Tyler BM

References (6)

Title : Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms -
Author(s) : Ali SS , Shao J , Lary DJ , Kronmiller B , Shen D , Strem MD , Amoako-Attah I , Akrofi AY , Begoude BA , Ten Hoopen GM , Coulibaly K , Kebe BI , Melnick RL , Guiltinan MJ , Tyler BM , Meinhardt LW , Bailey BA
Ref : Genome Biol Evol , 9 :536 , 2017
PubMedID: 28186564
Gene_locus related to this paper: 9stra-a0a2p4wvr1 , 9stra-a0a2p4xzk1 , 9stra-a0a2p4ybh6 , 9stra-a0a2p4yd47 , 9stra-a0a2p4yde6

Title : Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica - Jiang_2013_PLoS.Genet_9_e1003272
Author(s) : Jiang RH , de Bruijn I , Haas BJ , Belmonte R , Lobach L , Christie J , Van den Ackerveken G , Bottin A , Bulone V , Diaz-Moreno SM , Dumas B , Fan L , Gaulin E , Govers F , Grenville-Briggs LJ , Horner NR , Levin JZ , Mammella M , Meijer HJ , Morris P , Nusbaum C , Oome S , Phillips AJ , van Rooyen D , Rzeszutek E , Saraiva M , Secombes CJ , Seidl MF , Snel B , Stassen JH , Sykes S , Tripathy S , van den Berg H , Vega-Arreguin JC , Wawra S , Young SK , Zeng Q , Dieguez-Uribeondo J , Russ C , Tyler BM , van West P
Ref : PLoS Genet , 9 :e1003272 , 2013
Abstract : Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.
ESTHER : Jiang_2013_PLoS.Genet_9_e1003272
PubMedSearch : Jiang_2013_PLoS.Genet_9_e1003272
PubMedID: 23785293
Gene_locus related to this paper: sappc-a0a067bqc9 , sappc-a0a067cbi1

Title : Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations - Rouxel_2011_Nat.Commun_2_202
Author(s) : Rouxel T , Grandaubert J , Hane JK , Hoede C , van de Wouw AP , Couloux A , Dominguez V , Anthouard V , Bally P , Bourras S , Cozijnsen AJ , Ciuffetti LM , Degrave A , Dilmaghani A , Duret L , Fudal I , Goodwin SB , Gout L , Glaser N , Linglin J , Kema GH , Lapalu N , Lawrence CB , May K , Meyer M , Ollivier B , Poulain J , Schoch CL , Simon A , Spatafora JW , Stachowiak A , Turgeon BG , Tyler BM , Vincent D , Weissenbach J , Amselem J , Quesneville H , Oliver RP , Wincker P , Balesdent MH , Howlett BJ
Ref : Nat Commun , 2 :202 , 2011
Abstract : Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
ESTHER : Rouxel_2011_Nat.Commun_2_202
PubMedSearch : Rouxel_2011_Nat.Commun_2_202
PubMedID: 21326234
Gene_locus related to this paper: lepmc-q6q891 , lepmj-e4zh04 , lepmj-e4ziv6 , lepmj-e4zju4 , lepmj-e4zqu4 , lepmj-e4zvh3 , lepmj-e4zvl4 , lepmj-e4zx66 , lepmj-e5a0i2 , lepmj-e5a510 , lepmj-e5aau5 , lepmj-e5acd1 , lepmj-e5a4g5 , lepmj-e4zhg2 , lepmj-e4zuw5 , lepmj-e5a2e0 , lepmj-e4zpv2 , lepmj-e4zxp4 , lepmj-e4zpy5 , lepmj-e5ae17 , lepmj-e4ziv2 , lepmj-e5a374 , lepmj-e5ab81 , lepmj-e4zgy1 , lepmj-e4zg43 , lepmj-kex1 , lepmj-cbpya

Title : Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome - Baxter_2010_Science_330_1549
Author(s) : Baxter L , Tripathy S , Ishaque N , Boot N , Cabral A , Kemen E , Thines M , Ah-Fong A , Anderson R , Badejoko W , Bittner-Eddy P , Boore JL , Chibucos MC , Coates M , Dehal P , Delehaunty K , Dong S , Downton P , Dumas B , Fabro G , Fronick C , Fuerstenberg SI , Fulton L , Gaulin E , Govers F , Hughes L , Humphray S , Jiang RH , Judelson H , Kamoun S , Kyung K , Meijer H , Minx P , Morris P , Nelson J , Phuntumart V , Qutob D , Rehmany A , Rougon-Cardoso A , Ryden P , Torto-Alalibo T , Studholme D , Wang Y , Win J , Wood J , Clifton SW , Rogers J , Van den Ackerveken G , Jones JD , McDowell JM , Beynon J , Tyler BM
Ref : Science , 330 :1549 , 2010
Abstract : Many oomycete and fungal plant pathogens are obligate biotrophs, which extract nutrients only from living plant tissue and cannot grow apart from their hosts. Although these pathogens cause substantial crop losses, little is known about the molecular basis or evolution of obligate biotrophy. Here, we report the genome sequence of the oomycete Hyaloperonospora arabidopsidis (Hpa), an obligate biotroph and natural pathogen of Arabidopsis thaliana. In comparison with genomes of related, hemibiotrophic Phytophthora species, the Hpa genome exhibits dramatic reductions in genes encoding (i) RXLR effectors and other secreted pathogenicity proteins, (ii) enzymes for assimilation of inorganic nitrogen and sulfur, and (iii) proteins associated with zoospore formation and motility. These attributes comprise a genomic signature of evolution toward obligate biotrophy.
ESTHER : Baxter_2010_Science_330_1549
PubMedSearch : Baxter_2010_Science_330_1549
PubMedID: 21148394
Gene_locus related to this paper: hyaae-m4b4d8 , hyaae-m4b4e0 , hyaae-m4bkr1 , hyaae-m4bkw7

