3300032918: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R4_MAIN_05JUN2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032918
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330580 | Ga0314726
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R4_MAIN_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: 54159075
• Sequencing Scaffolds: 29
• Novel Protein Genes: 35
• Associated Families: 32

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 → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum miliaceum	3
Not Available	13
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 → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Arundinoideae → Arundineae → Arundo → Arundo donax	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 → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	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 sect. Hiantes → Panicum virgatum	6
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	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): 42.3941
  • Long. (^o): -85.3741
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000459	Metagenome / Metatranscriptome	1109	Y
F000927	Metagenome / Metatranscriptome	831	Y
F001705	Metagenome / Metatranscriptome	648	Y
F010664	Metagenome / Metatranscriptome	300	Y
F014470	Metatranscriptome	262	Y
F016911	Metagenome / Metatranscriptome	243	Y
F018302	Metagenome / Metatranscriptome	235	Y
F019940	Metagenome / Metatranscriptome	226	Y
F020484	Metagenome / Metatranscriptome	223	Y
F023769	Metagenome / Metatranscriptome	208	Y
F025200	Metagenome / Metatranscriptome	202	Y
F026763	Metagenome / Metatranscriptome	196	Y
F027091	Metagenome / Metatranscriptome	195	Y
F030953	Metatranscriptome	183	N
F032552	Metagenome / Metatranscriptome	179	Y
F040723	Metagenome / Metatranscriptome	161	Y
F042357	Metagenome / Metatranscriptome	158	Y
F046814	Metagenome / Metatranscriptome	150	N
F050083	Metagenome / Metatranscriptome	145	Y
F053032	Metagenome / Metatranscriptome	141	Y
F056279	Metagenome / Metatranscriptome	137	Y
F065372	Metagenome / Metatranscriptome	127	Y
F067332	Metagenome / Metatranscriptome	125	N
F069562	Metagenome / Metatranscriptome	123	Y
F072944	Metagenome / Metatranscriptome	120	Y
F074257	Metagenome / Metatranscriptome	119	Y
F079533	Metagenome / Metatranscriptome	115	N
F089752	Metagenome / Metatranscriptome	108	N
F093055	Metagenome / Metatranscriptome	106	Y
F094644	Metagenome / Metatranscriptome	105	N
F100085	Metatranscriptome	102	N
F100243	Metagenome / Metatranscriptome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314726_100839	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	2425
Ga0314726_101295	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	2145
Ga0314726_103065	Not Available	1661
Ga0314726_103817	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	1543
Ga0314726_105884	Not Available	1321
Ga0314726_107233	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	1222
Ga0314726_108609	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Arundinoideae → Arundineae → Arundo → Arundo donax	1134
Ga0314726_115862	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	852
