3300022465: Metatranscriptome of phyllosphere microbial comminities from switchgrass, Michigan, USA - G5R1_MAIN_12JUL2016_LR1 MT pilot (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300022465
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0211511 | Ga0213505
• Sample Name: Metatranscriptome of phyllosphere microbial comminities from switchgrass, Michigan, USA - G5R1_MAIN_12JUL2016_LR1 MT pilot (Metagenome Metatranscriptome)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 30920988
• Sequencing Scaffolds: 30
• Novel Protein Genes: 32
• Associated Families: 31

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 sect. Hiantes → Panicum virgatum	5
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 miliaceum	2
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Malpighiales → Rhizophoraceae → Rhizophora → Rhizophora mucronata	1
Not Available	15
All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	3
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 → 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	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): Host-associated → Plant → Plant surface

Location Information

• Location: USA: Michigan
• Coordinates
  • Lat. (^o): 42.39
  • Long. (^o): -85.37
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000459	Metagenome / Metatranscriptome	1109	Y
F002578	Metagenome / Metatranscriptome	546	Y
F002654	Metagenome / Metatranscriptome	539	Y
F004317	Metagenome / Metatranscriptome	443	Y
F007513	Metagenome / Metatranscriptome	349	Y
F018302	Metagenome / Metatranscriptome	235	Y
F020484	Metagenome / Metatranscriptome	223	Y
F025200	Metagenome / Metatranscriptome	202	Y
F026477	Metagenome / Metatranscriptome	197	Y
F028072	Metagenome / Metatranscriptome	192	N
F030953	Metatranscriptome	183	N
F032552	Metagenome / Metatranscriptome	179	Y
F032897	Metagenome / Metatranscriptome	178	Y
F035610	Metagenome / Metatranscriptome	171	Y
F040414	Metagenome / Metatranscriptome	161	Y
F041531	Metatranscriptome	159	Y
F042666	Metatranscriptome	157	N
F044274	Metagenome / Metatranscriptome	154	Y
F046792	Metagenome / Metatranscriptome	150	Y
F046814	Metagenome / Metatranscriptome	150	N
F049431	Metagenome / Metatranscriptome	146	N
F057813	Metagenome / Metatranscriptome	135	Y
F062397	Metagenome / Metatranscriptome	130	Y
F065367	Metagenome / Metatranscriptome	127	N
F073003	Metagenome / Metatranscriptome	120	Y
F085057	Metagenome / Metatranscriptome	111	Y
F088054	Metagenome / Metatranscriptome	109	N
F089752	Metagenome / Metatranscriptome	108	N
F096516	Metagenome / Metatranscriptome	104	Y
F100243	Metagenome / Metatranscriptome	102	Y
F100268	Metagenome / Metatranscriptome	102	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0213505_100054	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	4087
Ga0213505_100376	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	2546
Ga0213505_104054	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	1204
Ga0213505_104253	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Malpighiales → Rhizophoraceae → Rhizophora → Rhizophora mucronata	1181
