3300025253: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Cvi_mCL_r2 (SPAdes)

Overview

Basic Information

• IMG/M Taxon OID: 3300025253
• GOLD Reference (Study | Sequencing Project | Analysis Project): Gs0053073 | Gp0101312 | Ga0209677
• Sample Name: Arabidopsis root microbial communities from North Carolina, USA - plate scrape CL_Cvi_mCL_r2 (SPAdes)
• Sequencing Status: Permanent Draft
• Sequencing Center: DOE Joint Genome Institute (JGI)
• Published?: N
• Use Policy: Open

Dataset Contents

• Total Genome Size: 131661349
• Sequencing Scaffolds: 41
• Novel Protein Genes: 43
• Associated Families: 40

Dataset Phylogeny
Taxonomy Groups	Number of Scaffolds
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	27
All Organisms → cellular organisms → Bacteria → Proteobacteria	7
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Rhizobacter → unclassified Rhizobacter → Rhizobacter sp. Root1221	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	1
All Organisms → cellular organisms → Bacteria	2
All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	1
All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Schlegelella → Schlegelella koreensis	1

Ecosystem and Geography

Ecosystem Assignment (GOLD)

• Name: Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations
• Type: Host-Associated
• Taxonomy: Host-Associated → Plants → Roots → Endophytes → Unclassified → Arabidopsis Root → Arabidopsis, Maize, Boechera And Miscanthus Rhizosphere Microbial Communities From Different Us Locations

Alternative Ecosystem Assignments

• Environment Ontology (ENVO): Unclassified
• Earth Microbiome Project Ontology (EMPO): Host-associated → Plant → Plant rhizosphere

Location Information

• Location: USA: North Carolina
• Coordinates
  • Lat. (^o): 35.6667
  • Long. (^o): -78.5097
  • Alt. (m): N/A
  • Depth (m): N/A

Associated Families

Family	Category	Number of Sequences	3D Structure?
F012876	Metagenome / Metatranscriptome	276	Y
F022481	Metagenome / Metatranscriptome	214	Y
F023377	Metagenome / Metatranscriptome	210	Y
F023378	Metagenome / Metatranscriptome	210	Y
F024826	Metagenome / Metatranscriptome	204	Y
F026918	Metagenome / Metatranscriptome	196	N
F027546	Metagenome / Metatranscriptome	194	Y
F028856	Metagenome / Metatranscriptome	190	Y
F031516	Metagenome / Metatranscriptome	182	Y
F033107	Metagenome / Metatranscriptome	178	Y
F034241	Metagenome / Metatranscriptome	175	Y
F035339	Metagenome / Metatranscriptome	172	Y
F036775	Metagenome / Metatranscriptome	169	Y
F036776	Metagenome / Metatranscriptome	169	Y
F037289	Metagenome / Metatranscriptome	168	Y
F039453	Metagenome / Metatranscriptome	163	Y
F040130	Metagenome / Metatranscriptome	162	Y
F040670	Metagenome / Metatranscriptome	161	Y
F040711	Metagenome / Metatranscriptome	161	Y
F040712	Metagenome	161	Y
F044538	Metagenome / Metatranscriptome	154	Y
F044583	Metagenome / Metatranscriptome	154	Y
F045820	Metagenome / Metatranscriptome	152	Y
F049682	Metagenome / Metatranscriptome	146	Y
F049748	Metagenome / Metatranscriptome	146	Y
F049749	Metagenome	146	Y
F050419	Metagenome / Metatranscriptome	145	Y
F051255	Metagenome / Metatranscriptome	144	Y
F052031	Metagenome / Metatranscriptome	143	Y
F053329	Metagenome / Metatranscriptome	141	Y
F055847	Metagenome / Metatranscriptome	138	Y
F056275	Metagenome / Metatranscriptome	137	Y
F062395	Metagenome / Metatranscriptome	130	Y
F062899	Metagenome / Metatranscriptome	130	Y
F070201	Metagenome / Metatranscriptome	123	Y
F073010	Metagenome / Metatranscriptome	120	Y
F077376	Metagenome / Metatranscriptome	117	Y
F078153	Metagenome / Metatranscriptome	116	Y
F080539	Metagenome / Metatranscriptome	115	Y
F092337	Metagenome / Metatranscriptome	107	Y

