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["Supplementary Table 1. MIGS mandatory information for the complete genome of Paenarthrobacter nicotinovorans ATCC 49919. "]
[]
["Section","Item","Paenarthrobacter nicotinovorans ATCC 49919 complete genome"]
["Investigation","project name","Paenarthrobacter nicotinovorans pAO1 strain ATCC 49919 whole genome sequencing"]
[null,"submitted to INSDC","yes; SAMN17383832"]
[null,"investigation type","bacteria_archaea"]
["Environment","broad-scale environmental context","anthropogenic environment [ENVO:01000313]"]
[null,"local environmental context","culturing environment [ENVO:01000312]"]
["Nucleic acid sequence source","number of replicons",2]
[null,"extrachromosomal elements",1]
[null,"estimated size","4481325 bp"]
[null,"reference for biomaterial","Eberwein et al., 1961(2)"]
[null,"source material identifiers","ATCC:49919; DSM420"]
[null,"isolation and growth condition","Decker and Bleeg, 1965(3)"]
["Sequencing","sequencing method","MinION|IlluminaNovaSeq 6000"]
[null,"library reads sequenced",84018969]
[null,"library layout","single|paired"]
[null,"assembly name","UAIC_BIO_Pnic_3.0"]
[null,"assembly quality","Finished genome"]
[null,"assembly software","Unicycler v.0.4.9"]
[null,"annotation","NCBI Prokaryotic Genome Annotation Pipeline (PGAP)"]
[null,"number of contigs",2]
[null,"completeness score","high;100%"]
[null,"completeness software","CheckM v1.1.3"]
[null,"contamination score",{"v":0,"d":"0%"}]
[null,"contamination screening input","Contigs"]
[null,"decontamination software","CheckM v1.1.3"]

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["Supplementary Table 2. Genomes of strains belonging to the Paenarthrobacter, Arthrobacter, Nocardioides and Rhodococcus genera evaluated in the study. The table lists all the Paenarthrobacter strains available in NCBI Genomes database as well as Arthrobacter, Nocardioides and Rhodococcus strains known to have the nic-genes."]
["Organism Name","Strain","Assembly Accession","Assembly Level","Size (Mb)","No of contigs","No of scaffolds","No of plasmids","nic genes location"]
["Strains harboring at least 5 different nic-genes"]
["Paenarthrobacter nicotinovorans","ATCC 49919","GCA_021919345.1","Complete Genome",{"v":4.481325,"d":"4.48"},2,2,1,"pAO1"]
["Paenarthrobacter nicotinovorans","JCM 3874","GCA_014648735.1","Scaffold",{"v":4.444711,"d":"4.44"},47,31,"nd","contig, BMRR01000008.1"]
["Paenarthrobacter nicotinovorans","DSM 420","GCA_017876445.1","Contig",{"v":4.491478,"d":"4.49"},2,"nd","nd","contig, JAGINZ010000002.1"]
["Paenarthrobacter ureafaciens","CZY1","GCA_016694995.1","Complete Genome",{"v":4.402759,"d":"4.40"},2,2,1,"pCZY"]
["Arthrobacter sp.","NicSoilB11","GCA_019977375.1","Complete Genome",{"v":4.653565,"d":"4.65"},3,3,2,"pNicSoilB11-2"]
["Arthrobacter sp.","NicSoilE8","GCA_019977415.1","Complete Genome",{"v":4.643472,"d":"4.64"},3,3,2,"pNicSoilE8-2 "]
["Arthrobacter sp.","NtRootA2","GCA_019976995.1","Complete Genome",{"v":4.585189,"d":"4.59"},3,3,2,"pNtRootA2-2"]
