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Volumn 60, Issue 4, 2014, Pages 303-313

Intronic and plasmid-derived regions contribute to the large mitochondrial genome sizes of Agaricomycetes

Author keywords

Homing endonuclease genes; Mitochondrial evolution; Mitochondrial genome; Pathogen; Plasmid DNA

Indexed keywords

BASIDIOMYCETES; COMPARATIVE STUDY; DNA SEQUENCE; FUNGAL GENOME; GENETICS; INTRON; MITOCHONDRIAL GENOME; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID;

EID: 84930190547     PISSN: 01728083     EISSN: 14320983     Source Type: Journal    
DOI: 10.1007/s00294-014-0436-z     Document Type: Article
Times cited : (46)

References (44)
  • 1
    • 33845869791 scopus 로고    scopus 로고
    • Repseek, a tool to retrieve approximate repeats from large DNA sequences
    • PID: 17038345, COI: 1:CAS:528:DC%2BD28XhtlGktLzM
    • Achaz G, Boyer F, Rocha EPC et al (2007) Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics 23:119–121
    • (2007) Bioinformatics , vol.23 , pp. 119-121
    • Achaz, G.1    Boyer, F.2    Rocha, E.P.C.3
  • 2
    • 0344719444 scopus 로고    scopus 로고
    • Evolution of mitochondrial gene content: gene loss and transfer to the nucleus
    • PID: 14615181, COI: 1:CAS:528:DC%2BD3sXovVWntbo%3D
    • Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–395
    • (2003) Mol Phylogenet Evol , vol.29 , pp. 380-395
    • Adams, K.L.1    Palmer, J.D.2
  • 3
    • 84856418702 scopus 로고    scopus 로고
    • Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame
    • Al-Reedy RM, Malireddy R, Dillman CB, Kennell JC (2012) Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame. Fungal Genet Biol 49:2–14
    • (2012) Fungal Genet Biol , vol.49 , pp. 2-14
    • Al-Reedy, R.M.1    Malireddy, R.2    Dillman, C.B.3    Kennell, J.C.4
  • 4
    • 0346123001 scopus 로고    scopus 로고
    • Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase
    • PID: 14665667, COI: 1:CAS:528:DC%2BD3sXpvVGiurs%3D
    • Belfort M (2003) Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase. Genes Dev 17:2860–2863
    • (2003) Genes Dev , vol.17 , pp. 2860-2863
    • Belfort, M.1
  • 5
    • 22544464155 scopus 로고    scopus 로고
    • Fungal evolution: the case of the vanishing mitochondrion
    • PID: 15993645, COI: 1:CAS:528:DC%2BD2MXmvVCms78%3D
    • Bullerwell CE, Lang BF (2005) Fungal evolution: the case of the vanishing mitochondrion. Curr Opin Microbiol 8:362–369
    • (2005) Curr Opin Microbiol , vol.8 , pp. 362-369
    • Bullerwell, C.E.1    Lang, B.F.2
  • 6
    • 0344861878 scopus 로고    scopus 로고
    • Mitochondrial genomes: anything goes
    • PID: 14642752, COI: 1:CAS:528:DC%2BD3sXpt1emsbY%3D
    • Burger G, Gray MW, Lang BF (2003) Mitochondrial genomes: anything goes. Trends Genet 19:709–716
    • (2003) Trends Genet , vol.19 , pp. 709-716
    • Burger, G.1    Gray, M.W.2    Lang, B.F.3
  • 7
    • 23044487158 scopus 로고    scopus 로고
    • Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi
    • COI: 1:CAS:528:DC%2BD2MXmsFWmurk%3D
    • Cahan P, Kennell JC (2005) Identification and distribution of sequences having similarity to mitochondrial plasmids in mitochondrial genomes of filamentous fungi. Mol Gen Genomics 273:462–473
    • (2005) Mol Gen Genomics , vol.273 , pp. 462-473
    • Cahan, P.1    Kennell, J.C.2
  • 8
    • 58049208278 scopus 로고    scopus 로고
    • DNAPlotter: circular and linear interactive genome visualization
    • PID: 18990721, COI: 1:CAS:528:DC%2BD1MXmvFSr
    • Carver T, Thomson N, Bleasby A et al (2009) DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25:119–120
