124908018: Switchgrass rhizosphere microbial communities from Rose Lake, Michigan, USA - BV2.2

Overview

Basic Information

• IMG/M Taxon OID: 2124908018
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0045398 | Gp0051776 | Ga0026480
• Sample Name: Switchgrass rhizosphere microbial communities from Rose Lake, Michigan, USA - BV2.2
• Sequencing Status: Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 8465840
• Sequencing Scaffolds: 15
• Novel Protein Genes: 15
• Associated Families: 15

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria	4
All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	1
All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium RBG_16_71_46	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	2
Not Available	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → Chthoniobacterales → Chthoniobacteraceae → Candidatus Udaeobacter → Candidatus Udaeobacter copiosus	2
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	1
All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → Chthoniobacterales → Chthoniobacteraceae → Chthoniobacter → Chthoniobacter flavus	1
All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Candidatus Brocadiia → Candidatus Brocadiales → Candidatus Brocadiaceae → Candidatus Brocadia → Candidatus Brocadia sapporoensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Switchgrass Rhizosphere Microbial Communities From Michigan, Usa
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Rhizoplane → Unclassified → Unclassified → Switchgrass Rhizosphere → Switchgrass Rhizosphere Microbial Communities From Michigan, Usa

Alternative Ecosystem Assignments

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

Location Information

• Location: Central Sands area of central Wisconsin.
• Coordinates
  • Lat. (^o): 44.166906
  • Long. (^o): -89.649965
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000283	Metagenome / Metatranscriptome	1379	Y
F000708	Metagenome / Metatranscriptome	926	Y
F002081	Metagenome / Metatranscriptome	596	Y
F003244	Metagenome / Metatranscriptome	498	Y
F017749	Metagenome	239	Y
F025162	Metagenome	203	Y
F026351	Metagenome / Metatranscriptome	198	N
F028279	Metagenome	192	Y
F040753	Metagenome / Metatranscriptome	161	Y
F051527	Metagenome / Metatranscriptome	144	Y
F053430	Metagenome / Metatranscriptome	141	Y
F062946	Metagenome / Metatranscriptome	130	Y
F065882	Metagenome / Metatranscriptome	127	Y
F073927	Metagenome	120	N
F104384	Metagenome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
SwRhBV22_Contig_2425	All Organisms → cellular organisms → Bacteria	714
SwRhBV22_Contig_2809	All Organisms → cellular organisms → Bacteria	772
SwRhBV22_Contig_2854	All Organisms → cellular organisms → Bacteria → Acidobacteria → unclassified Acidobacteria → Acidobacteria bacterium	560
SwRhBV22_Contig_2905	All Organisms → cellular organisms → Bacteria → Bacteria incertae sedis → Bacteria candidate phyla → Candidatus Eisenbacteria → Candidatus Eisenbacteria bacterium RBG_16_71_46	1685
SwRhBV22_Contig_3083	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	554
SwRhBV22_Contig_3109	Not Available	543
SwRhBV22_Contig_3123	All Organisms → cellular organisms → Bacteria	625
SwRhBV22_Contig_3171	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → Chthoniobacterales → Chthoniobacteraceae → Candidatus Udaeobacter → Candidatus Udaeobacter copiosus	603
SwRhBV22_Contig_3304	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia	558
SwRhBV22_Contig_3307	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → Chthoniobacterales → Chthoniobacteraceae → Candidatus Udaeobacter → Candidatus Udaeobacter copiosus	536
SwRhBV22_Contig_3396	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → Spartobacteria → Chthoniobacterales → Chthoniobacteraceae → Chthoniobacter → Chthoniobacter flavus	521
SwRhBV22_Contig_3399	All Organisms → cellular organisms → Bacteria → PVC group → Planctomycetes → Candidatus Brocadiia → Candidatus Brocadiales → Candidatus Brocadiaceae → Candidatus Brocadia → Candidatus Brocadia sapporoensis	520
SwRhBV22_Contig_3712	Not Available	520
SwRhBV22_Contig_6795	All Organisms → cellular organisms → Bacteria → PVC group → Verrucomicrobia → unclassified Verrucomicrobia → Verrucomicrobia bacterium	515
SwRhBV22_Contig_9576	All Organisms → cellular organisms → Bacteria	612