Ga0213505_105503	Not Available	1059
Ga0213505_106504	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	983
Ga0213505_106878	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	958
Ga0213505_107258	Not Available	935
Ga0213505_107356	Not Available	929
Ga0213505_108488	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	865
Ga0213505_108943	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	844
Ga0213505_109004	Not Available	840
Ga0213505_109383	Not Available	822
Ga0213505_110347	Not Available	780
Ga0213505_112193	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	712
Ga0213505_113130	Not Available	684
Ga0213505_113198	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fagales → Fagaceae → Castanea → Castanea mollissima	681
Ga0213505_113699	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	667
Ga0213505_115469	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	623
Ga0213505_115490	Not Available	623
Ga0213505_116488	Not Available	600
Ga0213505_116773	Not Available	594
Ga0213505_117248	Not Available	585
Ga0213505_118357	Not Available	564
Ga0213505_118893	Not Available	555
Ga0213505_119069	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	552
Ga0213505_119126	Not Available	551
Ga0213505_120497	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	530
Ga0213505_120505	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	529
Ga0213505_122764	Not Available	500

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0213505_100054	Ga0213505_1000542	F007513	VEVRETVVVTVLQRVVALPAVLLVVFSTAMDHGTEALEEALRLHAFLAVVFVSHAVDGTGDTLCLVLLTLL
Ga0213505_100376	Ga0213505_1003762	F028072	LNLEVNTGKTVSTKENVIIRCRINSSEEHTWHTSHGQINLIVDLIHNFYITWGKRQDDLELKFERLQKEHKHLEEQNLVANKKLELALQAFEESKIFLGKISQNSDYIKRDISYLFNKLESTNIAEHSKEIVLSSSGILEVTRSLNSDK
Ga0213505_104054	Ga0213505_1040541	F100243	LKASIEILVPRADTVSDSVLARKCVPPHGTAVVGGKW
Ga0213505_104253	Ga0213505_1042532	F002654	VLNYQTFNDKVVCQKGNSPEQVFKVPKFLLSESKEEFKLYNQEIGLEAAIF
Ga0213505_105503	Ga0213505_1055032	F046814	MRRNRTYPHNWVVVKEEDNKQDNLGFGFWNPVDLMSCSNEEFSLPNIDGASNSEMKNTDMIIARN
Ga0213505_106504	Ga0213505_1065042	F100268	LQVEPVHLPLGSEDWWAFEELADDMEMVAAAISEDVSIEEGIGNVFADD
Ga0213505_106613	Ga0213505_1066131	F030953	NHGQMQGAYLSFPLLCLHSYCAATWAARFDKEARFLVNGDDTVISAYRDVTVQDYPSGYRLNNDKTIRAGNAAEVNSTVFLKSKGRWREVRHLRRGGAVADYPGMLHMAKAVTITPGFVDAYQRCRIGRRWGFLPSQLGHTTYPAYKRERGLRVRRTYTPLPEPADGCVFPEEMVRITGRDPTPVEQEALRSVQWKHGRWGGAKRDVFSPSCGKVRRSYHYRARPGFAYLSFVGPGRPKLSPLWEKGADWGLVPASFQSEEEERGLAELEQFRKNWDSGFISVGD
Ga0213505_106878	Ga0213505_1068781	F041531	RGGAVTDYPGMLHMAKAVTVSPRFVDAYQRGRIGRRWGFLPSQLGHKTYPAYKRERGLRVRRTYTPLPEPSDGCVFPEEMVRITGRDPTPVEQEALRAVQWRHGRWGGSKRDVFSPSCGKVRRSYHYRARPGFSYLSFVGPGKTKLSPLWEKGADWGLVPADFRSEEEERGLAKLEQFRADWDSGFIAIGD
Ga0213505_107258	Ga0213505_1072581	F062397	MCMNGLRINMGFGPSFGLWPSSFSVLALDHGPRHFMLQNRPKTCKNEVPPKYMCKCENDQ
Ga0213505_107356	Ga0213505_1073561	F096516	MKEDSRSLTQASMLTEIEDVVNLKILIEEVRLDQDMKAQVLCMSFYVNLSIGCRTIKGDATSVV