Associated Scaffolds

Scaffold	Taxonomy	Length
Ga0209677_100269	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	35129
Ga0209677_100474	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	22972
Ga0209677_100632	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	18831
Ga0209677_100748	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	16467
Ga0209677_100760	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	16357
Ga0209677_100793	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	15900
Ga0209677_100968	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	13962
Ga0209677_100987	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	13741
Ga0209677_101016	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	13419
Ga0209677_101108	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	12657
Ga0209677_101113	All Organisms → cellular organisms → Bacteria → Proteobacteria	12618
Ga0209677_101119	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	12557
Ga0209677_101192	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	11905
Ga0209677_101460	All Organisms → cellular organisms → Bacteria → Proteobacteria	10212
Ga0209677_101518	All Organisms → cellular organisms → Bacteria → Proteobacteria	9932
Ga0209677_101665	All Organisms → cellular organisms → Bacteria → Proteobacteria	9341
Ga0209677_101668	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Rhizobacter → unclassified Rhizobacter → Rhizobacter sp. Root1221	9325
Ga0209677_101796	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales	8814
Ga0209677_101817	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	8730
Ga0209677_101931	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	8284
Ga0209677_101998	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	8114
Ga0209677_102293	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Burkholderiales genera incertae sedis → Methylibium	7368
Ga0209677_102377	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	7181
Ga0209677_102923	All Organisms → cellular organisms → Bacteria	5977
Ga0209677_103508	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	5028
Ga0209677_103517	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	5014
Ga0209677_103706	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	4789
Ga0209677_103833	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	4639
Ga0209677_104135	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	4336
Ga0209677_104629	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3886
Ga0209677_104731	All Organisms → cellular organisms → Bacteria → Proteobacteria → Alphaproteobacteria → Hyphomicrobiales → Bradyrhizobiaceae → Bradyrhizobium	3808
Ga0209677_105073	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3560
Ga0209677_105236	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	3448
Ga0209677_105366	All Organisms → cellular organisms → Bacteria → Proteobacteria	3366
Ga0209677_105966	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales → Comamonadaceae → Schlegelella → Schlegelella koreensis	3017
Ga0209677_106133	All Organisms → cellular organisms → Bacteria → Proteobacteria	2932
Ga0209677_107276	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	2393
Ga0209677_107548	All Organisms → cellular organisms → Bacteria → Proteobacteria	2283
Ga0209677_108565	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1964
Ga0209677_110931	All Organisms → cellular organisms → Bacteria → Proteobacteria → Betaproteobacteria → Burkholderiales	1463
Ga0209677_110980	All Organisms → cellular organisms → Bacteria	1455

