3300032759: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_NF_15MAY2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032759
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330574 | Ga0314720
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_NF_15MAY2017_LR1 (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 65433157
• Sequencing Scaffolds: 28
• Novel Protein Genes: 32
• Associated Families: 30

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	2
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 → PACMAD clade → Panicoideae → Panicodae → Paniceae → Dichantheliinae → Dichanthelium → Dichanthelium oligosanthes	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	6
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	3
Not Available	12
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Oryzoideae → Oryzeae → Oryzinae → Oryza → Oryza sativa	1
All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Flavobacterium → unclassified Flavobacterium → Flavobacterium sp. SaA2.13	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

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?
F000392	Metagenome / Metatranscriptome	1188	Y
F000459	Metagenome / Metatranscriptome	1109	Y
F002974	Metagenome / Metatranscriptome	516	Y
F007513	Metagenome / Metatranscriptome	349	Y
F012546	Metagenome / Metatranscriptome	279	Y
F018302	Metagenome / Metatranscriptome	235	Y
F023028	Metagenome / Metatranscriptome	211	Y
F026180	Metagenome / Metatranscriptome	198	Y
F027090	Metagenome / Metatranscriptome	195	Y
F028072	Metagenome / Metatranscriptome	192	N
F030332	Metagenome / Metatranscriptome	185	Y
F031344	Metagenome / Metatranscriptome	182	N
F035610	Metagenome / Metatranscriptome	171	Y
F036531	Metagenome / Metatranscriptome	169	Y
F040424	Metagenome / Metatranscriptome	161	Y
F040444	Metagenome / Metatranscriptome	161	Y
F046814	Metagenome / Metatranscriptome	150	N
F049431	Metagenome / Metatranscriptome	146	N
F055475	Metagenome / Metatranscriptome	138	Y
F060529	Metagenome / Metatranscriptome	132	Y
F065366	Metagenome / Metatranscriptome	127	Y
F067332	Metagenome / Metatranscriptome	125	N
F068338	Metagenome / Metatranscriptome	124	Y
F074257	Metagenome / Metatranscriptome	119	Y
F085057	Metagenome / Metatranscriptome	111	Y
F088054	Metagenome / Metatranscriptome	109	N
F094644	Metagenome / Metatranscriptome	105	N
F096411	Metagenome / Metatranscriptome	104	Y
F100243	Metagenome / Metatranscriptome	102	Y
F104214	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314720_1002631	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	1807
Ga0314720_1010496	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	1110
Ga0314720_1011178	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae → Dichantheliinae → Dichanthelium → Dichanthelium oligosanthes	1080
Ga0314720_1012682	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	1025
Ga0314720_1012882	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	1018
Ga0314720_1014685	Not Available	958
Ga0314720_1020305	Not Available	820
Ga0314720_1021141	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	804
