Sample 3300032825

3300032825: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_MAIN_05JUN2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information
IMG/M Taxon OID	3300032825 Open in IMG/M
GOLD Reference (Study \| Sequencing Project \| Analysis Project)	Gs0128851 \| Gp0330578 \| Ga0314724
Sample Name	Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_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	41934403
Sequencing Scaffolds	26
Novel Protein Genes	27
Associated Families	24

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
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	4
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	2
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	4
Not Available	7
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 → 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 → Panicodae → Paniceae → Panicinae → Panicum → Panicum sect. Panicum → Panicum hallii	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
Location on Map

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Associated Families

Family	Category	Number of Sequences	3D Structure?
F001705	Metagenome / Metatranscriptome	648	Y
F012944	Metagenome / Metatranscriptome	275	Y
F016911	Metagenome / Metatranscriptome	243	Y
F019078	Metagenome / Metatranscriptome	231	Y
F023124	Metagenome / Metatranscriptome	211	Y
F023769	Metagenome / Metatranscriptome	208	Y
F026477	Metagenome / Metatranscriptome	197	Y
F028072	Metagenome / Metatranscriptome	192	N
F029306	Metagenome / Metatranscriptome	188	Y
F032897	Metagenome / Metatranscriptome	178	Y
F037036	Metagenome / Metatranscriptome	168	Y
F041531	Metatranscriptome	159	Y
F042140	Metagenome / Metatranscriptome	158	Y
F046814	Metagenome / Metatranscriptome	150	N
F049431	Metagenome / Metatranscriptome	146	N
F068385	Metagenome / Metatranscriptome	124	Y
F069562	Metagenome / Metatranscriptome	123	Y
F070783	Metagenome / Metatranscriptome	122	Y
F076725	Metagenome / Metatranscriptome	117	Y
F084981	Metagenome / Metatranscriptome	111	Y
F091151	Metagenome / Metatranscriptome	107	Y
F093512	Metagenome / Metatranscriptome	106	N
F096410	Metagenome / Metatranscriptome	104	Y
F104214	Metagenome / Metatranscriptome	100	Y

Associated Scaffolds

Scaffold	Taxonomy	Length	IMG/M Link
Ga0314724_100179	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	3412	Open in IMG/M
Ga0314724_102710	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	1623	Open in IMG/M
Ga0314724_102975	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	1569	Open in IMG/M
Ga0314724_105998	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	1202	Open in IMG/M
Ga0314724_109887	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	960	Open in IMG/M
Ga0314724_111238	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	902	Open in IMG/M
Ga0314724_111309	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	900	Open in IMG/M
Ga0314724_114263	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	800	Open in IMG/M
Ga0314724_115384	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	768	Open in IMG/M
Ga0314724_117223	Not Available	722	Open in IMG/M
Ga0314724_117711	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	710	Open in IMG/M
Ga0314724_119821	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → eudicotyledons → Gunneridae → Pentapetalae → rosids → fabids → Fagales → Fagaceae → Castanea → Castanea mollissima	666	Open in IMG/M
Ga0314724_121367	Not Available	637	Open in IMG/M
Ga0314724_121465	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	635	Open in IMG/M
Ga0314724_122248	Not Available	621	Open in IMG/M
Ga0314724_124404	All Organisms → Viruses → Riboviria → Orthornavirae → Lenarviricota → Miaviricetes → Ourlivirales → Botourmiaviridae	588	Open in IMG/M
Ga0314724_124429	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	587	Open in IMG/M
Ga0314724_124589	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	Open in IMG/M
Ga0314724_126053	Not Available	563	Open in IMG/M
Ga0314724_126293	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	560	Open in IMG/M
Ga0314724_126605	Not Available	556	Open in IMG/M
Ga0314724_126984	Not Available	551	Open in IMG/M
Ga0314724_128241	Not Available	535	Open in IMG/M
Ga0314724_129166	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	525	Open in IMG/M
Ga0314724_129620	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	520	Open in IMG/M
Ga0314724_130370	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	512	Open in IMG/M