    • (2009) Bioinformatics , vol.25 , pp. 119-120
    • Carver, T.1    Thomson, N.2    Bleasby, A.3
  • 9
    • 84860455342 scopus 로고    scopus 로고
    • The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao
    • PID: 22559916, COI: 1:CAS:528:DC%2BC38XltVKmsrs%3D
    • Costa GGL, Cabrera OG, Tiburcio RA et al (2012) The mitochondrial genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biol 116:551–562
    • (2012) Fungal Biol , vol.116 , pp. 551-562
    • Costa, G.G.L.1    Cabrera, O.G.2    Tiburcio, R.A.3
  • 10
    • 0013936167 scopus 로고
    • Codon-anticodon pairing: the wobble hypothesis
    • Crick FHC (1966) Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 19:548–555
    • (1966) J Mol Biol , vol.19 , pp. 548-555
    • Crick, F.H.C.1
  • 11
    • 78449279363 scopus 로고    scopus 로고
    • Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato
    • PID: 20964759, COI: 1:STN:280:DC%2BC3cbkvVyrtg%3D%3D
    • Dalman K, Olson Å, Stenlid J (2010) Evolutionary history of the conifer root rot fungus Heterobasidion annosum sensu lato. Mol Ecol 19:4979–4993
    • (2010) Mol Ecol , vol.19 , pp. 4979-4993
    • Dalman, K.1    Olson, Å.2    Stenlid, J.3
  • 12
    • 84879027741 scopus 로고    scopus 로고
    • The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences
    • PID: 23428625, COI: 1:CAS:528:DC%2BC3sXktlGmu7s%3D
    • Ferandon C, Xu J, Barroso G (2013) The 135 kbp mitochondrial genome of Agaricus bisporus is the largest known eukaryotic reservoir of group I introns and plasmid-related sequences. Fungal Genet Biol 55:85–91
    • (2013) Fungal Genet Biol , vol.55 , pp. 85-91
    • Ferandon, C.1    Xu, J.2    Barroso, G.3
  • 13
    • 49749105312 scopus 로고    scopus 로고
    • The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid
    • PID: 18786820, COI: 1:CAS:528:DC%2BD1cXhsV2ksbfP
    • Formighieri EF, Tiburcio RA, Armas ED et al (2008) The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109 kb in size and contains a stable integrated plasmid. Mycol Res 112:1136–1152
    • (2008) Mycol Res , vol.112 , pp. 1136-1152
    • Formighieri, E.F.1    Tiburcio, R.A.2    Armas, E.D.3
  • 14
    • 69249240353 scopus 로고    scopus 로고
    • Viruses of plant pathogenic fungi
    • PID: 19400634, COI: 1:CAS:528:DC%2BD1MXht1Gjt7rM
    • Ghabrial SA, Suzuki N (2009) Viruses of plant pathogenic fungi. Annu Rev Phytopathol 47:353–384
    • (2009) Annu Rev Phytopathol , vol.47 , pp. 353-384
    • Ghabrial, S.A.1    Suzuki, N.2
  • 15
    • 0033598755 scopus 로고    scopus 로고
    • Recurrent invasion and extinction of a selfish gene
    • PID: 10570167, COI: 1:CAS:528:DyaK1MXns1OqtLY%3D
    • Goddard MR, Burt A (1999) Recurrent invasion and extinction of a selfish gene. Proc Natl Acad Sci USA 96:13880–13885
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 13880-13885
    • Goddard, M.R.1    Burt, A.2
  • 16
    • 33751233858 scopus 로고    scopus 로고
    • Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements
    • PID: 17101053
    • Gogarten JP, Hilario E (2006) Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements. BMC Evol Biol 6:94
    • (2006) BMC Evol Biol , vol.6 , pp. 94
    • Gogarten, J.P.1    Hilario, E.2
  • 18
    • 77953171916 scopus 로고    scopus 로고
    • The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata
    • COI: 1:CAS:528:DC%2BC3cXotFGqtr4%3D
    • Haridas S, Gantt J (2010) The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata. FEMS Microb Lett 308:29–34
    • (2010) FEMS Microb Lett , vol.308 , pp. 29-34
    • Haridas, S.1    Gantt, J.2