Sequences

Scaffold ID	Protein ID	Family	Sequence
Ga0209677_100269	Ga0209677_10026937	F062395	LKRVVAGSHVHAETKTSFRYEATWHVEGPLLAWKAEVSLSGRRWALAGGTPEWTGGNEAKAVREDIARSIDGLEA
Ga0209677_100474	Ga0209677_10047415	F092337	MDMMNSLRTATFTISIRDSSEDELEAAAAAFTCTLHRYGMTPEDALGAWRRMDEWERANFAADDDPGERWWRTMAVARDAVLAALHAAGLDGQRRPFTIEPVATRH
Ga0209677_100632	Ga0209677_1006328	F012876	MTQTTARFAALALSALMSFGVIAGVSGIANAQYAAADRLAMAPYGQTHVAVQHVTVIGHRANV
Ga0209677_100748	Ga0209677_1007481	F039453	MPALLTYLRSDAIRLTHGDVAYEPITSDAALGALLLALDLLDRRAFDVPAMRYADRVALVPALDAARQYGLILRRHVDRVDRAVPLLPPSVTVDTAHGWVHEAAALVPEAERDRFCWRLARRLGA
Ga0209677_100760	Ga0209677_1007606	F012876	MTKTFTTQAVAFALSAFMSLGVFAGVNGVAKAQYAKADSLVMAPYGQAHVAVQRVTVIGHRA
Ga0209677_100793	Ga0209677_10079310	F050419	MTNASRPTFLRHFGRPPAPDLADMGTAFALDEALENGSYDSLPPGQPPPLRAAVPVAPWRLWLGRKLGG
Ga0209677_100793	Ga0209677_10079311	F070201	MRTMPLQFLTWGTITAAVGSAAWLSSIDQAAIFCSVGYRATSQAIGLDTPVEPTRAGPSAKNAGSHVAKQVAATAG
Ga0209677_100968	Ga0209677_1009682	F045820	MNAKNSPDRTQDDLPDGRNGDVVGENDDSVMESIGKAVIAPIVGADEGAEPVDPTRDRAFADLTKPLPQGQQETPRSADALDPRGKAR
Ga0209677_100987	Ga0209677_1009877	F077376	MTTYVLSLTGDEEKAANATHWARFRRAKLISVSRKTRERLADGDGRDSIVITALGSADDHERSPRRRDDTHDPAALAALLVRTLDIQDGTGVVLADFDSEAFAADVVARIAALGRDVTCTGQVADFAFSTTVRAAARALLS
Ga0209677_101016	Ga0209677_10101610	F052031	MTIDLHATSPAVSEHHEELVQFVFSSAVCPGLLKNAREILDAAPRELAESFEQAVRGAGLAS
Ga0209677_101108	Ga0209677_1011086	F056275	MDWHCINFKRGGSHESAAADLVLALEDAYDSAGEPPAAEVFLSQGPIGDYAFYLSPEAASMAPAVLQRFHAVMCEPPSDLHRCTPMRL
Ga0209677_101113	Ga0209677_1011135	F035339	LAAAPLTLAQLRRDRLAIWLWLPIGGFALFAIIAGWRHVAGEPPQRLYMVLDIVWIAVTFSLIARRTTRRCPRCNHRWLRSFPWMSMKKIECGVCGHEMPEH
Ga0209677_101119	Ga0209677_1011198	F024826	MADATPYFGIAPFVLGMSRELVRAAAGQPDTVETSQDDEGGDVETWFYQGGDVELEFEAVADAKLESITAWSSDITINGVALIGADLGDLPGLARAADIHDLELTDDFADSGQCWQSEQHGLMLWVAKGKVVNLTIFPRFDDSGEEPQWPE
Ga0209677_101192	Ga0209677_1011925	F026918	MDSKQLFIEHLAGELQAMEVGRVPMNALRYRVHAKMLRKALIGASTPSLLERQGGAHPQVVHALSNRFFEETGHLLQPNATAHKARSLLERTMASCRQARQK
Ga0209677_101460	Ga0209677_1014603	F049682	MDQREFEAVVDEFGANVKDLVELVEQARYEQPTAIAISRLLDAREDLLALSGKLPALRAISPPIELPIKLAGLRKHIAEAREGLKSSADSAAILHLVIDVGETFAAAVAPLQAQGRWPKGRAR