["Arthrobacter sp.","NtRootA4","GCA_019977095.1","Complete Genome",{"v":4.546719,"d":"4.55"},2,2,1,"pNtRootA4"]
["Arthrobacter sp.","NtRootC45","GCA_019977155.1","Complete Genome",{"v":4.546722,"d":"4.55"},2,2,1,"pNtRootC45"]
["Arthrobacter sp.","NtRootC7","GCA_019977135.1","Complete Genome",{"v":4.546721,"d":"4.55"},2,2,1,"pNtRootC7-1 "]
["Arthrobacter sp.","NtRootD5","GCA_019977175.1","Complete Genome",{"v":4.546721,"d":"4.55"},2,2,1,"pNtRootD5-1"]
["Arthrobacter sp.","StoSoilB13","GCA_019977255.1","Complete Genome",{"v":4.956288,"d":"4.96"},3,3,2,"pStoSoilB13-1"]
["Arthrobacter sp.","TES","GCA_014863565.1","Complete Genome",{"v":4.786524,"d":"4.79"},4,4,3,"pTES1"]
["Arthrobacter sp.","ZXY-2","GCA_001854365.1","Complete Genome",{"v":5.058708,"d":"5.06"},6,6,5,"pZXY21"]
["Arthrobacter sp.","M2012083","GCA_000281065.1","Contig",{"v":4.629172,"d":"4.63"},67,"nd","nd","contig, NZ_AKKK01000058"]
["Arthrobacter sp.","StoSoilA2","GCA_019977195.1","Complete Genome",{"v":4.934451,"d":"4.93"},1,1,0,"chroomosome"]
["Arthrobacter sp.","NicSoilC5","GCA_019977395.1","Complete Genome",{"v":4.691366,"d":"4.69"},1,1,0,"chromosome"]
["Arthrobacter sp.","NtRootA1","GCA_019976975.1","Complete Genome",{"v":5.279883,"d":"5.28"},1,1,0,"chromosome"]
["Arthrobacter sp. ","NtRootA9","GCA_019977115.1","Complete Genome",{"v":4.177067,"d":"4.18"},1,1,0,"chromosome"]
["Arthrobacter sp.","StoSoilB5","GCA_019977235.1","Complete Genome",{"v":5.299525,"d":"5.30"},1,1,0,"chromosome"]
["Nocardioides sp.","JQ2195","GCA_012272695.1","Complete Genome",{"v":4.078334,"d":"4.08"},2,2,1,"chromosome"]
["Nocardioides sp.","JS614","GCA_000015265.1","Complete Genome",{"v":5.293685,"d":"5.29"},2,2,1,"chromosome"]
["Paenarthrobacter sp","YJN-5","GCA_015040095.1","Complete Genome",{"v":5.331418,"d":"5.33"},5,5,4,"chromosome"]
["Rhodococcus opacus","R7","GCA_000736435.1","Complete Genome",{"v":10.118052,"d":"10.12"},40,6,5,"chromosome"]
["Rhodococcus opacus","B4","GCA_000010805.1","Complete Genome",{"v":8.834939,"d":"8.83"},6,6,5,"chromosome"]
["Rhodococcus opacus","PD630","GCA_000599545.1","Complete Genome",{"v":9.169032,"d":"9.17"},10,10,9,"chromosome"]
["Rhodococcus opacus","PD630","GCA_020542785.1","Complete Genome",{"v":9.166298,"d":"9.17"},4,4,3,"chromosome",null,24168675]
["Rhodococcus opacus","DSM 43205","GCF_001646735.1","Contig",{"v":8.534314,"d":"8.53"},382,"nd","nd","multiple contigs"]
["Rhodococcus opacus","ATCC 51881","GCF_012396235.1","Contig",{"v":8.111152,"d":"8.11"},110,"nd","nd","multiple contigs"]
["Other Paenarthrobacter strains available in NCBI Genomes"]
["Paenarthrobacter nicotinovorans","nic-","GCF_021918005.1","Complete Genome",4.32,1,1,1,"-"]
["Paenarthrobacter aurescens","TC1","GCA_000014925.1","Complete Genome",{"v":5.226648,"d":"5.23"},3,3,2,"-"]
["Paenarthrobacter sp","JL.01a","GCA_025452095.1","Complete Genome",{"v":4.404497,"d":"4.40"},1,1,0,"-"]
["Paenarthrobacter sp","YJN-D","GCA_015040335.1","Complete Genome",{"v":4.479271,"d":"4.48"},4,4,3,"-"]