Ga0213505_108488	Ga0213505_1084881	F042666	KETLLTWSMPCADLHKNAFQRSSSRVAHVTRPVDNPTSGSTVKRCRDCLRGERDTKETIHNGLLLLRVRYGLPYAELPDCGPGDLSRFLSFLLLQGKERTSVAFPRRQRPGENGLCTLQRLCRRDRWALAHGCSSIKRNLPKGCFRHTPSVFAAWEAAALSQPPPLTSGYLEHVRRVVTGIFRPGWDGRYNSFVGSHVPNPSARACKTRADVLWRRRRDEFFTATTSESDINPSELSGRYKEIRSAGKSRPMLIFDEQIELLAPLHKTIFSHLSKQEWSLCGPPTEEK
Ga0213505_108943	Ga0213505_1089431	F018302	ARLTLLESRFAAALPSFTAPSPVPPQQHGEGIFYGGVDGTQAAAPPLPVAARCWHPVVPTAVALPQLGKKKAFAWEDACHVFAAVRLQAAARGLLARRRLQKMRLEMQEAALTAIDLGNWGRDLVPSEGHQRSRQLAVVFKRALGSELQFCSSDKGGAFLLVIGGGTSPSAITFRHRPPRGRLRWSLLRLISGGDTCPPLSFRWSPWDPGGYLRAGPAQGGCPPYLQESKIKNCSLFKISRDVKGLLLGFRFASSGVIVSVIIRLQLEDELHVQVGCSVRG
Ga0213505_109004	Ga0213505_1090041	F089752	QPGGCDNSPVGVVRPWEECFEARASLFVCLKDKTCLRAEGGQGDDGACCSTAGAFVVLSRASGHRPWLPWLLCGAPFEGGRPEPMLRRSASRGSAPLYFVRSRLGVVTEGIFCPWSAVSSRASQASAFRQAWSLVPGTAINRGRGVSPSSPAS
Ga0213505_109383	Ga0213505_1093831	F057813	MVIVNYRNIKKYAKYISVHINVKGVGTSKYDMNYMRYYIGIAKGEMIISFWNVR
Ga0213505_110347	Ga0213505_1103471	F035610	MHESTIYLITLIELFVHIDREKHYLRVLTPRETTKDKLANMLV
Ga0213505_112193	Ga0213505_1121931	F088054	MHTDQATESHLIRPFQQLHRYKIWQSILLATATLASSFQLATVTTSFSFPWSIAIVVVDGDDGVVVVVVGAGEAADMGRIVATGQTPT
Ga0213505_113130	Ga0213505_1131301	F044274	EIVDWACSLXQNKKWFRRHKLVHLMHPILIFIMGLVWQXNGVKPPETRVLDEKYMVRNQTDVVEQXNGVKIPKIXVLDLKECIEIFQVECLESYYSKTFNQMHANTSFRNGSGASTKWRETFENMSFGPKVVDWACSLLENKKRFWRHKLVH
Ga0213505_113198	Ga0213505_1131981	F049431	MTTGRINQVTILSPSAEAHERTPRRRPGCTGRKGRRRSEPQPQASEVCETPKPQATDSIAPTEFPKLRSATGGIRLLHRSLHRYIRPSGGEDSRQVNAQARVLDRAIPEDLVKRLAKPVIHRPQMLPANRETNRTSVPSTSTLRLPEGRQHRASRKESPSPK
Ga0213505_113651	Ga0213505_1136511	F000459	RSGVLERVDNVKRGRGRPKLTWDESVKRDLKDWNISKEITLDRSAWRLTFNMPET
Ga0213505_113699	Ga0213505_1136991	F032897	RSHCHQKTIDLQYVPSELQVADFFTRAQTQEQHWFNMLKLNASDPPLPP
Ga0213505_115469	Ga0213505_1154691	F040414	LRVSEAILDALFFTSVKIPRTLRAFAKSSLRPWFKGSRGEAVRVNHGQMQGAYLSFPLLCLHSYCAATWAARFDREARFLVNGDDTVISANRDILVQDYPSGYRLNMDKTIRAGNTVEVNSTVFLWSKGKWREVRHLRRGGAVTDYPGMLHMAKAVTVSPRFVDAYQRCRIGRRWGFLPSQLGHTTYPAYKRERGLRVRRTYTPLPE
Ga0213505_115490	Ga0213505_1154902	F085057	VSLAEQSLSLSSLAVIPCKKEHQGWMEESGMAPRYLSWVLDHLVAASKVSKVSQVKQ
Ga0213505_116488	Ga0213505_1164882	F020484	MARTLDVARSEIRRDRLQRWDKMDITLLFGINFGRIKTCWKEKFVHFAMEQCFSTGYVLEIGRKIHEDEAAMGQRGIEGGDDDVKQ
Ga0213505_116773	Ga0213505_1167731	F073003	AGVKIAGRKLKMIWDKSHRVEKLLKDSSSMASGGQGRRKEKQRLRDFFFGR
Ga0213505_117248	Ga0213505_1172481	F026477	MLVILMFVAWLLVDPLCLVVYHLQISCCFCAVTFQSYASSCRIELVAQRQHPASFMSSRSNLLWFALILGVGVISARLGLANGLDDPVA
Ga0213505_118357	Ga0213505_1183572	F002578	MQMFMHDVVLEFFATKAPDPPDWTLNSCFGVFHTIWAHLGPLCCLTKLKAKHFEQVQKFVARRRVGAFRYERTRSSALDPKHM
Ga0213505_118893	Ga0213505_1188931	F065367	MGDGEKACPCCQFYGVPCRQVRATEDEATTIRNQRLFPGTKRKRSHQEQLAEDSLFLDCPSVEELQTIQKRKDPKCSRDTQ
Ga0213505_119069	Ga0213505_1190691	F032552	MGLVISCSKIGQKPAKMNYLQNICANAKTTNNRAEVRMVSDFDIKYMPLSKLNRG
Ga0213505_119126	Ga0213505_1191261	F046792	MQTKLNKSNKIIMETKQEHKANKTGFAILSLSSKKF
Ga0213505_120497	Ga0213505_1204972	F007513	VVFTVLQRVVALPVVLLVVLSTAMDHGTEALEEVTMHHAFLLVGVVSLAVDGTGDTFLI
Ga0213505_120505	Ga0213505_1205051	F025200	TFSLLSNLVSNHLALGFLLDHIGGAMTLVPLVGLDVDERTLDCEFLLILLIRKLLLWLRTLVGLMAFFVTL
Ga0213505_122764	Ga0213505_1227641	F004317	WTGKVFGALRPCLSPNRDERQMNLSYMVLLDMWNMFG