  • 19
    • 12344329187 scopus 로고    scopus 로고
    • The natural history of group I introns
    • PID: 15661357, COI: 1:CAS:528:DC%2BD2MXmslKgtA%3D%3D
    • Haugen P, Simon DM, Bhattacharya D (2005) The natural history of group I introns. Trends Genet 21:111–119
    • (2005) Trends Genet , vol.21 , pp. 111-119
    • Haugen, P.1    Simon, D.M.2    Bhattacharya, D.3
  • 20
    • 84893434236 scopus 로고    scopus 로고
    • Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis
    • PID: 24071901, COI: 1:CAS:528:DC%2BC3sXhsFWrsbvO
    • Hegedusova E, Brejova B, Tomaska L et al (2014) Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Curr Genet 60:49–59. doi:10.1007/s00294-013-0410-1
    • (2014) Curr Genet , vol.60 , pp. 49-59
    • Hegedusova, E.1    Brejova, B.2    Tomaska, L.3
  • 21
    • 58149203231 scopus 로고    scopus 로고
    • InterPro: the integrative protein signature database
    • COI: 1:CAS:528:DC%2BD1cXhsFejtL%2FF
    • Hunter S, Apweiler R, Attwood TK et al (2009) InterPro: the integrative protein signature database. Nucl Acid Res 37:D211–D215
    • (2009) Nucl Acid Res , vol.37 , pp. D211-D215
    • Hunter, S.1    Apweiler, R.2    Attwood, T.K.3
  • 22
    • 84870870373 scopus 로고    scopus 로고
    • Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability
    • Joardar V, Abrams NF, Hostetler J et al (2012) Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability. BMC Genomics 13:698
    • (2012) BMC Genomics , vol.13 , pp. 698
    • Joardar, V.1    Abrams, N.F.2    Hostetler, J.3
  • 23
    • 84880916121 scopus 로고    scopus 로고
    • Molecular paleontology and complexity in the last eukaryotic common ancestor
    • PID: 23895660, COI: 1:CAS:528:DC%2BC3sXhtF2qsb7N
    • Koumandou VL, Wickstead B, Ginger ML et al (2013) Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit Rev Biochem Mol Biol 48:373–396
    • (2013) Crit Rev Biochem Mol Biol , vol.48 , pp. 373-396
    • Koumandou, V.L.1    Wickstead, B.2    Ginger, M.L.3
  • 24
    • 33847192548 scopus 로고    scopus 로고
    • Mitochondrial introns: a critical view
    • PID: 17280737, COI: 1:CAS:528:DC%2BD2sXitFOisLs%3D
    • Lang B, Laforest M, Burger G (2007) Mitochondrial introns: a critical view. Trends Genet 23:119–125
    • (2007) Trends Genet , vol.23 , pp. 119-125
    • Lang, B.1    Laforest, M.2    Burger, G.3
  • 25
    • 84883149321 scopus 로고    scopus 로고
    • Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum
    • PID: 23991034, COI: 1:CAS:528:DC%2BC3sXhsVSnurjI
    • Li J, Zhang J, Chen H et al (2013) Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum. PLoS ONE 8:e72038
    • (2013) PLoS ONE , vol.8 , pp. e72038
    • Li, J.1    Zhang, J.2    Chen, H.3
  • 26
    • 0030854739 scopus 로고    scopus 로고
    • tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence
    • PID: 9023104, COI: 1:CAS:528:DyaK2sXhvVahtrk%3D
    • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25:955–964
    • (1997) Nucl Acids Res , vol.25 , pp. 955-964
    • Lowe, T.M.1    Eddy, S.R.2
  • 27
    • 69149090138 scopus 로고    scopus 로고
    • The fatal fungal outbreak on Vancouver Island is characterized by enhanced intracellular parasitism driven by mitochondrial regulation
    • PID: 19651610, COI: 1:CAS:528:DC%2BD1MXhtVKru77J
    • Ma H, Hagen F, Stekel DJ et al (2009) The fatal fungal outbreak on Vancouver Island is characterized by enhanced intracellular parasitism driven by mitochondrial regulation. Proc Natl Acad Sci USA 106:12980–12985
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 12980-12985