Ga0209677_101518	Ga0209677_10151811	F037289	MSMWLSNQSVSVAVLAVTSLRAVQSGALSLVAPSTLRRARAGVLRVITVVAGH
Ga0209677_101665	Ga0209677_1016655	F062899	MNSLAANRTAVRPPACMRGLDRHCSFVEDLNWPAARPSPDKKAPRRTEVWVPGPSGQWEGVTPTLQ
Ga0209677_101668	Ga0209677_1016684	F049749	MRFFGRKRTSVTLVRAWCSPFGEDGPAGELLALVDQVLAAIPARPLEGSINLGDRQPMSSLRRALARMKPVELDALAVHDEAGEIICSFGAEGASVGDRARAFEIFALLPPASDALQDKLLRLLLGYRLHYGYARRLGPDFCPLTEAPIRRGLFSDKFVVDGGRADWLVPEMDVRAGAVRGLYPANVFPAVGLARLAGSGLKLPPSAPTVGETLWRPTPREQAQLLRANPTYRRFLHFED
Ga0209677_101796	Ga0209677_1017969	F080539	MPELNYVTSGDLDHMQEVLLVKQELSKIGIFLEGFDIRITGVYTKPRPFGFDFDCKRPRDLLVLARSKAVLNEDKDDTLEGAVSAEQTHGTGFRQIGTGQRLHLEIAMDRKCNVHIDSHGYVVGPGQYDWNRALEHGYWDLLSDKAPGLFGAFGKQGQVGPMIRPMQGVDGRMRWVIGLTGHW
Ga0209677_101817	Ga0209677_1018175	F078153	MGWMVFEAMLALAAVLAIVWWTFRGRSDGDDGEEDA
Ga0209677_101931	Ga0209677_1019317	F040711	MPPDTPRDHLANALGSDADQVVMERGFSLAFVGIHGQVRLLQFRLSKKGFSANHAADDAEFATLLDDFTAVVQRQLEARWGGPMAMRAAFDGDGELVERLYDVGTLTRCDEVDPVSPAGRLVKEGEVVDARELLVRASARLVENWGVFEKAPALDDGAHAHEARVRHWVEGTQPA
Ga0209677_101998	Ga0209677_1019983	F023378	MTKTYVVSGSGMKFDAALWPVPPNIEIHFYFQCMREPQFYKTRTILDKLMLDVGMFPDRVALPGEMIPSHFVWAHATEQPPSGVFRRQTGNLALDLSGTDKSHPVALSHIVKTMAGDRRGTTAIHWIVREEEGPADLSGLDCLYPTRLRNGLYDSEESGHVPLPDDVLEQLHKRVVPTEPVPLSGVGFGPMSEWPGVKRRASTR
Ga0209677_102293	Ga0209677_1022934	F040712	MATAEFRRLASMSLRSFIVRRCLQSCLKATGLRVVNLPHVVDARQHVDPPVRLDAGYLVVDRRAFARITFSRGADDDAGPSHVTGFATLSGVLRAICAERIGVAGRAAIPGPRRAVELRREGRWQEVLEASERVEAPMRARLDAWLRGWQFKAYLMALRLLKQF
Ga0209677_102377	Ga0209677_1023776	F012876	MTKTTAQFAALALSALMTLGTVAGVGSIANAQYAKADSLAMAPYGQAHVAVQHVTVVGRRANA
Ga0209677_102377	Ga0209677_1023778	F049748	MDIKQDPNSIPNFNSGGRVGELQRNEPEQTQSSVELDPTAGGDGAASEAAQHESLLGDGEDPAAGKTPDRSTTGAGAIDGLVGAP
Ga0209677_102923	Ga0209677_1029233	F036775	MVVQPDQIDMLSAPTEVPDQPGQQPRRGLSDAVFYAGCFALALLPASLAGIVLNDLIGEPILFLAAVVVTTWVVTTVALVRIAGPMLRCRAIVAAGGLVSVAMCSLFLIE
Ga0209677_103508	Ga0209677_1035085	F028856	MDNFSAGQARDANFEHGPMLAMADPFDLLHADDNLGDEAAFPSTWQVLASGDVPND
