3300032888: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_NF_05JUN2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032888
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330582 | Ga0314728
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_NF_05JUN2017_LR1 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 27984871
• Sequencing Scaffolds: 18
• Novel Protein Genes: 19
• Associated Families: 16

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum sect. Hiantes → Panicum virgatum	3
All Organisms → cellular organisms → Bacteria	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum	2
Not Available	6
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Andropogonodae → Andropogoneae → Tripsacinae → Zea → Zea mays	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fagales → Fagaceae → Castanea → Castanea mollissima	1
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum miliaceum	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Phyllosphere Microbial Comminities From Bioenergy Crops Switchgrass And Miscanthus From Michigan, Usa
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Phyllosphere → Unclassified → Unclassified → Switchgrass Phyllosphere → Phyllosphere Microbial Comminities From Bioenergy Crops Switchgrass And Miscanthus From Michigan, Usa

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Unclassified

Location Information

• Location: USA: Michigan
• Coordinates
  • Lat. (^o): 42.3951
  • Long. (^o): -85.3736
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F001705	Metagenome / Metatranscriptome	648	Y
F007513	Metagenome / Metatranscriptome	349	Y
F009114	Metagenome / Metatranscriptome	322	Y
F012944	Metagenome / Metatranscriptome	275	Y
F023769	Metagenome / Metatranscriptome	208	Y
F032517	Metagenome / Metatranscriptome	179	Y
F034039	Metagenome / Metatranscriptome	175	Y
F042712	Metagenome / Metatranscriptome	157	Y
F047420	Metagenome / Metatranscriptome	149	Y
F049431	Metagenome / Metatranscriptome	146	N
F062397	Metagenome / Metatranscriptome	130	Y
F067332	Metagenome / Metatranscriptome	125	N
F069562	Metagenome / Metatranscriptome	123	Y
F069582	Metagenome / Metatranscriptome	123	N
F070755	Metagenome / Metatranscriptome	122	Y
F074257	Metagenome / Metatranscriptome	119	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314728_100487	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	2259
Ga0314728_101761	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum sect. Hiantes → Panicum virgatum	1575
Ga0314728_106619	All Organisms → cellular organisms → Bacteria	929
Ga0314728_107580	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum	872
Ga0314728_111208	Not Available	707
Ga0314728_111605	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Andropogonodae → Andropogoneae → Tripsacinae → Zea → Zea mays	694
Ga0314728_111644	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fagales → Fagaceae → Castanea → Castanea mollissima	692
Ga0314728_111806	Not Available	687
Ga0314728_112083	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum	679
Ga0314728_112098	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	678
Ga0314728_114537	Not Available	612
Ga0314728_117119	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum sect. Hiantes → Panicum virgatum	556
Ga0314728_117536	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum miliaceum	548
Ga0314728_117824	Not Available	543
Ga0314728_117930	Not Available	541
Ga0314728_119436	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	516
Ga0314728_120363	Not Available	503
Ga0314728_120422	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum sect. Hiantes → Panicum virgatum	502