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314724_100179	Ga0314724_1001791	F042140	NKSNITSYVIKKKTNGKVVAHKVGKQETSWNHSIWVPKDVITNMKGPQMVWVPKET
Ga0314724_102710	Ga0314724_1027103	F104214	MWSMYCIEPLGRLYRSTWLGGQVASPRDKEGYPGITINPKL
Ga0314724_102975	Ga0314724_1029751	F037036	VLETKRRRKEYFRTVSHVSEGKCFRTTWSHVPISFTQADLRLQHYPHNDPLVIRANIGKNSVHFARNDVGRTLV
Ga0314724_105998	Ga0314724_1059981	F068385	MISLVSYEIXKETPQFKIIMHVKDSFSMIKDLSSL
Ga0314724_109887	Ga0314724_1098872	F028072	LNLRVLQYSVKIEKLHYLNLEVNTGKTVSTKENINIRCRINSSEEHTWHTSHGQTNLIVDLIHNFYITWGKRQDDLELKFERLQKEHKHLEEQYLVANKKLELALQAFEESKIFLGKISQNSDYIKRDISYLFNKLESTNIAEHSKEIVLSSSGILEVTRSLNSDKWKYLIASLEDTSVS
Ga0314724_111238	Ga0314724_1112382	F069562	MSNYLIILPLIALLLLDLLNSNLGPQLCKSNVPKWLGEDVPELSSCLDILELDLSTVDAITDEVILGVDVLAPVVVDMVLC
Ga0314724_111309	Ga0314724_1113091	F041531	FVDAYQRCRIGRRWGFLPSQLGHTTYPAYKRERGLRVRRTYTPLPEPSDGCVFPEEMVRITGRDPTPVEQEALRAVQWRHGRWGGSKRDVFSPSCGKVRRSYHYRAQPGFSYLSFVGPGRTKLSPLWEKGADWGLVPADFRSEEEERGLAKLEQFRADWDSGFIAIGD
Ga0314724_114263	Ga0314724_1142631	F023124	LVATKLIPVETSSKVAADPLASGDSQVTLSHVECSHRALAHDPAGSLVALHVS
Ga0314724_115384	Ga0314724_1153841	F019078	MSAEQKDLGDSAMGDGEKTCPCCQFYGVPCRQARATEDEATTRRNQRLFSGTKRKMSHQEKLAEDSLFLDPPSVEELQTIQKRKDPKCSRDTQVENQALHDYVDVLTITMKVIQPRSHKESKEQATEIMQDVMLSSQGSQPSSVSHHHR
Ga0314724_117223	Ga0314724_1172231	F091151	SLRTSRRSVRPGLDSRFLRVGPSSGPRLPREDWAGWHHIGGQDV
Ga0314724_117711	Ga0314724_1177111	F001705	RGRGRPKLTWDESVKRDLKDWNISKEIALDRSAWRLAINVP
Ga0314724_119821	Ga0314724_1198211	F049431	GRINQVTILSPSAEAHERTPRRRPGCTGRKGRRRSEPQPQASQVCETPEPQATDSIAPTEFPKLRSATGGIRLLHRSLHRYIRPSGGEDSRQVNAQARVLDRAIPEDLVKRLAKPVIHRPQMLPANRETSRTSVPSASTLQLPEGGQHRASRKESPSPK
Ga0314724_121367	Ga0314724_1213671	F026477	MASSTSYHDVRSMALVDLLCFVAYHLRISCCLCAVTFQSLASSYRIELVAQGQHPASFIFSRSDLLWFALILRVGIISARLGLANGLDDPVA
Ga0314724_121465	Ga0314724_1214652	F032897	VDASFTRSHCHQKTIALQYVPSKLQLADLFTKAQTREQHRLHLLKLNASDPPLPP
Ga0314724_122248	Ga0314724_1222482	F084981	GTLRARPLGARLYKLMLLLRTCEAPVAGDLLMSSVQCDARSLVKTLLLGTSVECGQNVVESVTPMCSAPESTRTALHLNLSLLLLLSRLWWPWHLSLCPCPCLCLCLWDPP
