3300032932: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R3_MAIN_15MAY2017_LR1 (Metagenome Metatranscriptome)

Overview

Basic Information

• IMG/M Taxon OID: 3300032932
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0128851 | Gp0330571 | Ga0314717
• Sample Name: Metatranscriptome of switchgrass phyllosphere microbial communities from Michigan, USA - G5R3_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: 52285050
• Sequencing Scaffolds: 13
• Novel Protein Genes: 14
• Associated Families: 14

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	2
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	1
Not Available	4
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Pooideae → Triticodae → Triticeae → Hordeinae → Hordeum → Hordeum vulgare → Hordeum vulgare subsp. vulgare	1
All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	1
All Organisms → cellular organisms → Eukaryota	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	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): 42.3956
  • Long. (^o): -85.372
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F000459	Metagenome / Metatranscriptome	1109	Y
F001705	Metagenome / Metatranscriptome	648	Y
F007513	Metagenome / Metatranscriptome	349	Y
F014095	Metagenome / Metatranscriptome	265	Y
F020484	Metagenome / Metatranscriptome	223	Y
F029306	Metagenome / Metatranscriptome	188	Y
F033278	Metagenome / Metatranscriptome	177	Y
F042712	Metagenome / Metatranscriptome	157	Y
F061504	Metagenome / Metatranscriptome	131	N
F062345	Metagenome / Metatranscriptome	130	Y
F067310	Metagenome / Metatranscriptome	125	Y
F069562	Metagenome / Metatranscriptome	123	Y
F082073	Metagenome / Metatranscriptome	113	Y
F096516	Metagenome / Metatranscriptome	104	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0314717_107413	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	1134
Ga0314717_108205	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae	1087
Ga0314717_116768	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida	788
Ga0314717_118155	Not Available	758
Ga0314717_118635	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	748
Ga0314717_119026	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → PACMAD clade → Panicoideae	740
Ga0314717_120055	Not Available	720
Ga0314717_122958	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta → Tracheophyta → Euphyllophyta → Spermatophyta → Magnoliopsida → Mesangiospermae → Liliopsida → Petrosaviidae → commelinids → Poales → Poaceae → BOP clade → Pooideae → Triticodae → Triticeae → Hordeinae → Hordeum → Hordeum vulgare → Hordeum vulgare subsp. vulgare	672
Ga0314717_128616	All Organisms → cellular organisms → Eukaryota → Viridiplantae → Streptophyta → Streptophytina → Embryophyta	596
Ga0314717_130339	All Organisms → cellular organisms → Eukaryota	578
Ga0314717_136921	Not Available	515
Ga0314717_137540	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	511
Ga0314717_138815	Not Available	501

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0314717_107413	Ga0314717_1074131	F007513	MVVTVLQRVVDLPVVLLVVLSTDMDHGTKALEEVTMHHAFLAVVVVSLAVDGTGDT
Ga0314717_108205	Ga0314717_1082051	F061504	MENPSLNLSLLCLAPKYLDLILWALSFGLHWRVDVHKHASNHHGLRSFVRALAFVFLRVI
Ga0314717_116768	Ga0314717_1167682	F069562	MGNYLTILPLIALLLLDLLNSNLGPQLCRSNAPKWFGEDVPELSSCLDILEPDLSTIDAITDEVILGVDVLASVVVDGVLC
Ga0314717_118155	Ga0314717_1181551	F020484	MAKTLDAARSEIRNRLQRWDKMDTTLLFGINFVRISTSWKGKFVHFAMEQCFSTGSVLEIERKICEDETAMGQRGIEGGDDDVKQ
Ga0314717_118635	Ga0314717_1186352	F001705	MYVYNELTWDELVKRDFKDWNISKEIALDRSAWRLAINVPES
Ga0314717_119026	Ga0314717_1190261	F042712	MEYLFDESGRQKFLQLLADRPALELVEASQALLHRLGVGSDIKRVLGDLPRYARHVRGAPRKDICVGAEEIDEHHFLF
Ga0314717_120055	Ga0314717_1200551	F096516	MKEDSKSLAQAGMLTEIEDIVNLKILIEEVRLDQDMKAQVLCMSFYVNLSIGCRTIKGGAISVV
Ga0314717_122958	Ga0314717_1229581	F067310	PEDTLDTDLEAMMTRLNEIPNRVQAWKKSAARCGADVALSLVRVHCKDAKEEKLKTLQVANTKKLKFEDFMETFIEAATRIADGIDLDSFVEPASPTGA
Ga0314717_123437	Ga0314717_1234371	F000459	VHSGRIKLAENVKRGRGRPHLTWEESVKRDLKVWDIAKELAMDRGAWKLAIHVPEP
Ga0314717_128616	Ga0314717_1286162	F033278	NDEVKGSSRGFQVSSEISFLISARKTLPTSGQTIDVTFDPKIFTN
Ga0314717_130339	Ga0314717_1303392	F082073	KILAAAKELSLKESMPSKKPSQSSVKLTGDVGTKTIQLQEGDDSKTAIIGAGLGDK
Ga0314717_136921	Ga0314717_1369211	F029306	TKLNKSKKNILDTRHENKANKTGFAIFSLSRKKFYIKPYFGQQARNRNKTLTNRKESCEQAAPLKTTPHKESNKI
Ga0314717_137540	Ga0314717_1375401	F062345	GMPKVEWSYLNSIVGTIFGFLCIAVTAFGFLQLLSGVFVVVEESFVLELMAYNSDLRLCTENR
Ga0314717_138815	Ga0314717_1388151	F014095	MLHSLDCFVDPVSSGLIGILPDSTAGLLRFKCVLTLVA