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314728_100487	Ga0314728_1004872	F001705	VTWDESVERDLKVWNIFKEIALDMSAWKLAINVPEP
Ga0314728_101761	Ga0314728_1017611	F032517	MNLSLSSSSFDKIINPYYEFLGLYGGGADDLVERRGGGGIPSVNLMEELLGSLIPPRSNMSLLGAGLSSSMLRGDSETECLREELADASDVDERVLLLPVTNLMMPLMVTPYCTH
Ga0314728_106619	Ga0314728_1066191	F047420	VNIAEKDLADLAFNGLRSHIKERLEGYDFFTVTQVHQKVFAIESRSKKPQESHRHHRSSVHILECNSDCSDDESKDVYAAEFAWPSQAKPFTCSALKPIQKNR
Ga0314728_107580	Ga0314728_1075802	F007513	VVVTVLQRVVALPVVLLVVFSTAMDHETEALEEVLRLHAFLVVVFVSHAVDGMGDTLCLVLLTLL
Ga0314728_111208	Ga0314728_1112081	F069582	FIGIACLLSVINIRTTDGVVFDIMTLCETPSVLMNLLRSRCVVALVKFLNVLATCRKYGT
Ga0314728_111605	Ga0314728_1116052	F042712	MEYLFDESGRQKFLQLLADRPALELVEASQALLHRLGVGSDIKRVLGDLPRYARHVRGAPRKDICVGAEEIDEHHFLFVVEGGADLQHLAVGVARVE
Ga0314728_111644	Ga0314728_1116441	F049431	HMTTGRINQVTILSPSAEAHERTPRRRPGCTGRKGRRRSEPQPQASEVCETPKPQATDSIAPTEFPKLRSATGGIRLLHRSLHRYIRPSGGEDSRQVNAQARVLDRAIPEDLVKRLAKPVIHRPQMLPANRETSRTSVPSTSTLQLPEGGQHRASRKESPSPK
Ga0314728_111806	Ga0314728_1118061	F067332	MPPSIHVYCHIIMLANFGEDEIRRACIIISSCVEFLVVFLVHSILTRSLRAYIAVLKFCAALLSIQLLAIQIIFLEKLDYEKDMRNYRFTYYRNFNDLRGMFIWISRLNLALDPVPSMLIVTTQ
Ga0314728_112083	Ga0314728_1120831	F007513	MEVRETVVVTVLQRVVALPAVLLVIFSTAMDHRTEALEEVLRLHAFLAVVIVSLPVDGTGDMLCLTLHTLL
Ga0314728_112098	Ga0314728_1120981	F023769	KETLLTWSMPCADLHKNAFQRSSSRVAHVTRPVDNSTSGSTVKRCRDCLRGERDTKETIHNGLLLLRVRYGLPYAELPDCGPGDLSRFLSFLLLQGKERTSVAFPRRQRPGENGLCTMQRLCRRDRWALAHGCSSIKRNLPKGCFRHTPSVFAAWEAAALSQPPPLTSGYIEHVRRVVTGIFQPGWDKNYRSFVGSHVPNPSARACMTRADVLWRRRRDEFFTATT
Ga0314728_114537	Ga0314728_1145371	F009114	MVPFQMYSSFKFYLSNEVSNELLPETKVVDLEILNNF
Ga0314728_117119	Ga0314728_1171192	F069562	MGNYLTNLPLIALLLLDLLNSNLGPQLCESNAPKWLGEDVPKLSSCLDILELDLSTVDAITDEVILGVDVLAPVVVDMVLC
Ga0314728_117536	Ga0314728_1175361	F074257	MGGVRIPVLFHWRESAEYDRAEFFSPKGKRVGVGSEKDKFSISLAISGRRISAELISPSCSRRAVSVLAGSIRWLEKPPDPLAMQTHEPNTKVVPALITGKLNSKDAIEFFC
Ga0314728_117824	Ga0314728_1178241	F062397	MCMNGLRINMVLGPFFGLWPSSFSVLALDHGPRHFMLKNRPKTCKNEVPPKYMCKCENDQ
Ga0314728_117930	Ga0314728_1179302	F034039	VQCLKVLGLNLRDPAVVVPDGVQVVANTTLDSVVVFHLTALADHVSPLVVIAFLKWDLACLVFFLTLFQGI
Ga0314728_119258	Ga0314728_1192581	F070755	VAAPTSSAHSAEAPEIWLPLEVVGTKVVYIPSGAVLTYNLTAVAEADMWSDTVLVGTPADADKAHEGVRPESDETSD
Ga0314728_119436	Ga0314728_1194361	F001705	VKRGRGRPKLTWDESFKRDLKDWNISKKIALDRSAWRLAINVSEP
Ga0314728_120363	Ga0314728_1203631	F069582	SFVGIACLLSVINIRTTDWVVFDIMTSCETPSVLMNLLRSRCVVVLVKFLKVLVTCRKYGTRQA
Ga0314728_120422	Ga0314728_1204221	F012944	EIEAKLEDNSSSTRTMIIFKPKPTRVGTLLAQPVFGLHNSSSAYKQMIGSIYENSLDHLLCGKNHSVTASREAPIFDIYPDPVESSQDSLDFITNALVKIQLESCESHTLAELLDNLRKVASIDDLPFQHSTPLVTERETRSGGTILADYESDMESFSPERLVPVII