["Paenarthrobacter ureafaciens","YL1","GCA_014076395.1","Complete Genome",{"v":4.66343,"d":"4.66"},1,1,0,"-"]
["Paenarthrobacter ureafaciens","DnL1-1","GCA_017357445.1","Complete Genome",{"v":4.724281,"d":"4.72"},3,3,2,"-"]
["Paenarthrobacter ureafaciens","AT","GCA_022810785.1","Complete Genome",{"v":4.559818,"d":"4.56"},5,5,4,"-"]
["Paenarthrobacter ilicis","CECT 4207","GCA_011761315.1","Scaffold",{"v":4.090171,"d":"4.09"},24,22,0,"-"]
["Paenarthrobacter nicotinovorans","Hce-1","GCA_001662445.1","Scaffold",{"v":4.812174,"d":"4.81"},101,101,"nd","-"]
["Paenarthrobacter nicotinovorans","231Sha2.1M6","GCA_000514015.1","Scaffold",{"v":4.772546,"d":"4.77"},44,34,"nd","-"]
["Paenarthrobacter nicotinovorans","26Cvi1.1E","GCA_000514155.1","Scaffold",{"v":4.684304,"d":"4.68"},30,26,"nd","-"]
["Paenarthrobacter nitroguajacolicus","HG","GCA_001375615.1","Scaffold",{"v":4.849808,"d":"4.85"},5,3,"nd","-"]
["Paenarthrobacter nitroguajacolicus","SM1928","GCA_007786235.1","Scaffold",{"v":4.924076,"d":"4.92"},107,105,"nd","-"]
["Paenarthrobacter nitroguajacolicus","xwA8","GCA_013393175.1","Scaffold",{"v":4.960716,"d":"4.96"},61,59,"nd","-"]
["Paenarthrobacter nitroguajacolicus","xwA3","GCA_013393275.1","Scaffold",{"v":4.845531,"d":"4.85"},57,55,"nd","-"]
["Paenarthrobacter sp","Bin.011_Pasture","GCA_024508985.1","Scaffold",{"v":3.183583,"d":"3.18"},2527,956,"nd","-"]
["Paenarthrobacter sp","AR 02","GCA_021538675.1","Scaffold",{"v":4.423496,"d":"4.42"},38,37,"nd","-"]
["Paenarthrobacter sp","CM16","GCA_013179505.1","Scaffold",{"v":4.982797,"d":"4.98"},625,619,"nd","-"]
["Paenarthrobacter sp","DKR-5","GCA_018531425.1","Scaffold",{"v":3.7772,"d":"3.78"},16,15,"nd","-"]
["Paenarthrobacter sp","GOM3","GCA_018215265.1","Scaffold",{"v":4.418999,"d":"4.42"},58,50,"nd","-"]
["Paenarthrobacter sp","MMS21-TAE1-1","GCA_019038615.1","Scaffold",{"v":5.020099,"d":"5.02"},37,36,"nd","-"]
["Paenarthrobacter sp","MSM-2-10-13","GCA_011605365.1","Scaffold",{"v":4.716016,"d":"4.72"},25,24,"nd","-"]
["Paenarthrobacter sp","TYUT067","GCA_023656375.1","Scaffold",{"v":4.712148,"d":"4.71"},53,50,"nd","-"]
["Paenarthrobacter ureafaciens","xwA7","GCA_013393245.1","Scaffold",{"v":4.679052,"d":"4.68"},70,67,"nd","-"]
["Paenarthrobacter aurescens","NBRC 12136","GCA_006538985.1","Contig",{"v":4.313228,"d":"4.31"},61,"nd","nd","-"]
["Paenarthrobacter aurescens","TC1","GCA_025421775.1","Contig",{"v":5.09192,"d":"5.09"},843,"nd","nd","-"]
["Paenarthrobacter histidinolovorans","JCM 2520","GCA_014647595.1","Contig",{"v":4.652823,"d":"4.65"},23,"nd","nd","-"]
["Paenarthrobacter ilicis","DSM 20138","GCA_016907545.1","Contig",{"v":3.973023,"d":"3.97"},1,1,"nd","-"]
["Paenarthrobacter nicotinovorans","SSBW5","GCA_007670255.1","Contig",{"v":4.326735,"d":"4.33"},42,"nd","nd","-"]
["Paenarthrobacter sp","A20","GCA_024168825.1","Contig",{"v":5.379468,"d":"5.38"},3,"nd","nd","-"]
["Paenarthrobacter sp","UW852","GCA_024608385.1","Contig",{"v":4.222426,"d":"4.22"},27,"nd","nd","-"]