Ga0314726_116071	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	847
Ga0314726_120467	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	746
Ga0314726_121943	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	719
Ga0314726_122065	Not Available	716
Ga0314726_122820	Not Available	703
Ga0314726_124121	Not Available	681
Ga0314726_124311	Not Available	678
Ga0314726_125327	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	662
Ga0314726_125939	Not Available	653
Ga0314726_126444	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	645
Ga0314726_128124	Not Available	622
Ga0314726_128135	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	622
Ga0314726_128795	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	614
Ga0314726_130142	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	598
Ga0314726_131874	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	578
Ga0314726_132241	Not Available	574
Ga0314726_134271	Not Available	554
Ga0314726_134542	Not Available	551
Ga0314726_137135	Not Available	527
Ga0314726_138058	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	518
Ga0314726_139125	Not Available	510

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314726_100355	Ga0314726_1003552	F094644	MKFIFLLXALRYQRYHSGIWHHCYCCSMPTKCSLHSGYCHTCALRLLCNSNTWILQIXGKDIHLPFASPSSGFQQRMXYCQNHKXLFTHSFIKDLRSMAIYIRMDALECGYHFPSENDQVXQISHFNKSVIVQIHEHRNAKSNIWLNYTSNSLETSEFFGIFXSSLQQATLEKVYISIGNNISLNSYYHMWYVVHYKNIMYLRHDIHILLPCLYMGFNQIEMKHV
Ga0314726_100839	Ga0314726_1008391	F010664	MVLLQMDDNNAANHGNGGQEAQPPPPPSLAQAIAALIADRNEQTELLRQLVESHAGRGRQAPPAETDYVGFFATQPPLFHKANDPLEADAWIRTIE
Ga0314726_101295	Ga0314726_1012951	F074257	MGGVRIPVLFHWRESAEYDRAEFFSPKGKRVGVGSDKDKFSISLAISGRIISAEVISPSCSRRGVSVLAGSIRWLEKPPDPLAMQTHEPNTKVVPALIAGKLNSKDAIKFFC
Ga0314726_102614	Ga0314726_1026141	F000459	VDNVKRGRGRSKLTWDESVKRDLKDWNISKEIALDRSAWRLAINVPEP
Ga0314726_103065	Ga0314726_1030652	F089752	GSAPAGRVLRGARLFCFVCSGDKTCPRAEGGQGDDGACCSAAGAFVVLSRASGHRPWLPWLLCGAPFEGGRPEPMLRRSASRGSAPLYFVRSRLGVVTEGIFCPWSAVSSRATQASAFRQAWSLVPGTAINRGRGVSPSSPASQLFLPALPKSCNVSFAFS
Ga0314726_103817	Ga0314726_1038173	F065372	VHPTARHSAPDCREIQKLVRRVSGRREQSSKDGSPPPRQRAGKEKASDSGAAAGEKELGYQSPARELKGVYHNDDSDSDNGDRRKKLYVMYGRSWELVSRRDVKTLRREVL
Ga0314726_105884	Ga0314726_1058842	F067332	MPPSVHVYCHIIMLANFGEEEIRRACIIISSCVEFWVVFLVHPILTRSLRAYIAVLKFCAALLSIQLLAIQIIFLEKLDYEKDMRNYRFTYYRNFNDLRGMFIWISRLNLALDPVPSMLIVTTQ
Ga0314726_105943	Ga0314726_1059431	F093055	HALQEGSHANLPVGIVLAGKHRDLTKTRHGRRVVFEPVKVLKTSTKL
Ga0314726_107233	Ga0314726_1072333	F032552	VIVGLAISCSKIGQKPAKTKYLQNICANAKTTNNWAEVRMVSDFDIKFMPLSK
Ga0314726_108609	Ga0314726_1086091	F019940	KTTHDICHHIFMFDGRDKNINSQTNSSTKHILNTYGGVMQNEIYCN
Ga0314726_115862	Ga0314726_1158621	F100243	GFLLKASREIIVSRADVVSGSVLARKCVPPHGTVVVGGKW
Ga0314726_116071	Ga0314726_1160711	F025200	LRPLHVGDDVLGHPNGAVPTTFLLPNLVSNHLAICFHLDHIGGAIALVPPIGLGLDERILDCEFLFVLLIRKLLPWLRTLI
Ga0314726_120467	Ga0314726_1204671	F014470	FPEEMVRITGRDPTPVEQEALRAVQWRHGRWGGSKRDVFSPTCGKVRRSYHYRAQPGFSYLSFVGPGKTKLSPLWEKGADWGLVPADFRSEEEERGLAKLEQFRADWDSGFIAIGD
Ga0314726_121943	Ga0314726_1219431	F023769	LKETLLTWSMPCADLHKNAFQRSSSRVAHVTRPVDNSTSGSTVKRCRDCLRGERDTKETIHNGLLLLRVGYGLPYSELPDCSPGDLSRFLSFLLLQGKERTSVAFPRRQRHGENGLCTLQRLCRRDRWALAHGCSSIKRNLPKGCFRHTPSVFAAWEAAALSQPPPLTSGYLEHVRRVVTGIFRPGWDGRYNSFVGSHVPNPSARACKTRADVLWRRRRDEFFTATTSESDINPSELSG