Ga0314720_1023044	Not Available	769
Ga0314720_1025753	Not Available	725
Ga0314720_1029970	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	668
Ga0314720_1030243	Not Available	664
Ga0314720_1030567	Not Available	660
Ga0314720_1032610	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Oryzoideae → Oryzeae → Oryzinae → Oryza → Oryza sativa	637
Ga0314720_1032787	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	635
Ga0314720_1033699	All Organisms → cellular organisms → Bacteria → FCB group → Bacteroidetes/Chlorobi group → Bacteroidetes → Flavobacteriia → Flavobacteriales → Flavobacteriaceae → Flavobacterium → unclassified Flavobacterium → Flavobacterium sp. SaA2.13	625
Ga0314720_1034285	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	619
Ga0314720_1037710	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	585
Ga0314720_1039130	Not Available	573
Ga0314720_1039764	Not Available	568
Ga0314720_1040891	Not Available	559
Ga0314720_1045237	Not Available	527
Ga0314720_1046064	Not Available	521
Ga0314720_1046357	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	519
Ga0314720_1046740	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	517
Ga0314720_1048002	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	508
Ga0314720_1048150	Not Available	507
Ga0314720_1049290	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fagales → Fagaceae → Castanea → Castanea mollissima	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314720_1002631	Ga0314720_10026312	F028072	LNLEVNTGKTVSTKKNINIRCRINSSEEHTWHTSHGQINLIVDLIHNFYITWGKRQDDLELKFERLQKEHKHLEEQYLVANKKLELALQAFEESKIFLRKISQNSDYIKRDISYLFNKLESTNIAEHSKEIVLSSSGILEVTRSLNSDK
Ga0314720_1010496	Ga0314720_10104961	F074257	MGGVRIPVLFHWRESAEYDKAEFFSPKGKRVGVGSDKDKFSISLAISGRRISAELISPSCSRRAVSVLAGSIRWLEKPPDPLAMQTHEPNTKVVPALIAGKLNSKDAIEFFC
Ga0314720_1011178	Ga0314720_10111783	F100243	SFGRLRGFLLKASREIIVSRADVVSGSVLARKCVPPHGTVVVGGKW
Ga0314720_1012682	Ga0314720_10126822	F065366	MLAVQLLVPSGCRWKSSIDVTVVVEFASRIQDLVQNESGELLAHGVDPISRVTFIPHLRHLSFRKKTLTLCALVQL
Ga0314720_1012882	Ga0314720_10128821	F007513	VALPVVLLVVFSTAMDHGTEALEEVSMLHAFLAVVFVSHTVDGTGDTLYLTLLTLL
Ga0314720_1014685	Ga0314720_10146851	F104214	MWSMYCIEALGRLYRTTWLGGQVASPRDKEGYPGITTNPKLTISGVA
Ga0314720_1020305	Ga0314720_10203051	F067332	SIHVYCHIIILANFGEDEIRRACIIISSCVEFWVFFFLVHPILTHSLRAYIAVLKFCAALLSIQLLAIQIIFLEKLDYEKDMRNYRFTYYRNFNDLRGMFIWISRLNLALDPVPSMLIVTTQ
Ga0314720_1021141	Ga0314720_10211412	F040444	VTLDGLNGEAELSGHPGKEVEEGGEGLRLGAQRKSPRVMRKIINNDQIIFIARHAEYRRCPQVTVNKIKSMRSMRRRRRKRKSNMTT
Ga0314720_1021587	Ga0314720_10215871	F094644	MKFIFLLXALRYQRYHSGIWHHCYCCSMPTKCSLHSGYCHTCALRLLCNSNTWILQIXGKDIHLPFASPSSGFQQRMXYCQNHKXLFTHSFIKDLRSMAIYIRMDALECGYHFPSENDQVXQISHFNKSVIVQIHEHRNAKSNIWLNYTSNSLETSEFFGIFXSSLQQATLEKVHISIGNNISLNSYYHMWYVVHYKNSMYLRHDIHILLPCLYMGFNQ
Ga0314720_1023044	Ga0314720_10230441	F000392	MKTHIEYPDIFFXKYNSPYHFEMGTYVFINLLXAGGSVAPAQPTSLRXNXGIFAQTYSTCLEGPYRRDSSGAHPCRTIDMAXEPRIPSPCSLKAITHATGSKIGSSRSRWNRGTEYYPVGMKTHIEYPDIFFXKYDSPYHIYMGTYILIDLLXEGGSVAPAQPTSLRXN
Ga0314720_1025613	Ga0314720_10256133	F002974	GRPKLTWVESVKRDLKDWNISKEIALDRSAWRLAINVPEP