Ga0314724_124404	Ga0314724_1244041	F023769	WSMPCADLHKNAFQRSSSRVAHVTRSVDNPTSGSTVKRCRDCLRGERDTKETIHNGLLLLRVRYGLPYAELPDCGPGDLSRFLSFLLLQGKERTSVAFPRRQRPGENGLCTMQRLCRRDRWALAHGCSSIKRNLPKGCFRHTPSVFAAWEAAALSQPPPLTSGYLEHVRRVVTGIFRPGWDGRYNSFVGSHVPNPS
Ga0314724_124429	Ga0314724_1244291	F104214	EALGRLYRTTWLGGQVASPRDKEGYPGITTNPKLTISGVA
Ga0314724_124589	Ga0314724_1245891	F012944	KEIEAKLEDNLSSTWTQINLKPKSTRIGTPFAQPVFGLRNSSSAYKQMIKSIYENSLDHLLRVENHLVTASREAPVFDVYPDPVKSPPDSLDGITNALAKMQLKSCRSHTLAELLDNLREVASIDDLPFQHGTPLATERETGSRETVLANFDSDLDSFSSERLVPVIIQQSEASQHDPNEALDQISADNLTQDA
Ga0314724_126053	Ga0314724_1260531	F093512	MSKDDWKAVYAKDDDLKLTKAGGNKIRRTTTPSIFSSGMLDILLIE
Ga0314724_126293	Ga0314724_1262932	F016911	AIIGRPALYRFMAIAHYGYLVLKMPSPAGVLTVQGDRTAAVAAVERLHALAAEAARTEEDPSTSQPKAPAKAPKVQPSDPGHVPVKTVQIGADSTRTTRIAGNLEEK
Ga0314724_126605	Ga0314724_1266051	F046814	AFPARLRSVFLVLLPFFIPKLCFIQIMRRNRTYPHNWVVVKENDNKQDNLRFGFWNPVDLMSSSNEEFSLSNIDGASNSEMKNSDMIIARN
Ga0314724_126984	Ga0314724_1269841	F029306	MQTKLNKSKTITIETKLEKKANKTGFTIFSLSSKKFYIKPPFGQQARNRNKTLTTSKQTCERVVPLKTTPHKESNEIWFDIFRAVYK
Ga0314724_128241	Ga0314724_1282411	F001705	RGRPKLTWDESVKRDLKDWNISKEIALDMSARRLTINVSEP
Ga0314724_129166	Ga0314724_1291661	F070783	MALVDVDVAFDIMGSYMMRITCMLREIELMTLVGVIYIGYIGDMNFTCMLFFTRIY
Ga0314724_129620	Ga0314724_1296202	F001705	GRPKLTWDESVKRDLKDWNISKEIALDRSVWRLAINVPEP
Ga0314724_129692	Ga0314724_1296921	F096410	MSWVGSTVHAVNSNRVQILGNVRLDWFVISLNLGIGFLRVKS
Ga0314724_130370	Ga0314724_1303701	F076725	LILGNFVFLTPAGSSTLVATTKICIELLGCRTDPDPLAAGEGSGPLMTYSGERELVSGGGPESC

Bioinformatics & Integrated Biology Lab
Institute for Fundamental Biomedical Research
Biomedical Sciences Research Center "Alexander Fleming"

NMPFamsDB

NMPFamsDB

NMPFamsDB

A database of Novel Metagenome Protein Families

A database of Novel Metagenome Protein Clusters

A database of Novel Metagenome Protein Clusters

3300032825: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R2_MAIN_05JUN2017_LR1 (Metagenome Metatranscriptome)

Overview

Ecosystem and Geography

Associated Families

Associated Scaffolds

Sequences