Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
Joelle Amselem,Christina A. Cuomo,Jan A. L. van Kan,Muriel Viaud,Ernesto P. Benito,Arnaud Couloux,Pedro M. Coutinho,Ronald P. de Vries,Paul S. Dyer,Sabine Fillinger,Elisabeth Fournier,Elisabeth Fournier,Lilian Gout,Matthias Hahn,Linda M. Kohn,Nicolas Lapalu,Kim M. Plummer,Jean-Marc Pradier,Emmanuel Quévillon,Emmanuel Quévillon,Amir Sharon,Adeline Simon,Arjen ten Have,Bettina Tudzynski,Paul Tudzynski,Patrick Wincker,Marion Andrew,Véronique Anthouard,Ross E. Beever,Rolland Beffa,Isabelle Benoit,Ourdia Bouzid,Baptiste Brault,Zehua Chen,Mathias Choquer,Mathias Choquer,Jérôme Collemare,Jérôme Collemare,Pascale Cotton,Etienne Danchin,Corinne Da Silva,Angélique Gautier,Corinne Giraud,Tatiana Giraud,Celedonio González,Sandrine Grossetete,Ulrich Güldener,Bernard Henrissat,Barbara J. Howlett,Chinnappa D. Kodira,Matthias Kretschmer,Anne Lappartient,Michaela Leroch,Caroline Levis,Evan Mauceli,Cécile Neuvéglise,Birgitt Oeser,Matthew D. Pearson,Julie Poulain,Nathalie Poussereau,Hadi Quesneville,Christine Rascle,Julia Schumacher,Béatrice Segurens,Adrienne Sexton,Evelyn Silva,Catherine Sirven,Darren M. Soanes,Nicholas J. Talbot,Matthew D. Templeton,Chandri Yandava,Oded Yarden,Qiandong Zeng,Jeffrey A. Rollins,Marc-Henri Lebrun,Marc-Henri Lebrun,Marty Dickman +76 more
TLDR
Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea, and shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating.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.read more
Citations
More filters
Journal ArticleDOI
The Top 10 fungal pathogens in molecular plant pathology
Ralph A. Dean,Jan A. L. van Kan,Zacharias A. Pretorius,Kim E. Hammond-Kosack,Antonio Di Pietro,Pietro Spanu,Jason J. Rudd,Martin B. Dickman,Regine Kahmann,Jeff Ellis,Gary D. Foster +10 more
TL;DR: A short resumé of each fungus in the Top 10 list and its importance is presented, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark.
Journal ArticleDOI
Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways
Arne Weiberg,Ming Wang,Feng Mao Lin,Hongwei Zhao,Zhihong Zhang,Isgouhi Kaloshian,Hsien Da Huang,Hailing Jin +7 more
TL;DR: This fungal pathogen transfers “virulent” sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.
Journal ArticleDOI
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses
Richard J. O'Connell,Michael R. Thon,Stéphane Hacquard,Stefan G. Amyotte,Jochen Kleemann,Maria F. Torres,Ulrike Damm,Ester Alvarenga Santos Buiate,Lynn Epstein,Noam Alkan,Janine Altmüller,Lucia Alvarado-Balderrama,Christopher Bauser,Christian Becker,Bruce W. Birren,Zehua Chen,Jaeyoung Choi,Jo Anne Crouch,Jonathan P. Duvick,Jonathan P. Duvick,Mark A. Farman,Pamela Gan,David I. Heiman,Bernard Henrissat,Richard J. Howard,Mehdi Kabbage,Christian Koch,Barbara Kracher,Yasuyuki Kubo,Audrey D. Law,Marc-Henri Lebrun,Yong-Hwan Lee,Itay Miyara,Neil Moore,Ulla Neumann,Karl Nordström,Daniel G. Panaccione,Ralph Panstruga,Ralph Panstruga,Michael Place,Robert H. Proctor,Dov Prusky,Gabriel E. Rech,Richard Reinhardt,Jeffrey A. Rollins,Steve Rounsley,Christopher L. Schardl,David C. Schwartz,Narmada Shenoy,Ken Shirasu,Usha Rani Sikhakolli,Kurt Stüber,Serenella A. Sukno,James A. Sweigard,Yoshitaka Takano,Hiroyuki Takahara,Hiroyuki Takahara,Frances Trail,H. Charlotte van der Does,H. Charlotte van der Does,Lars M. Voll,Isa Will,Sarah Young,Qiandong Zeng,Jingze Zhang,Shiguo Zhou,Martin B. Dickman,Paul Schulze-Lefert,Emiel Ver Loren van Themaat,Li-Jun Ma,Li-Jun Ma,Lisa J. Vaillancourt +71 more
TL;DR: Findings show that preinvasion perception of plant-derived signals substantially reprograms fungal gene expression and indicate previously unknown functions for particular fungal cell types.
Journal ArticleDOI
The Top 10 fungal pathogens in molecular plant pathology: Top 10 fungal pathogens
Journal ArticleDOI
Genome evolution in filamentous plant pathogens: why bigger can be better
Sylvain Raffaele,Sophien Kamoun +1 more
TL;DR: Cases in which genome plasticity has contributed to the emergence of new virulence traits are illustrated and how genome expansions may have had an impact on the co-evolutionary conflict between these filamentous plant pathogens and their hosts are discussed.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
TL;DR: ClUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W, providing an integrated system for performing multiple sequence and profile alignments and analysing the results.
Journal ArticleDOI
MRBAYES: Bayesian inference of phylogenetic trees
TL;DR: The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo, and an executable is available at http://brahms.rochester.edu/software.html.
Journal ArticleDOI
MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Related Papers (5)
Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium
Li-Jun Ma,H. Charlotte van der Does,Katherine A. Borkovich,Jeffrey J. Coleman,Marie Josée Daboussi,Antonio Di Pietro,Marie Dufresne,Michael Freitag,Manfred Grabherr,Bernard Henrissat,Petra M. Houterman,Seogchan Kang,Won-Bo Shim,Charles P. Woloshuk,Xiaohui Xie,Jin-Rong Xu,John F. Antoniw,Scott E. Baker,B. H. Bluhm,Andrew Breakspear,Daren W. Brown,Robert A. E. Butchko,Sinéad B. Chapman,Richard M.R. Coulson,Pedro M. Coutinho,Etienne Danchin,Etienne Danchin,Andrew C. Diener,Liane R. Gale,Donald M. Gardiner,Stephen A. Goff,Kim E. Hammond-Kosack,Karen Hilburn,Aurélie Hua-Van,Wilfried Jonkers,Kemal Kazan,Chinnappa D. Kodira,Michael Koehrsen,Lokesh Kumar,Yong-Hwan Lee,Liande Li,Liande Li,John M. Manners,Diego Miranda-Saavedra,Mala Mukherjee,Gyungsoon Park,Jongsun Park,Sook Young Park,Sook Young Park,Robert H. Proctor,Aviv Regev,M. Carmen Ruiz-Roldán,Divya Sain,Sharadha Sakthikumar,Sean M. Sykes,David C. Schwartz,B. Gillian Turgeon,Ilan Wapinski,Olen C. Yoder,Sarah Young,Qiandong Zeng,Shiguo Zhou,James E. Galagan,Christina A. Cuomo,H. Corby Kistler,Martijn Rep +65 more