3300032811: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R4_MAIN_15MAY2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032811
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330572 | Ga0314718
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R4_MAIN_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: 62735778
• Sequencing Scaffolds: 20
• Novel Protein Genes: 22
• Associated Families: 22

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	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	4
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	1
Not Available	8
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 → PACMAD clade → Panicoideae → Panicodae → Paniceae → Panicinae → Panicum → Panicum miliaceum	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. Panicum → Panicum hallii	1
All Organisms → cellular organisms → Eukaryota	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → Caryophyllales → Cactineae → Cactaceae → Opuntioideae → Opuntia → Opuntia streptacantha	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?
F000412	Metagenome / Metatranscriptome	1169	Y
F000459	Metagenome / Metatranscriptome	1109	Y
F004317	Metagenome / Metatranscriptome	443	Y
F007513	Metagenome / Metatranscriptome	349	Y
F018668	Metagenome / Metatranscriptome	233	Y
F019078	Metagenome / Metatranscriptome	231	Y
F022580	Metagenome / Metatranscriptome	213	Y
F025200	Metagenome / Metatranscriptome	202	Y
F026180	Metagenome / Metatranscriptome	198	Y
F026477	Metagenome / Metatranscriptome	197	Y
F030332	Metagenome / Metatranscriptome	185	Y
F032517	Metagenome / Metatranscriptome	179	Y
F032552	Metagenome / Metatranscriptome	179	Y
F040424	Metagenome / Metatranscriptome	161	Y
F042140	Metagenome / Metatranscriptome	158	Y
F042712	Metagenome / Metatranscriptome	157	Y
F059695	Metagenome / Metatranscriptome	133	N
F065367	Metagenome / Metatranscriptome	127	N
F067332	Metagenome / Metatranscriptome	125	N
F076802	Metagenome / Metatranscriptome	117	N
F094790	Metagenome / Metatranscriptome	105	Y
F102251	Metagenome / Metatranscriptome	101	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314718_1000192	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	3412
Ga0314718_1003624	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	1607
Ga0314718_1008665	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	1189
Ga0314718_1020457	Not Available	804
Ga0314718_1021353	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	786
Ga0314718_1021684	Not Available	779
Ga0314718_1023132	Not Available	753
Ga0314718_1024289	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	734
Ga0314718_1029900	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	653
Ga0314718_1029915	Not Available	653
Ga0314718_1031385	Not Available	635
Ga0314718_1035304	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	593
Ga0314718_1036634	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	581
Ga0314718_1037090	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. Panicum → Panicum hallii	577
Ga0314718_1037510	All Organisms → cellular organisms → Eukaryota	573
Ga0314718_1038631	Not Available	563
Ga0314718_1039609	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → Caryophyllales → Cactineae → Cactaceae → Opuntioideae → Opuntia → Opuntia streptacantha	555
