High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat. Here we report a 110-Mb draft sequence of Pst isolate CY32, obtained using a ‘fosmid-to-fosmid’ strategy, to better understand its race evolution and pathogenesis. The Pst genome is highly heterozygous and contains 25,288 protein-coding genes. Compared with non-obligate fungal pathogens, Pst has a more diverse gene composition and more genes encoding secreted proteins. Re-sequencing analysis indicates significant genetic variation among six isolates collected from different continents. Approximately 35% of SNPs are in the coding sequence regions, and half of them are non-synonymous. High genetic diversity in Pst suggests that sexual reproduction has an important role in the origin of different regional races. Our results show the effectiveness of the ‘fosmid-to-fosmid’ strategy for sequencing dikaryotic genomes and the feasibility of genome analysis to understand race evolution in Pst and other obligate pathogens.

[1]  P. Cheng,et al.  Virulence races of Puccinia striiformis f. sp. tritici in 2006 and 2007 and development of wheat stripe rust and distributions, dynamics, and evolutionary relationships of races from 2000 to 2007 in the United States , 2010 .

[2]  Jonathan D. G. Jones,et al.  Obligate biotroph parasitism: can we link genomes to lifestyles? , 2012, Trends in plant science.

[3]  Y. Van de Peer,et al.  The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis , 2008, Nature.

[4]  X. Chen,et al.  Inheritance of stripe rust resistance in wheat cultivars used to differentiate races of Puccinia striiformis in North America , 1992 .

[5]  J. Kolmer.  Tracking wheat rust on a continental scale. , 2005, Current opinion in plant biology.

[6]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[7]  S. Kamoun,et al.  RXLR effectors of plant pathogenic oomycetes. , 2007, Current opinion in microbiology.

[8]  Christina A. Cuomo,et al.  The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization , 2007, Science.

[9]  G. Weinstock,et al.  Creating a honey bee consensus gene set , 2007, Genome Biology.

[10]  Pari Skamnioti,et al.  Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism , 2010, Science.

[11]  J. Fellers,et al.  Cereal rust fungi genomics and the pursuit of virulence and avirulence factors. , 2006, FEMS microbiology letters.

[12]  James K. M. Brown,et al.  Aerial Dispersal of Pathogens on the Global and Continental Scales and Its Impact on Plant Disease , 2002, Science.

[13]  K. Mendgen,et al.  A putative amino acid transporter is specifically expressed in haustoria of the rust fungus Uromyces fabae. , 1997, Molecular plant-microbe interactions : MPMI.

[14]  Aaron L. Halpern,et al.  Consensus generation and variant detection by Celera Assembler , 2008, Bioinform..

[15]  Keith Bradnam,et al.  CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes , 2007, Bioinform..

[16]  A. Justesen,et al.  Escalating Threat of Wheat Rusts , 2010, Science.

[17]  Jeppe Emmersen,et al.  Powdery mildew fungal effector candidates share N-terminal Y/F/WxC-motif , 2010, BMC Genomics.

[18]  Huanming Yang,et al.  Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers , 2011, Nature Biotechnology.

[19]  C. Wellings.  Puccinia striiformis in Australia: a review of the incursion, evolution, and adaptation of stripe rust in the period 1979–2006 , 2007 .

[20]  J. Brownstein,et al.  Emerging fungal threats to animal, plant and ecosystem health , 2012, Nature.

[21]  Sarah Calvo,et al.  Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis , 2006, Nature.

[22]  B. Birren,et al.  Stable propagation of cosmid sized human DNA inserts in an F factor based vector. , 1992, Nucleic acids research.

[23]  L. Szabo,et al.  Century-old mystery of Puccinia striiformis life history solved with the identification of Berberis as an alternate host. , 2010, Phytopathology.

[24]  Loretta Auvil,et al.  The yak genome and adaptation to life at high altitude , 2012, Nature Genetics.

[25]  J. Jurka,et al.  Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust , 2011, PloS one.