Ga0314726_122007	Ga0314726_1220071	F100085	RGPLAYRATRRFGLSTTVTHTPIPSLVVDNGLSLAASGCEFVDPLELSDEDKERNLCELAAWKWRTKFNISDQCRSNLRFMLAVSATRVDRPDFRPLFWGSDSCLLTRKWHSAKMFRKPIEKRERGFPVLAGYAGRLPSYEEVLAGETDVGSVELIVKADKKN
Ga0314726_122065	Ga0314726_1220651	F046814	MRRNRTYPYNWVVVKEKDNKQDNLGFGFWNPVDLMSCSNEEFSLPNIDGASNSEMKNTDTIIAQN
Ga0314726_122820	Ga0314726_1228201	F079533	SREEARVSTQLVLNKYNTNYEALRLADSTALAFKYWQIFIKAIYYKLMNYL
Ga0314726_124121	Ga0314726_1241211	F016911	VLTVQGDRTAAVAAVERLHTLAAEAARPEEDPSTSQPRAPAKAPKVQPSDPDQVPVKTVQIGADSTRTTRIAGNLEEK
Ga0314726_124311	Ga0314726_1243111	F056279	MTSGKLPKVKEKPTVASIWAMMLAEKTTPVLVAIELDV
Ga0314726_125327	Ga0314726_1253271	F027091	GALIAQPVFGLCNSSSVYKQMIRSSYENSSDRLLHVENQSATASREAPVFDVYPDPIESSQDSLDFITNALIKMQLKSCRDHTLAELLDNLREVASIDDLPFQHGAPLVTERETGSGRTVLADYGSDLESFSHERLVPVIIQHGEAPSHHDPNRDLDQISADNLTQDAPGDEDEVTRTAHRERNQRKEVRRTRAAERAHLPPCNLNNEFNNAADPIFRTP
Ga0314726_125939	Ga0314726_1259391	F072944	XTKKNKILNKIKSTESYTRDMVLKFLPEPSHELKILQKNYQALSQQDKLVMHLTYHELA
Ga0314726_126444	Ga0314726_1264441	F018302	LHEMRRQMHEASLTAINLGKGGRVLALPDGHQQSRGSAAVYMREQGVVSTVGELQLCGSGSFRFVTGEDAQFSATTFRYRPPRGPLRWSWSRLIPGGRTRAPLSFRWSPWDLGGYIHAGPACGECPPYLQQSKIKSRSLFKISRDVKGLFLGVRFASSGVIVRLQLEDELPMLLAR
Ga0314726_128124	Ga0314726_1281241	F000927	MDYSSCFIFLYRMFNMGSGATNFMEGTSKHKLSTEIFPDFIHLYSRGDKKIKNSKPFTKINSTERFTEDLVLKFLPETIHEINILQ
Ga0314726_128135	Ga0314726_1281351	F042357	MDLKPTRNSLGRNPLSDAPHRNPGVVISGQGPGRHPTNGASYRDLGMMISEQGLGRHLSGALHLRPGVVINEQGSSHFPRRVRRVRKLAEPTRIRIVSWNVGSLTGKL
Ga0314726_128795	Ga0314726_1287951	F069562	LLLLDFLNSNLGPQLCESNAPKWLGEDVPKLSSSLDMLELDLSTIDAVTDEVILGVDVLAPVMVDGVLC
Ga0314726_129839	Ga0314726_1298391	F030953	TVQDYPSGYRLNNDKTIRAGNAAEVNSTVFLKSKERWREVRHLRRGGAVTDFPGMMHMAKAVTVAPGFVDAYQRCRIGRRWGFLPSQLGHTTYPAYKRERGLRVRRTYTPLPEPADGCVFPEEMVRITGRDPTPVEQEALRSVQWKHGRWGGAKRDVFSPSCGKVRRSYQYRARPGFAYLSFVGPGRPKLSPLWEKGADW
Ga0314726_130142	Ga0314726_1301421	F050083	VANSIIFITDSIVVSHIDDMENDMTVDLAMTWIAMMTWSLTWLLTCQ
Ga0314726_131788	Ga0314726_1317881	F000459	VRSGVLERVDNVKRGRGRPKLTWDESAKRDLKDWNISKEIALDRSGWKLAINVLEP
Ga0314726_131874	Ga0314726_1318741	F001705	RPKLTWDESVKRDLKDCNISKEIALDRSAWRLAINVPEH
Ga0314726_132241	Ga0314726_1322411	F040723	MSFHSYMIVFCALFQWDRELPILDPVAXVIAFKLHGEGIQGSQALSIVLQGXAPDKSFLYGLSRQV
Ga0314726_134271	Ga0314726_1342711	F020484	MARTLDAAHSEIRNRLQRWDKMDTTLLFGINFGRIRTRWKEKFVHFTMEQCFSTCSVLEIERKIREDEAAMRQRGIEGGDDNMKQ
Ga0314726_134542	Ga0314726_1345421	F053032	SPRKSSCSILHRNFSFSLNTLWQDQASPLEMSVLGHPEIGNPKDVTQQDPTQRPQICLIGRCKDMMSRMDPMRAWEWQDEVAGTSLVTRKFSSSIFCWKGLHKLQEGESKNTKDKPWPLHFGASGKGLSPTFYSYKGAY
Ga0314726_137135	Ga0314726_1371352	F020484	MTRTLDVVCSEIRRDRLQRWDEMGITLLFGINFGRMRTRWKVKFVHFTIEQCFSTCSILEVERKIHEDETTMGQRGIEGGDDDVKQ
Ga0314726_138058	Ga0314726_1380581	F026763	VCIASGSGSFDSHLTNSPTLKAASPESLGKLAESDDQGIMLLPYLTKEIEMKLEDNLGSTRTQIDLKLISTRIGTPLAQPLFGLRNSSSTYKQMIRSIYENSLDHLLCGKNHSVTASREAPIFDIYPDPVESSQDSLDFITNALVKIQLESCESHTLAELLDNLRKVASIDD
Ga0314726_139125	Ga0314726_1391251	F067332	MPPSIHVYCHIIIWANFGEDEIRRACIIISSCVEFWVVFLVHPILTHSLRAYIAVLKFCDALISVQLLAIQIIFPKKLDYERDVRSYRFTYYRSFNNLM