    • Ma, H.1    Hagen, F.2    Stekel, D.J.3
  • 28
    • 0029017911 scopus 로고
    • A cytoplasmically transmissible hypovirulence phenotype associated with mitochondrial DNA mutations in the chestnut blight fungus Cryphonectria parasitica
    • PID: 11607549, COI: 1:CAS:528:DyaK2MXmsFWqtLg%3D
    • Monteiro-Vitorello CB, Bell JA, Fulbright DW, Bertrand H (1995) A cytoplasmically transmissible hypovirulence phenotype associated with mitochondrial DNA mutations in the chestnut blight fungus Cryphonectria parasitica. Proc Natl Acad Sci USA 92:5935–5939
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 5935-5939
    • Monteiro-Vitorello, C.B.1    Bell, J.A.2    Fulbright, D.W.3    Bertrand, H.4
  • 29
    • 70149095682 scopus 로고    scopus 로고
    • The Cryphonectria parasitica mitochondrial RNS gene: plasmid-like elements, introns and homing endonucleases
    • PID: 19607930, COI: 1:CAS:528:DC%2BD1MXhtFGnsLvO
    • Monteiro-Vitorello C, Hausner G, Searles D et al (2009) The Cryphonectria parasitica mitochondrial RNS gene: plasmid-like elements, introns and homing endonucleases. Fungal Genet Biol 46:837–848
    • (2009) Fungal Genet Biol , vol.46 , pp. 837-848
    • Monteiro-Vitorello, C.1    Hausner, G.2    Searles, D.3
  • 30
    • 0034284036 scopus 로고    scopus 로고
    • Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases
    • PID: 10981697, COI: 1:CAS:528:DC%2BD3cXlvV2lsb0%3D
    • Nakai R, Sen K, Kurosawa S, Shibai H (2000) Basidiomycetous fungus Flammulina velutipes harbors two linear mitochondrial plasmids encoding DNA and RNA polymerases. FEMS Microbiol Lett 190:99–102
    • (2000) FEMS Microbiol Lett , vol.190 , pp. 99-102
    • Nakai, R.1    Sen, K.2    Kurosawa, S.3    Shibai, H.4
  • 31
    • 0035942837 scopus 로고    scopus 로고
    • Plant pathogens: mitochondrial control of fungal hybrid virulence
    • PID: 11373666, COI: 1:CAS:528:DC%2BD3MXkt1aqs7g%3D
    • Olson A, Stenlid J (2001) Plant pathogens: mitochondrial control of fungal hybrid virulence. Nature 411:438
    • (2001) Nature , vol.411 , pp. 438
    • Olson, A.1    Stenlid, J.2
  • 32
    • 84860511529 scopus 로고    scopus 로고
    • Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen
    • PID: 22463738
    • Olson A, Aerts A, Asiegbu F et al (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytol 194:1001–1013
    • (2012) New Phytol , vol.194 , pp. 1001-1013
    • Olson, A.1    Aerts, A.2    Asiegbu, F.3
  • 33
    • 77949914791 scopus 로고    scopus 로고
    • Heterobasidion occidentale sp nov and Heterobasidion irregulare nom. nov.: a disposition of North American Heterobasidion biological species
    • PID: 20965057
    • Otrosina W, Garbelotto M (2010) Heterobasidion occidentale sp nov and Heterobasidion irregulare nom. nov.: a disposition of North American Heterobasidion biological species. Fungal Biol 114:16–25
    • (2010) Fungal Biol , vol.114 , pp. 16-25
    • Otrosina, W.1    Garbelotto, M.2
  • 34
    • 0030993742 scopus 로고    scopus 로고
    • The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression
    • PID: 9162109, COI: 1:CAS:528:DyaK2sXjvFOksbs%3D
    • Paquin B, Laforest MJ, Forget L et al (1997) The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression. Curr Genet 31:380–395
    • (1997) Curr Genet , vol.31 , pp. 380-395
    • Paquin, B.1    Laforest, M.J.2    Forget, L.3
  • 36
    • 0001066637 scopus 로고
    • A mitochondrial target for double-stranded RNA in diseased isolates of the fungus that causes Dutch elm disease
    • COI: 1:CAS:528:DyaL2sXmtFCkt7Y%3D
