Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

[1]  K. Jordan,et al.  Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races , 2022, Nature Communications.

[2]  D. Villegas,et al.  Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance , 2022, Frontiers in Plant Science.

[3]  T. James,et al.  Sexual reproduction is the null hypothesis for life cycles of rust fungi , 2022, PLoS pathogens.

[4]  E. Stone,et al.  Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data , 2022, Genome biology.

[5]  Heng Li,et al.  Haplotype-resolved assembly of diploid genomes without parental data , 2022, Nature Biotechnology.

[6]  P. Dodds,et al.  A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts , 2022, bioRxiv.

[7]  R. Park,et al.  A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution , 2021, Frontiers in Microbiology.

[8]  Zev N. Kronenberg,et al.  Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C , 2021, Nature Communications.

[9]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[10]  Marisa E. Miller,et al.  Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci , 2020, PLoS genetics.

[11]  Christina A. Cuomo,et al.  Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations , 2020, bioRxiv.

[12]  R. Park,et al.  Long-Read–Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes , 2020, Frontiers in Genetics.

[13]  Cédric Feschotte,et al.  RepeatModeler2 for automated genomic discovery of transposable element families , 2020, Proceedings of the National Academy of Sciences.

[14]  P. Dodds,et al.  Evolution of virulence in rust fungi - multiple solutions to one problem. , 2020, Current opinion in plant biology.

[15]  S. Koren,et al.  Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies , 2020, Genome Biology.

[16]  Sergey Koren,et al.  HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads , 2020, bioRxiv.

[17]  Z. Pretorius,et al.  Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing , 2019, Heredity.

[18]  Olga Chernomor,et al.  IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era , 2019, bioRxiv.

[19]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[20]  Marisa E. Miller,et al.  Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation , 2019, Nature Communications.

[21]  Sergey Koren,et al.  Mash Screen: high-throughput sequence containment estimation for genome discovery , 2019, Genome Biology.

[22]  Z. Pretorius,et al.  Tackling the re-emergence of wheat stem rust in Western Europe , 2019, Communications Biology.

[23]  Christophe Klopp,et al.  D-GENIES: dot plot large genomes in an interactive, efficient and simple way , 2018, PeerJ.

[24]  K. Hammond-Kosack,et al.  A review of wheat diseases-a field perspective. , 2018, Molecular plant pathology.

[25]  R. Park,et al.  Puccinia coronata f. sp. avenae: a threat to global oat production. , 2018, Molecular plant pathology.

[26]  Sergey Koren,et al.  Integrating Hi-C links with assembly graphs for chromosome-scale assembly , 2018, bioRxiv.

[27]  Adam M. Phillippy,et al.  MUMmer4: A fast and versatile genome alignment system , 2018, PLoS Comput. Biol..

[28]  Heng Li,et al.  Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..

[29]  Kin Chung Lam,et al.  High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.

[30]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[31]  Christina A. Cuomo,et al.  Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci , 2016, G3: Genes, Genomes, Genetics.

[32]  Jean-Philippe Vert,et al.  HiC-Pro: an optimized and flexible pipeline for Hi-C data processing , 2015, Genome Biology.

[33]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[34]  James K. Hane,et al.  CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts , 2015, BMC Genomics.

[35]  S. Salzberg,et al.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.

[36]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[37]  Matthew Fraser,et al.  InterProScan 5: genome-scale protein function classification , 2014, Bioinform..

[38]  Alexandros Stamatakis,et al.  RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies , 2014, Bioinform..

[39]  J. Kolmer,et al.  Genetic differentiation of the wheat leaf rust fungus Puccinia triticina in Europe , 2013 .

[40]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[41]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[42]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[43]  R. Singh,et al.  Global status of wheat leaf rust caused by Puccinia triticina , 2011, Euphytica.

[44]  D. Garvin,et al.  Wheat leaf rust caused by Puccinia triticina. , 2008, Molecular plant pathology.

[45]  P. Bartoš,et al.  Occurrence of wheat leaf rust (Puccinia triticina) races and virulence changes in Slovakia in 1994–2004 , 2008, Biologia.

[46]  Jonathan E. Allen,et al.  Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments , 2007, Genome Biology.

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

[48]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[49]  R. Park,et al.  Physiological specialization and pathotype distribution of Puccinia recondita in western Europe, 1995 , 1998 .

[50]  J. Burdon,et al.  Isozyme analysis indicates that a virulent cereal rust pathogen is a somatic hybrid , 1981, Nature.

[51]  D. J. Samborski,et al.  Studies on asexual variation in the virulence of oat crown rust, Puccinia coronata f. sp. avenae, and wheat leaf rust, Puccinia recondita , 1969 .

[52]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[53]  Sequence analysis Advance Access publication June 7, 2011 The variant call format and VCFtools , 2010 .

[54]  Peer Bork,et al.  Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation , 2007, Bioinform..

[55]  R. Park,et al.  Wheat Rusts: An Atlas of Resistance Genes , 1995 .

[56]  Heng Li,et al.  BIOINFORMATICS ORIGINAL PAPER , 2022 .