Ga0209677_103517	Ga0209677_1035173	F073010	MNRWLSRPRVMVGLALAVFLCIGLFQWPGSPASSGRFAALVGAAPFDERPAGYTLSGVLQAFRLLGAQGVADYTAYRCVDLVFPWLLCALLAAVMLRLEAPRATAWCWLAAGADSIENLFQWRILATRDDLSPDLVRWASAATQVKFALYAAMLLALAAVGARLAWRHRRVAG
Ga0209677_103706	Ga0209677_1037064	F034241	MSQAKPRQYLGALRAAIVAAKAANAARVAAYHVLPNGISCKMDWDGWSDPWYNASPRQQALLDVLQDLLDGGETDVPMIALKTALRLEVPESEILRSRDNTGADGESGYFFDDVLHALYALDAQDTEQVFYGLIDRLMQPGCVQAGLIAAR
Ga0209677_103833	Ga0209677_1038333	F044538	MRLIARFVVLMVAVFGVSLAFAWAWDKSDTPQDTATTHAPAHT
Ga0209677_104135	Ga0209677_1041356	F033107	MRLLTSLALITIAYAAFSRVNKVHAGRTHARPAAKPEEVQTWEGEGGGLPSGGPGPGVKVAPAAVHDPDLAHGGA
Ga0209677_104629	Ga0209677_1046293	F036776	MNSIVRMLAVYAGFALLLCGFTHMEWSPLQPNGFGQWLALLLLIFPAAAAAEFLGERAFGRNTPALEFEESKSHHDCSWGRIATGVFVFVATVAVVLCAAWWLSHPAAA
Ga0209677_104731	Ga0209677_1047315	F022481	MWTAAIVQRRLRTPTGPFFARFFIGIIPGLVAEFAFMGRSTRLTMSFFAAPWTDRKQTVGWKFQHGCSTGRPALTPSF
Ga0209677_105073	Ga0209677_1050733	F051255	MNAAAAYIASTHHAANDWARSQAARTMVRAAMNSNAVVYRRTWPTLEAIETLGEAEYDPSLRFNGFLDSTLDLRDGLSVVEVFAPIEEPAALQEFALLRGRA
Ga0209677_105236	Ga0209677_1052364	F040670	MNPLVNRNTATADIGRPPPADAPMQVLPWAEDSSRSIGAEDANTRYQGELFLPGWLKIELQPTAEQGPGA
Ga0209677_105366	Ga0209677_1053662	F031516	MMHFDTAQMAAITQAHFFSRVAEFIRDQTPVAAYRQAALDTRLRTELWAPHWHTLRDTSEHDAALFMCFLLACHTLGIDAQRAAQAVRQSSQPEASMKLFLSERGLLRLSAFDVPHPARPGAVA
Ga0209677_105966	Ga0209677_1059662	F053329	MPADLENPSAHDPALSRNHAAGVPQDTASPAERALAPAGDAPMQSANATADDGTYVGQAGGYMGAPLPAVEGGVAQVNEANKRGDGAYGFPAGPGVGVPGGEHQPVAQKPDIVPNPYPER
Ga0209677_106133	Ga0209677_1061333	F044583	MSQVLTPRQEILRARIRFALRRATGFVFDIDAMLNRPELRSRRIGLWRDVADHELSSLLDELETEFQHDDADDDSAERTVVMRRVEPGTARR
Ga0209677_107276	Ga0209677_1072762	F027546	MKVAGESDPAPWQPLGERVARPQPQQPEWQPLAHAPCIEINRQGQLRTNLPLPK
Ga0209677_107548	Ga0209677_1075484	F023377	MTHRPVCSPRAIRIAMATALVFTTVAAPAMSVSYQCTGRRVLDAELSPRQGQLHFEGHDWTVTRVPGGREARYVNKKAGIEVVTKERQMTFTHDGETLQCFLFSSALPGDAPQKSAN
Ga0209677_108565	Ga0209677_1085652	F040130	MRVAGLVKRSVAVLVGVMLGMLLVAGSGPWRELLKKADPPPEPAPIQRERAPDLRV
Ga0209677_110931	Ga0209677_1109313	F055847	MNQRYAYRDYEILVSARPAGSQPGWRPEICVIAPDDHWQFVPTHHSLVADDLGYCLEIGRRCAESAIQSMDPAREKATRGVLH
Ga0209677_110980	Ga0209677_1109801	F062899	NRTDARPLPLPRPRAKHCSFVEDLNWPAHMPTPDRKPARPTEVWVPGPNGQWEGVTPTLQ