Hori C

References (5)

Title : Genome Sequence of Striga asiatica Provides Insight into the Evolution of Plant Parasitism - Yoshida_2019_Curr.Biol_29_3041
Author(s) : Yoshida S , Kim S , Wafula EK , Tanskanen J , Kim YM , Honaas L , Yang Z , Spallek T , Conn CE , Ichihashi Y , Cheong K , Cui S , Der JP , Gundlach H , Jiao Y , Hori C , Ishida JK , Kasahara H , Kiba T , Kim MS , Koo N , Laohavisit A , Lee YH , Lumba S , McCourt P , Mortimer JC , Mutuku JM , Nomura T , Sasaki-Sekimoto Y , Seto Y , Wang Y , Wakatake T , Sakakibara H , Demura T , Yamaguchi S , Yoneyama K , Manabe RI , Nelson DC , Schulman AH , Timko MP , dePamphilis CW , Choi D , Shirasu K
Ref : Current Biology , 29 :3041 , 2019
Abstract : Parasitic plants in the genus Striga, commonly known as witchweeds, cause major crop losses in sub-Saharan Africa and pose a threat to agriculture worldwide. An understanding of Striga parasite biology, which could lead to agricultural solutions, has been hampered by the lack of genome information. Here, we report the draft genome sequence of Striga asiatica with 34,577 predicted protein-coding genes, which reflects gene family contractions and expansions that are consistent with a three-phase model of parasitic plant genome evolution. Striga seeds germinate in response to host-derived strigolactones (SLs) and then develop a specialized penetration structure, the haustorium, to invade the host root. A family of SL receptors has undergone a striking expansion, suggesting a molecular basis for the evolution of broad host range among Striga spp. We found that genes involved in lateral root development in non-parasitic model species are coordinately induced during haustorium development in Striga, suggesting a pathway that was partly co-opted during the evolution of the haustorium. In addition, we found evidence for horizontal transfer of host genes as well as retrotransposons, indicating gene flow to S. asiatica from hosts. Our results provide valuable insights into the evolution of parasitism and a key resource for the future development of Striga control strategies.
ESTHER : Yoshida_2019_Curr.Biol_29_3041
PubMedSearch : Yoshida_2019_Curr.Biol_29_3041
PubMedID: 31522940
Gene_locus related to this paper: straf-a0a5a7qxe3

Title : Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood - Hori_2014_PLoS.Genet_10_e1004759
Author(s) : Hori C , Ishida T , Igarashi K , Samejima M , Suzuki H , Master E , Ferreira P , Ruiz-Duenas FJ , Held B , Canessa P , Larrondo LF , Schmoll M , Druzhinina IS , Kubicek CP , Gaskell JA , Kersten P , St John F , Glasner J , Sabat G , Splinter BonDurant S , Syed K , Yadav J , Mgbeahuruike AC , Kovalchuk A , Asiegbu FO , Lackner G , Hoffmeister D , Rencoret J , Gutierrez A , Sun H , Lindquist E , Barry K , Riley R , Grigoriev IV , Henrissat B , Kues U , Berka RM , Martinez AT , Covert SF , Blanchette RA , Cullen D
Ref : PLoS Genet , 10 :e1004759 , 2014
Abstract : Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes.
ESTHER : Hori_2014_PLoS.Genet_10_e1004759
PubMedSearch : Hori_2014_PLoS.Genet_10_e1004759
PubMedID: 25474575
Gene_locus related to this paper: phlgi-a0a0c3nds0 , phlgi-a0a0c3niq6 , phlgi-a0a0c3pc91 , phlgi-a0a0c3pv58 , phlgi-a0a0c3rra0 , phlgi-a0a0c3rvc4 , phlgi-a0a0c3rvu0 , phlgi-a0a0c3s394 , phlgi-a0a0c3s606 , phlgi-a0a0c3s673 , phlgi-a0a0c3s8d3 , phlgi-a0a0c3sce4 , phlgi-a0a0c3sdt8

Title : Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize - Suzuki_2012_BMC.Genomics_13_444
Author(s) : Suzuki H , MacDonald J , Syed K , Salamov A , Hori C , Aerts A , Henrissat B , Wiebenga A , vanKuyk PA , Barry K , Lindquist E , LaButti K , Lapidus A , Lucas S , Coutinho P , Gong Y , Samejima M , Mahadevan R , Abou-Zaid M , de Vries RP , Igarashi K , Yadav JS , Grigoriev IV , Master ER
Ref : BMC Genomics , 13 :444 , 2012
Abstract : BACKGROUND: Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.
RESULTS: P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.
CONCLUSIONS: The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.
ESTHER : Suzuki_2012_BMC.Genomics_13_444
PubMedSearch : Suzuki_2012_BMC.Genomics_13_444
PubMedID: 22937793
Gene_locus related to this paper: phacs-k5whx2 , phacs-k5v2s8 , phacs-k5v5r2 , phacs-k5vyk5 , phacs-k5vzf8 , phacs-k5wbu9 , phacs-k5wc10 , phacs-k5wpw0 , phacs-k5wzn6 , phacs-k5x1t8 , phacs-k5x5g6 , phacs-k5x5p4