["Paenarthrobacter ureafaciens","KI72","GCA_002049485.1","Contig",{"v":4.568574,"d":"4.57"},105,"nd","nd","-"]
["Paenarthrobacter ureafaciens","DSM 20126","GCA_004028095.1","Contig",{"v":4.401812,"d":"4.40"},11,"nd","nd","-"]
["Paenarthrobacter ureafaciens","SCN18_26_2_15_R1_B_64_47","GCA_017306175.1","Contig",{"v":4.082655,"d":"4.08"},49,"nd","nd","-"]
["Paenarthrobacter ureafaciens","MPD2","GCA_019067065.1","Contig",{"v":4.38951,"d":"4.39"},65,"nd","nd","-"]

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["Supplementary Table 3. Annotations of the nic-genes cluster on the two pAO1 plasmid sequences. Bold indicates genes experimentally related to nicotine degradation."]
[]
["Gene/CDS","Product","AJ507836",{"$nulls":3},"CP089294"]
[null,null,"Min","Max","Length","Direction","Min","Max","Length","Direction"]
["nbr","NAD(P)H-Nicotine Blue (4,4',5,5'-tetrahydroxy-3,3'-diazadiphenoquinone-(2,2')) Oxidoreductase",53903,54517,615,"reverse",83753,84367,615,"reverse"]
["hypothetical","hypothetical, cupin domain-containing protein",54899,55243,345,"reverse",84749,85093,345,"reverse"]
["mao","monoamine oxidase",55240,56505,1266,"reverse",85090,86355,1266,"reverse"]
["hypothetical","hypothetical protein",56912,57442,531,"forward"]
["sad","succinic semialdehyde dehydrogenase",57584,58936,1353,"forward",87282,88787,1506,"forward"]
["hypothetical","DUF2437 domain-containing protein CDS",{"$nulls":4},88829,89047,219,"forward"]
["hypothetical","fumarylacetoacetate hydrolase",59275,59715,441,"forward",89093,89566,474,"forward"]
["nepB","efflux pump of SMR family, related to nicotine catabolism",59915,60415,501,"reverse"]
["nepA","efflux pump of SMR family, related to nicotine catabolism",60466,60816,351,"reverse",90317,90634,318,"reverse"]
["folD","putative methylene-tetrahydrofolate dehydrogenase cyclohydrolase (folD) homolog",60844,61770,927,"reverse",90695,91621,927,"reverse"]
["abo","gamma-N-methylaminobutyrate oxidase",61867,64341,2475,"reverse",91718,94192,2475,"reverse"]
["purU","putative formyltetrahydrofolate deformylase",64397,65260,864,"reverse",94248,95111,864,"reverse"]
["hypothetical","hypothetical protein",65268,65555,288,"reverse"]
["hypothetical","putative amino acid permease, APC family permease",66082,67527,1446,"reverse",95934,97379,1446,"reverse"]
["pmfR","transcriptional activator pmfR",68009,69421,1413,"forward",97861,99273,1413,"forward"]
["hypothetical","putative transposase",70398,70655,258,"reverse"]
["hypothetical","hypothetical protein",70884,71327,444,"reverse"]
["hypothetical","hypothetical protein",71475,72146,672,"forward",100517,101203,687,"forward"]
["hypothetical","hypothetical protein",72227,72439,213,"reverse"]
["mobA","MobA, related to molybdopterin cytosine dinucleotide cofactor biosynthesis",72530,73144,615,"reverse",102382,102996,615,"reverse"]
["hypothetical","hypothetical protein",73137,73490,354,"reverse",102989,103342,354,"reverse"]