Sequences

Scaffold ID	Protein ID	Family	Sequence
SwRhBV22_Contig_2425	SwRhBV22_00064880	F000283	VEPNRRKIDDLKERHMNSTLVSRNVFLCAAAILIASCGTATFTKTGSDATIESLRSFHLAFIDQFAVPGKKFNATAFNAKVNEGNAKFQQAIADEKFTARRPVLVDLKAQFDADAAHLKSKASHGKITPALASEMKKDVNKIYDHALGR
SwRhBV22_Contig_2809	SwRhBV22_00140170	F025162	MKVGFLVSSISRKAGGLFQSVRGLAKAVASTNADVQVF
SwRhBV22_Contig_2854	SwRhBV22_00148920	F028279	MVLEEIFRALFEEIDTDKIRKEVDELRASAPDFSPKSHARRMARRTAIRCAAAGAVSGLPGGLVAIGTLGADLAYLVYQQFR
SwRhBV22_Contig_2905	SwRhBV22_00158050	F026351	MKIKIAVMMCAALGLPGVIFGQHHAPPATPTAEQSITGDWVIHFQAGHESVSGSLHLQADGERLAGTVETGHTGPGTVENGKWSKQKLEATLVFKKHESVVLEGELKSNGTLAGNYTTEGRTETWQAERKSARL
SwRhBV22_Contig_3083	SwRhBV22_00144060	F104384	YLIVFSKADLFKIAGSTAIAAIPLVSWVLLKNRSNAQIVTKFEPWLYVSHAMQMLGLGKLLSGPLAFTVVALPIYLLGCLGLRVIGIPAILTAIFRPRPEGALRFLLGIFVVIGVVIALTCSFTPAGWTFRYNPISSTFLVQSEYVAWIFAVEVFQTFYQWAIRRGMYPALAAGGIMVTAGGLS
SwRhBV22_Contig_3109	SwRhBV22_00001880	F051527	MDKHARYALAHPVFDPDRQITMGHFWAYNFRVTAGLTVNIGMG
SwRhBV22_Contig_3123	SwRhBV22_00004390	F003244	VKWKNRGDPKGKLGDERVRTKFAWFPVEADDGFTYWLAPVVVREQLLPKVTRGGFEDDEQTWHVVEA
SwRhBV22_Contig_3171	SwRhBV22_00014170	F002081	MKISNDDQRAIGLILFCVGVLAFLIGLAGHLKENYHYRGEISCTGFTIAIILAAIGVVLF
SwRhBV22_Contig_3304	SwRhBV22_00041090	F040753	MKRLTKISLTVAISGMVLLFKGSSPLVTTAIAQSQNTPQQQPAESTRDAPPDTTPYRRPAVREDFAPKGIRPIPLLPSLFIVDVVVNNTDPNLTNTDTFNDGET
SwRhBV22_Contig_3307	SwRhBV22_00041440	F065882	MLFGNVFATFGAAPSLALFLLSALYFIASLCVYVSLIYQISTRIRGASGADAPARAFGLPEA
SwRhBV22_Contig_3396	SwRhBV22_00058960	F073927	MLTQRSEGLRRLLLICQIWITAGLFWLGVWVMVKFYSPPGGLTWRRYSIYCVLLVLGLTLEYLGRDSSRDYPLQTDLLREHRVSLRQTVASIGTLVIYLIATKDGFISRVFLFNFVPCFYLALLFSHHYLPAFLARRFFKGIRAEKTLL
SwRhBV22_Contig_3399	SwRhBV22_00059410	F017749	GKRRSRDRHLQPSGDVLAYIARGRKGILRSMVAKYDLVKAAGLLDENHYYYDGFILTLRLAKLTPFVYLPDPLMEKRDHGGGASKGISFVEKERCFQDVLAEVMRVTVELPEKDKRAISKNWLEKISQLYFEAKMEEGNWSGAWMEIARRLVRDPRRIKASLKMARNILSRAG
SwRhBV22_Contig_3712	SwRhBV22_00120980	F062946	LASAAEGDSAVQGTPPQGAPSTPGIDRHELCKIQVWRWSMQNRTYEPTGEDLEIQRLRGSRINFAWSNESDRLVIVNARGTNEAECAFFQVGGTFLELVDRSRRLNEMKIVALAFATYHSGIAAVSVDSDTPALRNVKLFSFSGDYLEVIPVSGKDSIRLSEGFLPNGIGFGP
SwRhBV22_Contig_6795	SwRhBV22_00137700	F053430	LIVSPLTHRDGNYVGDYQLKVRPYFFKSEKGSLLLAASDDAVRKLQTGTAINFTGQALTHKDGRTHIVLGRATPSSRDRGSVTFSIVTDDARIVFNTSYHFGT
SwRhBV22_Contig_9576	SwRhBV22_00094670	F000708	MTKLDLALSQIAARFTQHDVEWSRGAFMIIDRRTTNPIARLRPIPDTDRFELFYWSNAKGRWTTFGNFGRMKLMLESAHEIVESDPMFRIPRGR