Title : Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions - Jiang_2006_Mol.Plant.Microbe.Interact_19_1311
Author(s) : Jiang RH , Tyler BM , Govers F
Ref : Mol Plant Microbe Interact , 19 :1311 , 2006
Abstract : Comparative analysis of two Phytophthora genomes revealed overall colinearity in four genomic regions consisting of a 1.5-Mb sequence of Phytophthora sojae and a 0.9-Mb sequence of P. ramorum. In these regions with conserved synteny, the gene order is largely similar; however, genome rearrangements also have occurred. Deletions and duplications often were found in association with genes encoding secreted proteins, including effectors that are important for interaction with host plants. Among secreted protein genes, different evolutionary patterns were found. Elicitin genes that code for a complex family of highly conserved Phytophthora-specific elicitors show conservation in gene number and order, and often are clustered. In contrast, the race-specific elicitor gene Avrlb-1 appeared to be missing from the region with conserved synteny, as were its five homologs that are scattered over the four genomic regions. Some gene families encoding secreted proteins were found to be expanded in one species compared with the other. This could be the result of either repeated gene duplications in one species or specific deletions in the other. These different evolutionary patterns may shed light on the functions of these secreted proteins in the biology and pathology of the two Phytophthora spp.
ESTHER : Jiang_2006_Mol.Plant.Microbe.Interact_19_1311
PubMedSearch : Jiang_2006_Mol.Plant.Microbe.Interact_19_1311
PubMedID: 17153915

Title : Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis - Tyler_2006_Science_313_1261
Author(s) : Tyler BM , Tripathy S , Zhang X , Dehal P , Jiang RH , Aerts A , Arredondo FD , Baxter L , Bensasson D , Beynon JL , Chapman J , Damasceno CM , Dorrance AE , Dou D , Dickerman AW , Dubchak IL , Garbelotto M , Gijzen M , Gordon SG , Govers F , Grunwald NJ , Huang W , Ivors KL , Jones RW , Kamoun S , Krampis K , Lamour KH , Lee MK , McDonald WH , Medina M , Meijer HJ , Nordberg EK , Maclean DJ , Ospina-Giraldo MD , Morris PF , Phuntumart V , Putnam NH , Rash S , Rose JK , Sakihama Y , Salamov AA , Savidor A , Scheuring CF , Smith BM , Sobral BW , Terry A , Torto-Alalibo TA , Win J , Xu Z , Zhang H , Grigoriev IV , Rokhsar DS , Boore JL
Ref : Science , 313 :1261 , 2006
Abstract : Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes.
ESTHER : Tyler_2006_Science_313_1261
PubMedSearch : Tyler_2006_Science_313_1261
PubMedID: 16946064
Gene_locus related to this paper: phyrm-h3ga89 , phyrm-h3gbl6.1 , phyrm-h3gbl6.2 , phyrm-h3gbl7 , phyrm-h3gdd4 , phyrm-h3gl36 , phyrm-h3gq42 , phyrm-h3gx86 , phyrm-h3gyi2 , phyrm-h3gyi3 , phyrm-h3gyi4 , phyrm-h3h292 , phyrm-h3h293 , phyrm-h3h967 , phyrm-h3hcf9 , physp-g4ynp3 , physp-g4yut6 , physp-g4yut8 , physp-g4yw23 , physp-g4zis3 , physp-g4zqe3 , physp-g4zqe4 , physp-g4zqf0 , physp-g4zqn9 , physp-g4zwy9 , physp-g5a582 , physp-g5a583 , physp-g5aav9 , phyrm-h3g9e7 , physp-g4zwu9 , phyrm-h3ggp1 , physp-g4ztq5 , physp-g4zwu8 , physp-g4zwv7 , physp-g4zwv6 , physp-g4zwv0 , physp-g4zwv8 , phyrm-h3gp95 , phyrm-h3g6r5 , physp-g4zwv9 , physp-g5a510 , phyrm-h3glu3 , physp-g5aci1 , phyrm-h3h2d0 , physp-g4ztb2 , physp-g4yg47 , phyrm-h3h2c9 , physp-g4ztb3 , phyrm-h3gvj3 , phyrm-h3gy62 , physp-g4yg46 , physp-g4zdt9 , phyrm-h3gdh5 , physp-g4zm41 , physp-g5abj7 , phyrm-h3gz76 , physp-g5a425 , phyrm-h3h080 , physp-g4ytv0 , phyrm-h3gcw7