Amselem J

References (8)

Title : Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges - Gouin_2017_Sci.Rep_7_11816
Author(s) : Gouin A , Bretaudeau A , Nam K , Gimenez S , Aury JM , Duvic B , Hilliou F , Durand N , Montagne N , Darboux I , Kuwar S , Chertemps T , Siaussat D , Bretschneider A , Mone Y , Ahn SJ , Hanniger S , Grenet AG , Neunemann D , Maumus F , Luyten I , Labadie K , Xu W , Koutroumpa F , Escoubas JM , Llopis A , Mabeche-Coisne M , Salasc F , Tomar A , Anderson AR , Khan SA , Dumas P , Orsucci M , Guy J , Belser C , Alberti A , Noel B , Couloux A , Mercier J , Nidelet S , Dubois E , Liu NY , Boulogne I , Mirabeau O , Le Goff G , Gordon K , Oakeshott J , Consoli FL , Volkoff AN , Fescemyer HW , Marden JH , Luthe DS , Herrero S , Heckel DG , Wincker P , Kergoat GJ , Amselem J , Quesneville H , Groot AT , Jacquin-Joly E , Negre N , Lemaitre C , Legeai F , d'Alencon E , Fournier P
Ref : Sci Rep , 7 :11816 , 2017
Abstract : Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world's worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains ("C" and "R") that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
ESTHER : Gouin_2017_Sci.Rep_7_11816
PubMedSearch : Gouin_2017_Sci.Rep_7_11816
PubMedID: 28947760

Title : Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus - Perlin_2015_BMC.Genomics_16_461
Author(s) : Perlin MH , Amselem J , Fontanillas E , Toh SS , Chen Z , Goldberg J , Duplessis S , Henrissat B , Young S , Zeng Q , Aguileta G , Petit E , Badouin H , Andrews J , Razeeq D , Gabaldon T , Quesneville H , Giraud T , Hood ME , Schultz DJ , Cuomo CA
Ref : BMC Genomics , 16 :461 , 2015
Abstract : BACKGROUND: The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. RESULTS: We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14% of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. CONCLUSIONS: The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.
ESTHER : Perlin_2015_BMC.Genomics_16_461
PubMedSearch : Perlin_2015_BMC.Genomics_16_461
PubMedID: 26076695
Gene_locus related to this paper: ustv1-u5h5e5

Title : Obligate biotrophy features unraveled by the genomic analysis of rust fungi - Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
Author(s) : Duplessis S , Cuomo CA , Lin YC , Aerts A , Tisserant E , Veneault-Fourrey C , Joly DL , Hacquard S , Amselem J , Cantarel BL , Chiu R , Coutinho PM , Feau N , Field M , Frey P , Gelhaye E , Goldberg J , Grabherr MG , Kodira CD , Kohler A , Kues U , Lindquist EA , Lucas SM , Mago R , Mauceli E , Morin E , Murat C , Pangilinan JL , Park R , Pearson M , Quesneville H , Rouhier N , Sakthikumar S , Salamov AA , Schmutz J , Selles B , Shapiro H , Tanguay P , Tuskan GA , Henrissat B , Van de Peer Y , Rouze P , Ellis JG , Dodds PN , Schein JE , Zhong S , Hamelin RC , Grigoriev IV , Szabo LJ , Martin F
Ref : Proc Natl Acad Sci U S A , 108 :9166 , 2011
Abstract : Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
ESTHER : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedSearch : Duplessis_2011_Proc.Natl.Acad.Sci.U.S.A_108_9166
PubMedID: 21536894
Gene_locus related to this paper: pucgt-e3k840 , pucgt-e3kaq6 , pucgt-e3kw59 , pucgt-e3kz16 , pucgt-e3l9v6 , pucgt-e3l279 , pucgt-h6qt25 , mellp-f4reh4 , mellp-f4rhc8 , mellp-f4reh2 , mellp-f4r3y0 , mellp-f4rz15 , mellp-f4rz64 , mellp-f4rl14 , mellp-f4rz66 , mellp-f4s751 , mellp-f4s2g6 , pucgt-e3l1z7 , pucgt-e3l803 , pucgt-e3kst2 , pucgt-e3kst5 , mellp-f4ru03 , pucgt-e3l1z8 , pucgt-e3ktz7 , pucgt-e3jun4 , mellp-f4rl65 , mellp-f4rz16 , mellp-f4ru02 , mellp-f4sav4 , mellp-f4sav3 , mellp-f4s1j0 , mellp-f4rkp0 , mellp-f4s483 , pucgt-e3kzu5 , pucgt-h6qtq8 , mellp-f4r5l5 , pucgt-e3krw7 , pucgt-e3l7w5 , pucgt-e3k2w6 , pucgt-e3kfg2 , pucgt-kex1