Title : The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes - Floudas_2012_Science_336_1715
Author(s) : Floudas D , Binder M , Riley R , Barry K , Blanchette RA , Henrissat B , Martinez AT , Otillar R , Spatafora JW , Yadav JS , Aerts A , Benoit I , Boyd A , Carlson A , Copeland A , Coutinho PM , de Vries RP , Ferreira P , Findley K , Foster B , Gaskell J , Glotzer D , Gorecki P , Heitman J , Hesse C , Hori C , Igarashi K , Jurgens JA , Kallen N , Kersten P , Kohler A , Kues U , Kumar TK , Kuo A , LaButti K , Larrondo LF , Lindquist E , Ling A , Lombard V , Lucas S , Lundell T , Martin R , McLaughlin DJ , Morgenstern I , Morin E , Murat C , Nagy LG , Nolan M , Ohm RA , Patyshakuliyeva A , Rokas A , Ruiz-Duenas FJ , Sabat G , Salamov A , Samejima M , Schmutz J , Slot JC , St John F , Stenlid J , Sun H , Sun S , Syed K , Tsang A , Wiebenga A , Young D , Pisabarro A , Eastwood DC , Martin F , Cullen D , Grigoriev IV , Hibbett DS
Ref : Science , 336 :1715 , 2012
Abstract : Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
ESTHER : Floudas_2012_Science_336_1715
PubMedSearch : Floudas_2012_Science_336_1715
PubMedID: 22745431
Gene_locus related to this paper: aurde-j0d098 , aurde-j0dc31 , glota-s7rlc1 , fompi-s8f7s4 , dacsp-m5fpg2 , dicsq-r7sm16 , dacsp-m5g7q5 , dacsp-m5fr12 , glota-s7q5w3 , fompi-s8f826.1 , fompi-s8f826.2 , dicsq-r7sy09 , glota-s7rt87 , dicsq-r7t032 , glota-s7rym7 , fompi-s8fiv2 , dacsp-m5gda3.2 , dicsq-r7swi6 , dacsp-m5frf2 , fompi-s8ebb6 , dicsq-r7sln3 , dicsq-r7sya6 , dacsp-m5g7g1 , dicsq-r7syx7 , dicsq-r7sx57 , dacsp-m5fps7 , glota-s7pwi7 , dicsq-r7swj6 , fompi-s8ejq6 , dicsq-r7spc3 , glota-s7q258 , dacsp-m5ft65 , glota-s7q3m7 , fompi-s8dkc7 , glota-s7q1z1 , fompi-s8eqi2 , glota-s7q1z8 , fompi-s8du50 , dacsp-m5gg33 , dacsp-m5g3a7 , fompi-s8ecd7 , fompi-s8dps1 , dacsp-m5fwr0 , dicsq-r7sub7 , glota-s7q8k9 , fompi-s8ffc3 , dacsp-m5g2f9 , fompi-s8ecc2 , dacsp-m5g868 , fompi-s8f890 , dicsq-r7t1a8 , fompi-s8ebx4 , fompi-s8eb97 , glota-s7q222 , glota-s7puf0 , fompi-s8f6v9 , dacsp-m5g0z2 , dacsp-m5gdh9 , fompi-s8fb37 , dacsp-m5fy91 , glota-s7q5v6 , fompi-s8fl44 , dicsq-r7stv9 , dicsq-r7szk3 , fompi-s8epq9 , glota-s7rh56 , dacsp-m5gbt1 , punst-r7s3x9 , punst-r7s0t5 , glota-s7q312 , glota-s7rhh6 , dicsq-r7t117 , dicsq-r7slz3

Title : Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis - Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
Author(s) : Fernandez-Fueyo E , Ruiz-Duenas FJ , Ferreira P , Floudas D , Hibbett DS , Canessa P , Larrondo LF , James TY , Seelenfreund D , Lobos S , Polanco R , Tello M , Honda Y , Watanabe T , Ryu JS , Kubicek CP , Schmoll M , Gaskell J , Hammel KE , St John FJ , Vanden Wymelenberg A , Sabat G , Splinter BonDurant S , Syed K , Yadav JS , Doddapaneni H , Subramanian V , Lavin JL , Oguiza JA , Perez G , Pisabarro AG , Ramirez L , Santoyo F , Master E , Coutinho PM , Henrissat B , Lombard V , Magnuson JK , Kues U , Hori C , Igarashi K , Samejima M , Held BW , Barry KW , LaButti KM , Lapidus A , Lindquist EA , Lucas SM , Riley R , Salamov AA , Hoffmeister D , Schwenk D , Hadar Y , Yarden O , de Vries RP , Wiebenga A , Stenlid J , Eastwood D , Grigoriev IV , Berka RM , Blanchette RA , Kersten P , Martinez AT , Vicuna R , Cullen D
Ref : Proc Natl Acad Sci U S A , 109 :5458 , 2012
Abstract : Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium.
ESTHER : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedSearch : Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
PubMedID: 22434909
Gene_locus related to this paper: cers8-m2r3x2 , cers8-m2qf37 , cers8-m2pcy7 , cers8-m2pcz3 , cers8-m2qn26 , cers8-m2r654 , cers8-m2r8g9 , cers8-m2ps90 , cers8-m2qn44 , cers8-m2q837 , cers8-m2pjy6 , cers8-m2r609 , cers8-m2qy35 , cers8-m2r1n1 , cers8-m2rl22 , cers8-m2qkx5 , cers8-m2qib7 , cers8-m2rgs8 , cers8-m2rlx6 , cers8-m2r4p3 , cers8-m2rf62 , cers8-m2qyx5 , cers8-m2pcz2 , cers8-m2rm22 , cers8-m2qwb7 , cers8-m2r9u3 , cers8-m2pp23 , cers8-m2r613 , cers8-m2rup8 , cers8-m2piv7 , cers8-m2rch3 , cers8-m2qvf7 , cers8-m2qvb7 , cers8-m2qvb2 , cers8-m2pip7 , cers8-m2rb73 , cers8-m2qgd3 , cers8-m2rcg8 , cers8-m2rb68