Ga0314720_1025753	Ga0314720_10257531	F027090	LFQDENALGPRLKPDKEYVHSWVTKEGQIISHDYRRNEISPDEPLLQPCLTIFGVRPPARAEDCQDKSEMRALSYELTKAHMANIRLDTSQQRLREEVREMQGDLDLYLEFLDERMDRLAKALGIQNFE
Ga0314720_1027369	Ga0314720_10273691	F000459	VRSGVLKRVDKVKRGRGRPKLTWDESVKRDLKDWDISEELVLDRSAWRLSINVPEP
Ga0314720_1029970	Ga0314720_10299701	F030332	MDLREQLAALFLGNAPHEDTIGATAVEIPFYHRVAFSQSYYALSGYIIFRKDVVFQVVPDLGDPCIGTSLSNWGWPYEVSGILGSAHDPWRAPRMECRRDH
Ga0314720_1030243	Ga0314720_10302431	F026180	VHPTARHSAADCREIQKLAKRVSGRREQSSKDDSPPPRQRAGKEKASDSRAAAGEKELGYQSPARELKGVYHNDDSDSDNGDRRKKLYVMYGGSWELVSRRDVKTLRREVLSVKPGVPRAAPHQRWMNTTISFGPSDCPENMAGAGVLPL
Ga0314720_1030567	Ga0314720_10305672	F023028	MSRMDPMRAWEWQDEVAGTSLVTRKFSSSIFCWKGLHKLQEGESKNTKDKPWLLHFGASGKGLSLAFYSHKGAY
Ga0314720_1032610	Ga0314720_10326101	F055475	LFKTGFAQPQGRRPGLDPPLWHRGGPDEDITPTDTNDTPQDDIQGPITRARARQLNLQVSSFLSNVYCESENRLLPNDLIVLRNKGEDQQGCGEGLGGVEDQQGRPDQDGGPNRFDFVSVSDSRNRPH
Ga0314720_1032787	Ga0314720_10327872	F088054	MHTDQATEIHLTRPFQQLHRYKIRQSILLATVTLASSFQLATVTTSFSFPWSIAIVVVDGDDGVVVVVVGAGEAADMGRIVATGQTPT
Ga0314720_1033699	Ga0314720_10336991	F036531	LTISEKDLADLAFNGLRSYLKEKLEGFEYHTVNFLQVKVMGLEFKLKNAKDTFKPHRSNTHILDHDSDGSDDDSKEVYAAEFVWPSKAKPGSVPSLKPIQKNRQDEPKFTFDVSKCDRIFDELLKNGNIRLSHAIPSPDELKRHAY
Ga0314720_1034285	Ga0314720_10342851	F060529	PNSKFKFEFKKMKNSQKNPKNISRCKESNDVKFSQKFVHLVWFVEFIS
Ga0314720_1037710	Ga0314720_10377102	F018302	LTAIDLGNWGRDLVPLEGHQRSWQLAVVFKRALGSELQFYSSDRGGAFLLVIGGGTLPSAITFCHRPPRGRLRWSLLRLVSDGHTYPPLSFRWSPWDPGGCRCTGPVCRWCSPSVQEATKIKSPSLFQVENNKISRDVKGLFLGVRFISSRIISVIIRLQLEDELHGPRAACPGGM
Ga0314720_1039130	Ga0314720_10391301	F031344	VENIGKKVKKSKRGSLIEGTSASAQQEDLEVNLPPPSSAYWSNEFQGASSGQGYPQGWTSQWEGSQEQAWGHAATAPPPFSNYGYPPSSYQGEMPDPSFGAQYFDLPQPEQGVRIMGAYARRNMEDIDVIRRHTTQLEDGTAGIAYQMGLLGLAPPEQFNRGAFQQYYDQGYNARANQGD
Ga0314720_1039764	Ga0314720_10397641	F096411	CSQSWEEGKELEPLHLGAKGYHHQYEGALNGVGFKEDLKPKNGFGGFGCLAYKLKVKVQAKTS
Ga0314720_1040891	Ga0314720_10408911	F046814	AFPARLRCVFLVLLPFFIPKLFFIQLMRRNRTYPYNWVVVKEKDNKQDNLGFGFWNPVDLMSCSNEEFSLPNIDGASNSEMKNTDMIIARN
Ga0314720_1042213	Ga0314720_10422131	F002974	MLFFSPWGRGRPKLTWVESVKRDLKDWNISKEIALDRSAWRLAINVP
Ga0314720_1045237	Ga0314720_10452371	F035610	MHESTIYLITLIELFVHIDRDKHSLRVLTPRETTKDNLANMLVSKSQAIE
Ga0314720_1046064	Ga0314720_10460641	F068338	EVKFFQTLTKREGQVLTIAGRDAMIVGSGRATFILPMGTQIHIEEALLYPDSTRTLLSYRDIWKNGIHVETHEEHNEEFFLFTKNTGYGKQTLEKMPSLPSGLYYTYIKPVPHFAYKVIFQNVDTFKTWHERLGHPSWHRDDEKNHE
Ga0314720_1046357	Ga0314720_10463571	F007513	VEVRETVVVTVLQRVVALPVVLLVIFSTAMDHGTEALEEVLRLHAFLAVVFVSHAVDGTGDTLCLVLLTLL
Ga0314720_1046740	Ga0314720_10467401	F085057	GVSLAEQSLSLFSLAVIPCKREHQGRMEESGMAPRYLSWVLDHLVAASKVSRVSQEKWER
Ga0314720_1048002	Ga0314720_10480022	F040424	FECNKEAIDHAATIRVPSSVSEILVVAKELSLKESMPSKKPSQSSVKPTSDVGTKTIQLQERDDSKTAIIGAELGDK
Ga0314720_1048150	Ga0314720_10481501	F012546	MGSSLALSCNIRLFVIELDYGYRYLLEVGSELSDICFLIWLFYCSMLALHDRLVLEMISISCLELYQLL
Ga0314720_1049290	Ga0314720_10492901	F049431	GRINQVTILSPSAEAREQTPRRRPGCTGRKGRRRSEPQPQASEVCETPKPQATDSIAPTEFPKLRSATGGIRLLHRSLHRYIRPSGGEDSRQVNAQARVLDRAIPEDLVKRLAKPVIHRPQMLPANRETSRTSVPSTSTLQLPEGGQHRASRKESPSPK