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 : Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea - Amselem_2011_PLoS.Genet_7_e1002230
Author(s) : Amselem J , Cuomo CA , van Kan JA , Viaud M , Benito EP , Couloux A , Coutinho PM , de Vries RP , Dyer PS , Fillinger S , Fournier E , Gout L , Hahn M , Kohn L , Lapalu N , Plummer KM , Pradier JM , Quevillon E , Sharon A , Simon A , ten Have A , Tudzynski B , Tudzynski P , Wincker P , Andrew M , Anthouard V , Beever RE , Beffa R , Benoit I , Bouzid O , Brault B , Chen Z , Choquer M , Collemare J , Cotton P , Danchin EG , Da Silva C , Gautier A , Giraud C , Giraud T , Gonzalez C , Grossetete S , Guldener U , Henrissat B , Howlett BJ , Kodira C , Kretschmer M , Lappartient A , Leroch M , Levis C , Mauceli E , Neuveglise C , Oeser B , Pearson M , Poulain J , Poussereau N , Quesneville H , Rascle C , Schumacher J , Segurens B , Sexton A , Silva E , Sirven C , Soanes DM , Talbot NJ , Templeton M , Yandava C , Yarden O , Zeng Q , Rollins JA , Lebrun MH , Dickman M
Ref : PLoS Genet , 7 :e1002230 , 2011
Abstract : Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
ESTHER : Amselem_2011_PLoS.Genet_7_e1002230
PubMedSearch : Amselem_2011_PLoS.Genet_7_e1002230
PubMedID: 21876677
Gene_locus related to this paper: botci-cutas , botci-q6rki2 , botf4-g2y7k8 , botfb-dapb , botfu-g2xyd8 , botfu-g2ynh8 , scls1-a7e814 , scls1-a7edc9 , scls1-a7edh1 , scls1-a7emm0 , scls1-a7eti8 , scls1-a7eu48 , scls1-a7f208 , scls1-dapb , botf4-g2xqp7 , scls1-a7eqq8 , botf4-g2xqc6 , scls1-a7ebs4 , botf4-g2xn51 , scls1-a7f5m9 , botf4-g2xti4 , botf4-g2xtu7 , botf4-g2yfp1 , scls1-a7f534 , botf4-g2yys3 , scls1-a7erz9 , botf4-g2y037 , botf4-g2y0e1 , scls1-a7f706 , scls1-a7ewt6 , botf4-g2yuj6 , botf1-m7u3d1 , botf1-m7u430 , botf1-m7tei8 , botf1-m7u0w9 , botf1-m7tij6 , botf1-m7u819 , botf1-m7u6d8 , botf1-m7tzd4 , botf1-m7tqd7 , botf1-m7tyz9 , botf1-m7unl9 , botf1-m7u429 , botf1-m7u4s5 , botf1-m7ul92 , botf1-m7tx42 , botf1-m7u9h4 , botf1-m7u187 , botf1-m7uz64 , botf1-m7u4q4 , botf1-m7u2f6 , botf1-m7tt59 , botf1-m7v3h2 , botf1-m7u6c9 , botf1-m7tud9 , botf1-m7u309 , scls1-a7et87 , botf4-g2ylt4 , scls1-a7f5a0 , scls1-a7f900 , botf4-g2yib9 , scls1-a7f3m9 , scls1-a7er46 , botf4-g2y3y4 , botf4-g2xyy5 , botf1-m7uct5 , scls1-a7ea78 , scls1-kex1 , scls1-cbpya , botfb-cbpya , scls1-a7ecx1

Title : Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism - Spanu_2010_Science_330_1543
Author(s) : Spanu PD , Abbott JC , Amselem J , Burgis TA , Soanes DM , Stuber K , Ver Loren van Themaat E , Brown JK , Butcher SA , Gurr SJ , Lebrun MH , Ridout CJ , Schulze-Lefert P , Talbot NJ , Ahmadinejad N , Ametz C , Barton GR , Benjdia M , Bidzinski P , Bindschedler LV , Both M , Brewer MT , Cadle-Davidson L , Cadle-Davidson MM , Collemare J , Cramer R , Frenkel O , Godfrey D , Harriman J , Hoede C , King BC , Klages S , Kleemann J , Knoll D , Koti PS , Kreplak J , Lopez-Ruiz FJ , Lu X , Maekawa T , Mahanil S , Micali C , Milgroom MG , Montana G , Noir S , O'Connell RJ , Oberhaensli S , Parlange F , Pedersen C , Quesneville H , Reinhardt R , Rott M , Sacristan S , Schmidt SM , Schon M , Skamnioti P , Sommer H , Stephens A , Takahara H , Thordal-Christensen H , Vigouroux M , Wessling R , Wicker T , Panstruga R
Ref : Science , 330 :1543 , 2010
Abstract : Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
ESTHER : Spanu_2010_Science_330_1543
PubMedSearch : Spanu_2010_Science_330_1543
PubMedID: 21148392
Gene_locus related to this paper: blugr-d2cql4 , blug1-n1jlh9 , blug1-n1j5n4 , blug1-n1j9r9 , blug1-n1je34 , blug1-n1jkm5 , blug1-n1jhv6 , blug1-n1j8l0 , blug1-n1jqj7 , blug1-n1j543