[26]  Robert S. Harris,et al.  Improved pairwise alignment of genomic dna , 2007 .

[27]  S. Chen,et al.  Genetic diversity in Puccinia striiformis Westend. f.sp. tritici revealed by pathogen genome-specific repetitive sequence , 1998 .

[28]  Ramon Wahl,et al.  A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis , 2010, PLoS biology.

[29]  P. Dodds,et al.  Haustorially Expressed Secreted Proteins from Flax Rust Are Highly Enriched for Avirulence Elicitors[W] , 2005, The Plant Cell Online.

[30]  K. Mendgen,et al.  The role of haustoria in sugar supply during infection of broad bean by the rust fungus Uromyces fabae , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Cathryn J. Rehmeyer,et al.  The genome sequence of the rice blast fungus Magnaporthe grisea , 2005, Nature.

[32]  Huanming Yang,et al.  SNP detection for massively parallel whole-genome resequencing. , 2009, Genome research.

[33]  S. Brunak,et al.  Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.

[34]  Christina A. Cuomo,et al.  Obligate biotrophy features unraveled by the genomic analysis of rust fungi , 2011, Proceedings of the National Academy of Sciences.

[35]  J. Enjalbert,et al.  Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp. tritici. , 2010, Fungal genetics and biology : FG & B.

[36]  Huanming Yang,et al.  De novo assembly of human genomes with massively parallel short read sequencing. , 2010, Genome research.

[37]  Gang Liu,et al.  Automatic clustering of orthologs and inparalogs shared by multiple proteomes , 2006, ISMB.

[38]  K. Mendgen,et al.  Identification of a protein from rust fungi transferred from haustoria into infected plant cells. , 2005, Molecular plant-microbe interactions : MPMI.

[39]  P. Spanu.  The genomics of obligate (and nonobligate) biotrophs. , 2012, Annual review of phytopathology.

[40]  H. Martin,et al.  The Uromyces fabae UfAAT3 gene encodes a general amino acid permease that prefers uptake of in planta scarce amino acids. , 2004, Molecular plant pathology.

[41]  Kristian Kristensen,et al.  Evidence for increased aggressiveness in a recent widespread strain of Puccinia striiformis f. sp. tritici causing stripe rust of wheat. , 2009, Phytopathology.

[42]  Ruiqiang Li,et al.  SOAP: short oligonucleotide alignment program , 2008, Bioinform..

[43]  M. Ruggero,et al.  Similarity of Traveling-Wave Delays in the Hearing Organs of Humans and Other Tetrapods , 2007, Journal for the Association for Research in Otolaryngology.

[44]  T. Flutre,et al.  Considering Transposable Element Diversification in De Novo Annotation Approaches , 2011, PloS one.

[45]  S. Brunak,et al.  Improved prediction of signal peptides: SignalP 3.0. , 2004, Journal of molecular biology.

[46]  Dawei Li,et al.  The diploid genome sequence of an Asian individual , 2008, Nature.

[47]  Christina A. Cuomo,et al.  Obligate Biotrophy Features Unraveled by the Genomic Analysis of the Rust Fungi, Melampsora larici-populina and Puccinia graminis f. sp. tritici , 2011 .

[48]  A. Justesen,et al.  Diversity of Puccinia striiformis on cereals and grasses. , 2011, Annual review of phytopathology.

[49]  M. Ernst,et al.  Characterization of a developmentally regulated amino acid transporter (AAT1p) of the rust fungus Uromyces fabae. , 2002, Molecular plant pathology.

[50]  S. Raffaele,et al.  Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi , 2012, PloS one.

[51]  Zhao Jie.  Confirmation of Berberis spp.as alternate hosts of Puccinia striiformis f.sp.tritici on wheat in China , 2011 .

[52]  R. Line,et al.  Stripe rust of wheat and barley in North America: a retrospective historical review. , 2002, Annual review of phytopathology.

[53]  Bernard Henrissat,et al.  Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea , 2011, PLoS genetics.