    • Rogers HJ, Buck KW, Brasier CM (1987) A mitochondrial target for double-stranded RNA in diseased isolates of the fungus that causes Dutch elm disease. Nature 329:558–560
    • (1987) Nature , vol.329 , pp. 558-560
    • Rogers, H.J.1    Buck, K.W.2    Brasier, C.M.3
  • 37
    • 0033635022 scopus 로고    scopus 로고
    • Artemis: sequence visualization and annotation
    • PID: 11120685, COI: 1:CAS:528:DC%2BD3MXjvVWksw%3D%3D
    • Rutherford K, Parkhill J, Crook J et al (2000) Artemis: sequence visualization and annotation. Bioinformatics 16:944–945
    • (2000) Bioinformatics , vol.16 , pp. 944-945
    • Rutherford, K.1    Parkhill, J.2    Crook, J.3
  • 38
    • 77955875364 scopus 로고    scopus 로고
    • Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae
    • PID: 20648755, COI: 1:CAS:528:DC%2BC3cXpsFOit7k%3D
    • Stone C, Buitrago M, Boore J, Frederick R (2010) Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae. Mycologia 102:887–897
    • (2010) Mycologia , vol.102 , pp. 887-897
    • Stone, C.1    Buitrago, M.2    Boore, J.3    Frederick, R.4
  • 39
    • 84890803314 scopus 로고    scopus 로고
    • Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion
    • Torriani SFF, Penselin D, Knogge W et al (2014) Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion. Fungal Genet Biol 62:34–42
    • (2014) Fungal Genet Biol , vol.62 , pp. 34-42
    • Torriani, S.F.F.1    Penselin, D.2    Knogge, W.3
  • 40
    • 22244455429 scopus 로고    scopus 로고
    • Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins
    • PID: 15985556, COI: 1:CAS:528:DC%2BD2MXmsFaruro%3D
    • Touchon M, Nicolay S, Audit B et al (2005) Replication-associated strand asymmetries in mammalian genomes: toward detection of replication origins. Proc Natl Acad Sci USA 102:9836–9841
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 9836-9841
    • Touchon, M.1    Nicolay, S.2    Audit, B.3
  • 41
    • 38849095278 scopus 로고    scopus 로고
    • The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom)
    • PID: 18248422, COI: 1:CAS:528:DC%2BD1cXivFejsb0%3D
    • Wang Y, Zeng F, Hon CC et al (2008) The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiol Lett 280:34–41
    • (2008) FEMS Microbiol Lett , vol.280 , pp. 34-41
    • Wang, Y.1    Zeng, F.2    Hon, C.C.3
  • 42
    • 84867842428 scopus 로고    scopus 로고
    • The mitochondrial genome of the white-rot fungus Flammulina velutipes
    • PID: 22990494, COI: 1:CAS:528:DC%2BC38XhsVWrsr%2FE
    • Yoon H, You Y-H, Woo J-R et al (2012) The mitochondrial genome of the white-rot fungus Flammulina velutipes. J Gen Appl Microbiol 58:331–337
    • (2012) J Gen Appl Microbiol , vol.58 , pp. 331-337
    • Yoon, H.1    You, Y.-H.2    Woo, J.-R.3
  • 43
    • 0024283658 scopus 로고
    • 2 linear plasmid-like DNA elements simultaneously maintained in Pleurotus Ostreatus
    • PID: 2847798, COI: 1:CAS:528:DyaL1MXjsVKgug%3D%3D
    • Yui Y, Katayose Y, Shishido K (1988) 2 linear plasmid-like DNA elements simultaneously maintained in Pleurotus Ostreatus. Biochim Biophys Acta 951:53–60
    • (1988) Biochim Biophys Acta , vol.951 , pp. 53-60
    • Yui, Y.1    Katayose, Y.2    Shishido, K.3
  • 44
    • 84884500091 scopus 로고    scopus 로고
    • Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes
    • COI: 1:CAS:528:DC%2BC3sXlslyksbc%3D
    • Zhao XQ, Aizawa T, Schneider J et al (2013) Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes. Microbiol Open 2:308–317
    • (2013) Microbiol Open , vol.2 , pp. 308-317
    • Zhao, X.Q.1    Aizawa, T.2    Schneider, J.3


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