["coxF","putative carbon monoxide dehydrogenase subunit F, XdhC family protein",73517,74650,1134,"reverse",103369,104502,1134,"reverse"]
["coxE","putative carbon monoxide dehydrogenase subunit  E, VWA domain-containing protein",74643,75734,1092,"reverse",104495,105586,1092,"reverse"]
["coxD","putative carbon monoxide dehydrogenase subunit D, AAA family ATPase",75752,76645,894,"reverse",105604,106308,705,"reverse"]
["nit","omega-amidase for alpha-ketoglutaramate",76848,77732,885,"reverse",106700,107575,876,"reverse"]
["coxG","putative carbon monoxide dehydrogenase subunit G, SRPBCC family protein",77729,78436,708,"reverse",107581,108288,708,"reverse"]
["hph","2,6-dihydroxypyridine 3-hydroxylase",78452,79645,1194,"reverse",108304,109497,1194,"reverse"]
["pkc","putative polyketide cyclase",79642,80574,933,"reverse",109494,110426,933,"reverse"]
["hypothetical","hypothetical, Dabb family protein",80574,80894,321,"reverse",110426,110731,306,"reverse"]
["kdhL","6-hydroxy-pseudooxynicotine:acceptor oxidoreductase, hydroxylating, (ketone  dehydrogenase), large subunit",80977,83361,2385,"reverse",110829,113213,2385,"reverse"]
["pnh","2,6-dihydroxy-pseudo-oxynicotine hydrolase",83529,84632,1104,"forward",113381,114484,1104,"forward"]
["hypothetical","hypothetical, cupin domain-containing protein",84625,84975,351,"forward",114477,114827,351,"forward"]
["hypothetical","putative transcriptional regulator, helix-turn-helix domain-containing protein",85010,86233,1224,"reverse",114862,116085,1224,"reverse"]
["hypothetical","putative transcriptional regulator, helix-turn-helix domain-containing protein",86297,87481,1185,"forward",116149,117333,1185,"forward"]
["kdhM","6-hydroxy-pseudooxynicotine:acceptor oxidoreductase, hydroxylating, (ketone dehydrogenase), medium subunit",87630,88520,891,"forward",117482,118372,891,"forward"]
["kdhS","6-hydroxy-pseudooxynicotine:acceptor oxidoreductase, hydroxylating, (ketone dehydrogenase), small subunit",88520,89002,483,"forward",118372,118854,483,"forward"]
["hypothetical","hypothetical protein",89719,90030,312,"forward"]
["hypothetical","hypothetical protein",90030,90224,195,"forward"]
["hypothetical","hypothetical protein",90370,90606,237,"reverse",120222,120458,237,"reverse"]
["hypothetical","hypothetical, DUF948 domain-containing protein",90622,91212,591,"reverse",120474,120848,375,"reverse"]
["6-hlno","6-hydroxy-L-nicotine oxidase",91550,92827,1278,"reverse",121402,122679,1278,"reverse"]
["ndhL","nicotine dehydrogenase (large subunit)",92895,95345,2451,"reverse",122747,125197,2451,"reverse"]
["ndhS","nicotine dehydrogenase (small subunit)",95338,95835,498,"reverse",125190,125687,498,"reverse"]
["ndhM","nicotine dehydrogenase (medium subunit)",95832,96683,852,"reverse",125684,126535,852,"reverse"]
["is1473","putative transposase, related to IS1473",97125,97835,711,"reverse"]
["is1473","putative transposase, related to IS1473","<97835",">98095",">260","reverse",126977,127947,971,"reverse"]