Title : Perigord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis - Martin_2010_Nature_464_1033
Author(s) : Martin F , Kohler A , Murat C , Balestrini R , Coutinho PM , Jaillon O , Montanini B , Morin E , Noel B , Percudani R , Porcel B , Rubini A , Amicucci A , Amselem J , Anthouard V , Arcioni S , Artiguenave F , Aury JM , Ballario P , Bolchi A , Brenna A , Brun A , Buee M , Cantarel B , Chevalier G , Couloux A , Da Silva C , Denoeud F , Duplessis S , Ghignone S , Hilselberger B , Iotti M , Marcais B , Mello A , Miranda M , Pacioni G , Quesneville H , Riccioni C , Ruotolo R , Splivallo R , Stocchi V , Tisserant E , Viscomi AR , Zambonelli A , Zampieri E , Henrissat B , Lebrun MH , Paolocci F , Bonfante P , Ottonello S , Wincker P
Ref : Nature , 464 :1033 , 2010
Abstract : The Perigord black truffle (Tuber melanosporum Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of T. melanosporum is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal Laccaria bicolor, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of T. melanosporum, which at approximately 125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for approximately 58% of the genome. In contrast, this genome only contains approximately 7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that T. melanosporum degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both L. bicolor and T. melanosporum, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis-'the symbiosis toolbox'-evolved along different ways in ascomycetes and basidiomycetes.
ESTHER : Martin_2010_Nature_464_1033
PubMedSearch : Martin_2010_Nature_464_1033
PubMedID: 20348908
Gene_locus related to this paper: 9pezi-d5g8f4 , 9pezi-d5gi84 , 9pezi-d5gph4 , tubmm-d5g4w2 , tubmm-d5g4w3 , tubmm-d5g4w6 , tubmm-d5g5r5 , tubmm-d5g8z4 , tubmm-d5g938 , tubmm-d5ga65 , tubmm-d5gcz1 , tubmm-d5giz0 , tubmm-d5gkr8 , tubmm-d5glm4 , tubmm-d5gnw0 , tubmm-dapb , tubmm-d5gfj1 , tubmm-d5gpf4 , tubmm-TmEst2 , tubmm-TmEst1 , tubmm-TmEst3 , 9pezi-a0a292py12 , tubmm-kex1

Title : Further progress towards a catalogue of all Arabidopsis genes: analysis of a set of 5000 non-redundant ESTs - Cooke_1996_Plant.J_9_101
Author(s) : Cooke R , Raynal M , Laudie M , Grellet F , Delseny M , Morris PC , Guerrier D , Giraudat J , Quigley F , Clabault G , Li YF , Mache R , Krivitzky M , Gy IJ , Kreis M , Lecharny A , Parmentier Y , Marbach J , Fleck J , Clement B , Philipps G , Herve C , Bardet C , Tremousaygue D , Lescure B , Lacomme C , Roby D , Jourjon MF , Chabrier P , Charpenteau JL , Desprez T , Amselem J , Chiapello H , Hofte H
Ref : Plant J , 9 :101 , 1996
Abstract : Nearly 7000 Arabidopsis thaliana-expressed sequence tags (ESTs) from 10 cDNA libraries have been sequenced, of which almost 5000 non-redundant tags have been submitted to the EMBL data bank. The quality of the cDNA libraries used is analysed. Similarity searches in international protein data banks have allowed the detection of significant similarities to a wide range of proteins from many organisms. Alignment with ESTs from the rice systematic sequencing project has allowed the detection of amino acid motifs which are conserved between the two organisms, thus identifying tags to genes encoding highly conserved proteins. These genes are candidates for a common framework in genome mapping projects in different plants.
ESTHER : Cooke_1996_Plant.J_9_101
PubMedSearch : Cooke_1996_Plant.J_9_101
PubMedID: 8580968