3300032970: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_MAIN_15MAY2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032970
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330570 | Ga0314716
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_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: 59336469
• Sequencing Scaffolds: 19
• Novel Protein Genes: 22
• Associated Families: 20

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida	1
Not Available	6
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 → 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	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
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 → 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 → Malpighiales → Salicaceae → Saliceae → Populus → Populus trichocarpa	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

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?
F000459	Metagenome / Metatranscriptome	1109	Y
F007513	Metagenome / Metatranscriptome	349	Y
F018302	Metagenome / Metatranscriptome	235	Y
F025200	Metagenome / Metatranscriptome	202	Y
F029306	Metagenome / Metatranscriptome	188	Y
F032897	Metagenome / Metatranscriptome	178	Y
F034039	Metagenome / Metatranscriptome	175	Y
F034784	Metagenome / Metatranscriptome	173	Y
F035610	Metagenome / Metatranscriptome	171	Y
F038063	Metagenome / Metatranscriptome	166	Y
F054498	Metagenome / Metatranscriptome	139	Y
F057814	Metagenome / Metatranscriptome	135	Y
F060513	Metagenome / Metatranscriptome	132	Y
F062378	Metagenome / Metatranscriptome	130	Y
F062397	Metagenome / Metatranscriptome	130	Y
F065372	Metagenome / Metatranscriptome	127	Y
F067332	Metagenome / Metatranscriptome	125	N
F068338	Metagenome / Metatranscriptome	124	Y
F070783	Metagenome / Metatranscriptome	122	Y
F096411	Metagenome / Metatranscriptome	104	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314716_101387	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida	2122
Ga0314716_107508	Not Available	1239
Ga0314716_112835	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	986
Ga0314716_116787	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	865
Ga0314716_117272	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae → Panicodae → Paniceae	852
Ga0314716_118598	Not Available	821
Ga0314716_119434	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	801
Ga0314716_120629	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	776
Ga0314716_121135	Not Available	767
Ga0314716_127470	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	665
Ga0314716_130731	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	623
Ga0314716_131480	Not Available	614
Ga0314716_132263	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	604
Ga0314716_133484	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	591
Ga0314716_135132	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	574
Ga0314716_142641	Not Available	512
Ga0314716_142814	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Malpighiales → Salicaceae → Saliceae → Populus → Populus trichocarpa	510
Ga0314716_143199	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	508
Ga0314716_143769	Not Available	503