["moaD","putative molybdopterin cofactor synthesis protein moaD",98374,98640,267,"reverse",128225,128491,267,"reverse"]
["moaA","molybdopterin cofactor synthesis protein moaA",98647,99762,1116,"reverse",128498,129616,1119,"reverse"]
["moeA","molybdopterin cofactor synthesis protein moeA",100053,101342,1290,"forward",129958,131196,1239,"forward"]
["moaC","molybdopterin cofactor synthesis protein moaC",101339,101845,507,"forward",131193,131699,507,"forward"]
["moaE","molybdopterin synthase (large subunit moaE)",101958,102425,468,"forward",131812,132279,468,"forward"]
["modA","molybdate-binding periplasmic protein modA",102436,103224,789,"forward",132239,133078,840,"forward"]
["modB","molybdenum transport transmembrane protein modB",103343,104062,720,"forward",133053,133916,864,"forward"]
["modC","molybdenum transport ATPase modC",104059,105108,1050,"forward",133913,134962,1050,"forward"]
["hypothetical","putative beta-glucosidase",106666,108417,1752,"reverse",136521,138272,1752,"reverse"]
["hypothetical","hypothetical MFS transporter  protein",108429,109703,1275,"reverse",138284,139558,1275,"reverse"]
["hypothetical","putative LacI-family transcriptional regulatory protein",109837,110940,1104,"forward",139692,140795,1104,"forward"]
["hypothetical","hypothetical antibiotic biosynthesis monooxygenase",111227,111532,306,"reverse",141082,141366,285,"reverse"]
["putative amino acid permease CDS","putative amino acid transporter, APC family permease",111798,113291,1494,"reverse",141653,143146,1494,"reverse"]
["6-hdno","6-hydroxy-D-nicotine oxidase",113841,115220,1380,"forward",143699,145075,1377,"forward"]
["hypothetical","putative amino acid transporter, APC family permease",115728,117125,1398,"forward",145583,147004,1422,"forward"]
["hdnoR","transcriptional repressor of the 6-hydroxy-D-nicotine oxidase gene",117206,117790,585,"reverse",147060,147644,585,"reverse"]

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["Supplementary Table 4. MEGA BLAST results of different plasmids and contigs against the pAO1 megaplasmid of P. nicotinovorans ATCC 49919"]
[]
["Query","Accession","Max Score","Total Score","Query Cover","E value","Per. Ident","Acc. Len"]
[" pNtRootA2-2, Arthrobacter sp. NtRootA2","AP024633.1","1.714e+05","2.965e+05","96%","0.0","99.92%","160561"]
[" pNtRootA4, Arthrobacter sp. NtRootA4","AP024635.1","1.881e+05","2.965e+05","96%","0.0","99.93%","160560"]
["pNtRootC7-1, Arthrobacter sp. NtRootC7","AP024638.1","1.881e+05","2.965e+05","96%","0.0","99.93%",160559]
["pNtRootC45, Arthrobacter sp. NtRootC45","AP024640.1","1.175e+05","2.965e+05","96%","0.0","99.89%","160560"]
["pNtRootD5-1, Arthrobacter sp. NtRootD5","AP024642.1","1.001e+05","2.965e+05","96%","0.0","99.87%","160559"]
["Contig NZ_JAGINZ010000002.1, Paenarthrobacter nicotinovorans strain DSM 420","NZ_JAGINZ010000002.1","2.745e+05","3.086e+05","100%","0.0","100.00%","165142"]
["Contig BMRR01000008.1, Paenarthrobacter nicotinovorans JCM 3874","BMRR01000008.1","2.209e+05","3.073e+05","99%","0.0","100.00%","164931"]