Ga0314718_1040821	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	545
Ga0314718_1042524	Not Available	532
Ga0314718_1044990	Not Available	514

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314718_1000192	Ga0314718_10001921	F032552	VISCSKIGQKPAKTKYLQNICANAKTTNNWTDVRMVSDFDIKFMPLSKLNRG
Ga0314718_1003624	Ga0314718_10036241	F032517	MNLSISYSSFDKIINPYSEFLGLYGGGADDLVEHCGGGGIPSVNLIEELLGSLIPPRSNMLLLGAGLSSSMLRGDSETECLREELADASDVDERVLLLPVTNLMMPLMVTPCCPHTKTNTPGVSCRRENNISKSGAN
Ga0314718_1008665	Ga0314718_10086651	F022580	MACSGSWPHIDYLVPDDNGIIEAAIPCGWPNNFSCHLPVFAADLVDNEDSPAFAAGFSDDGKLGYGFTSADDLEEVDIGPGDKPRPTFISKKLDLALREEMIALLKEYRDYF
Ga0314718_1020457	Ga0314718_10204571	F004317	GALRPCLSPYMDERQMNLSYMVLLDMWNMFGQKFLSFIGG
Ga0314718_1021353	Ga0314718_10213531	F026180	VHPTARHSAADCREIQKLAKRVSGRRDQSSKDSSPPPRQRPGKEKASDSGAADGEKELGYQSPARELKGVYSHDNSDSDNEERRKKLYVMYGGSWELVSQRDVKTLRREVLSVRPGVPKAAPHQRWMNTTISFEP
Ga0314718_1021684	Ga0314718_10216841	F059695	VLARLKGPFDVVPQLVYSKTIAKSDKKPSRHFIRSEAFVNEKVIYRKGPSNRANKVLEVGLWVSYTFGLKQKF
Ga0314718_1023132	Ga0314718_10231321	F067332	MPPSIHVYCHIIILANFGEDEIRRACIIMPSCVVFWVVFLVHSILTRSLRAYIAVLKFCAALLSIQLLAIQIIFLEKLDYEKDMRNYRFTYYRNFNDLRGMFIWISRLNLALDPVPSMLIVTTQ
Ga0314718_1024289	Ga0314718_10242891	F025200	LRPLHIDDDVLGHPNGAVPTSFLLPNLVSNHLAIYFLLDHIGGAIALVPPVGFGVDERTLDCKLLLVLLIRKLLPWLRALVGLVAFFVAL
Ga0314718_1029900	Ga0314718_10299001	F019078	MGDGEKTCPCCQFYGIPCRQVRATEDEATTRRNQRLFSSTKRKRSHQEQLAEDSLFLDSPSVDELQTIQKRKDPECSRDTQVKDQALYDYVDGLTITMKVIQPQSHKDSKEQATEIMQDVMLSSQGGQPSSAFHRRRLCY
Ga0314718_1029915	Ga0314718_10299152	F042712	MEYLLDEFGHHKFLQLLANRPTLELVEASQALLHRLGVGSDIKGVLGDLPRYARHVRGAPREDVCVGAEKVDEHHFLFAVEGGADLQRLVVGAIRV
Ga0314718_1031385	Ga0314718_10313851	F000412	RXNXGNFAQTCSTCLEGPNRKDSSGAHPCRAIDRAXEPRIPSLCSLKAITHATGSKIRSSRSRXNRGTEYYRVGMKTHIEYSDIFFXKYNSPYHIEMGTYVLIDLLXAGGSVAPAQPTSLRXNXGIFAQTCSTCLEGPNRKDSSGAHPCRAIDRAXEPDSLCSLKAITHATGSKIWSSRSRWNRCTEYYPVGMKTHIEYPDIIVXKYNSPY
Ga0314718_1035304	Ga0314718_10353042	F007513	VVLTVLQRVVALPVVLLVVFSTAMDHGTGALEEVLRLHAFLVVVFVRHAVDGTGDMLCLVLLTLL
Ga0314718_1035799	Ga0314718_10357991	F102251	NNDAKIIITFLNMHGDVHYYTANFGIKIQLLYEETKKTNCFMG
Ga0314718_1036634	Ga0314718_10366342	F030332	CEQLAALFLGNAPHEDTIGAMAVEIPFYHRVAFRQLYYALSGHIIIRKDIVFKVVPDLGDPCIGTSLRRWEWRYEVSRVLNSAHNPGRAPLMECRRTASFEVLT
Ga0314718_1037090	Ga0314718_10370901	F094790	MVFLNCRDWGSTSGPFLHTPVSGMPEALLSNCFTADRGCGSCLGLSCSYLLQSHRELCLLGSMGLLPQNVGLLIKELIQGG
Ga0314718_1037510	Ga0314718_10375101	F040424	DKEAIDHASTIRVPSSVSEILAAAKELSLKESMPSKKPSQSSDKPTDDVGTKTIQLQEGDDSKTAIIGAGLGDK
Ga0314718_1038631	Ga0314718_10386311	F026477	MFVAWLVVDLLCFVAYYLRISCCLCAVTFQSLASSYCIELVAQGQRPASFMSSRSDLLWFALVLRVGIISARLGLANGLDDPVAC
Ga0314718_1039609	Ga0314718_10396091	F018668	HSLLSTPPPKQHQTIKMAFFKSLLIASVAAVAFAAPQGASDKNTEVKVSGQDNSPKCGNGQKIACCNSGEDLIGLNCLSIPILAIPIQQACGSNVAACCQTGDAEGNLINLEANCLAIPL
Ga0314718_1040821	Ga0314718_10408211	F042140	TNGKVVAHKVGKKKSSWNHSIWVTKDILTNMKGPQMVWVPKET
Ga0314718_1042524	Ga0314718_10425242	F065367	MSAEQKDLGVSAMGDGEKACPCCQFYGVPCRQARATEDEATIRRNQRLFSGTKRKRSHQEQLTEDSLFLDGPSVDELQTIQKRKDP
Ga0314718_1044990	Ga0314718_10449902	F076802	AQYFDLPQPEQGMRIMGAYARRNMEDIDAIRRHTTQLEDGTAGIAYQMGLLGLAPSEQFNGGAFQQYYDQGYNARANQGD
Ga0314718_1046886	Ga0314718_10468861	F000459	VRIGVLERVDNIKRGRGRPKLTWNKLVKRDLKDWNISKEIALDRSAWRLAINV