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314716_101387	Ga0314716_1013871	F060513	MSTTEIPEETGQTASADRSDRSCLVQHTGSTGQTGHPDRSDRSNAEWLQQRLDQYRARTNDMCEAIEDSDDLDKLGQGFTSADPLEKVDIGDGTIPRPTFVNKNLSAEYKTDLVNLLKEYVDCFAW
Ga0314716_107508	Ga0314716_1075081	F067332	VYCHIIILANFGEDEIRRACIIISSCVEFWVVFLVHPILTRSLRAYIAVLKFCAALLSIQLLAIQIIFLEKLDYEKDMRNYRFTYYRNFNDLRGMFIWISRLNLALDPVPSMLIVTTQ
Ga0314716_112835	Ga0314716_1128351	F032897	VDASFTRSHCHQNTIALQYVPSELQLADFFTKAQTREQHRLHMLKLNASDPPPPP
Ga0314716_116787	Ga0314716_1167871	F018302	VPPQQHGEGIFYGGVDGTQAVAPPLPVAARCWHPVVPAAVALPQLGKKKAFAWEDACHVFAAVRLQAAARGLLARRRLQKMRLEMQEAALTAIDLGNWGRNLGKWGRDLVPSEGHQRSRQLAVVFKRALGSELQFYSSDKGGAFLLVIGGGTSPSAITFRHRPPRGRLRWSLLRLISGGDTCPPLSFRWSPWDPGGYLRAGPTQGGCPPHLQESKIKNCSLFKISRDVKGLFLGFRFASSGVIVSVIVRLQLEDELQVQVGCSVRGVKGLLGLNPLGLISRLLRD
Ga0314716_117272	Ga0314716_1172722	F096411	WQGSCSQGWEARKELEPSHLGAQGCHHQYEGISNGVGSKGNLKPKNDFRGFGGLAYKLK
Ga0314716_118598	Ga0314716_1185981	F062378	MAAPKPISXANRINTTLISLNNNLGTLFTLVLGCFPLDIQPYRTMSDNLINI
Ga0314716_119434	Ga0314716_1194341	F007513	VEDSETVMVTVLQRVVALPAVLLVIFNTAMDHGTEALEEVTRHHTFLTMVVVSLAVDGTGDTLCLILLTLL
Ga0314716_120629	Ga0314716_1206291	F070783	ALMDVDVAFDIMDSYMMRITYMLREIELMTLVGVIYIGYIVDMNFTCMLFFIKIW
Ga0314716_121135	Ga0314716_1211352	F035610	MHESTKYLITLIELFVHIDREKHSLRVLTPLETTKDKLRKHVSLKL
Ga0314716_123130	Ga0314716_1231301	F000459	VRNRVLERVDNVKRGRDRPKLTWDESAKRDLKDWNISKDIALDRSAWRLTINVPEP
Ga0314716_127470	Ga0314716_1274702	F065372	VHPTACHSAADCREIQKLAKRVSGRREQSSKDGSPPPRQWPGKEKASDSGAAAGEKELGYQSPARELKGVYHDDDSDSDNGDRRKKLYVMYGGSWELVSRRDVKTLRREVL
Ga0314716_127754	Ga0314716_1277541	F000459	GVLERVDNVKRGRGRPKLTCDESVKRDLKDWNIFKEIALDRSAWRLAINVPEP
Ga0314716_127904	Ga0314716_1279042	F057814	MIEKIGAIHMIKSYGGECRKYPEVPRIKYLVLPKCGTKYQKVGSNINLI
Ga0314716_130731	Ga0314716_1307311	F034039	MVYMYLLFRGTVLDREVQCLKVLGLNLRDPAVVVPDGVQVVANTTLDSAVVFHLTALADHVFPLVVIAFLKWDLICL
Ga0314716_131480	Ga0314716_1314801	F062397	MCMNGLRINMGFGPSFGLWPSSFSVLALDHGPRHFMLQNRPKTCKNEVPPKYMCKCENDQNICANVKMTNN
Ga0314716_132263	Ga0314716_1322632	F065372	VHPTARHSAADCRKIQKLAKRVGGRREQASKDGSPPPRQRSGKEKASDSETAVGEKELGYQSPARDLKGVYSH
Ga0314716_133484	Ga0314716_1334841	F034784	MQSHLQAKGLNVWRVTSEGTKSNSQQEKQYDAIAKCAILNSLGENVFNRVFACENGNVLWKTISENHEGTKDVAIKNYHVLIDKLNSFKQLDDESA
Ga0314716_135132	Ga0314716_1351321	F054498	SQHDPNEALDQISEDNLTLDAPQDEDESTRTARRVRNQHKGERRVQATERARLPPRNLNNKFNNVADPVFRTPIAAMTEAALRLMQMPQNSEMEHVIKLAKNVVEQLERQNPLSSLHGTQSRATATVIPQDK
Ga0314716_142641	Ga0314716_1426411	F038063	ITRTEAFFMASNASYPDVRSMAFSRFIVLLLPTIYEYHVVSVQSRFNLMLILVA
Ga0314716_142814	Ga0314716_1428141	F068338	MEEEICLVDSCTTNTILREVKFFQTLTKREGQVLTIAGRDAMIVGSGRATFILPMGTQIYIEEALLYPDSTCTLLSYRDIRKNEIHVETYEEHNEEFLLFTKNTGYGKQTLEKVPSLPSGLYYTYIK
Ga0314716_143199	Ga0314716_1431991	F025200	LRPLHIGDDILGHPNGVIPTPFLLPNLVSNHLAIGFLLDYIGGAMALVPSVGLGVNERTLDCKLLFVLLIRKLLLWLRELVGLVAFLMAFRESHGGPLLKLLHHASR
Ga0314716_143769	Ga0314716_1437692	F029306	MQTKLNKSKTITIETKLENKANKTGFTIFSLSSKKFYIKPPFGQQARNRNKTLTTSKQTCERVVPLKTTPHKESKKIWFDIFRAVYK