title: Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini.
abstract: Rust fungi are an important group of plant pathogens that cause devastating losses in agricultural, silvicultural and natural ecosystems. Plants can be protected from rust disease by resistance genes encoding receptors that trigger a highly effective defence response upon recognition of specific pathogen avirulence proteins. Identifying avirulence genes is crucial for understanding how virulence evolves in the field.
  
  
  
  To facilitate avirulence gene cloning in the flax rust fungus, Melampsora lini, we constructed a high-density genetic linkage map using single nucleotide polymorphisms detected in restriction site-associated DNA sequencing (RADseq) data. The map comprises 13,412 RADseq markers in 27 linkage groups that together span 5860 cM and contain 2756 recombination bins. The marker sequences were used to anchor 68.9 % of the M. lini genome assembly onto the genetic map. The map and anchored assembly were then used to: 1) show that M. lini has a high overall meiotic recombination rate, but recombination distribution is uneven and large coldspots exist; 2) show that substantial genome rearrangements have occurred in spontaneous loss-of-avirulence mutants; and 3) identify the AvrL2 and AvrM14 avirulence genes by map-based cloning. AvrM14 is a dual-specificity avirulence gene that encodes a predicted nudix hydrolase. AvrL2 is located in the region of the M. lini genome with the lowest recombination rate and encodes a small, highly-charged proline-rich protein.
  
  
  
  The M. lini high-density linkage map has greatly advanced our understanding of virulence mechanisms in this pathogen by providing novel insights into genome variability and enabling identification of two new avirulence genes.
authors.affiliation: Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
authors.forename: Claire
authors.initials: C
authors.lastname: Anderson
authors.affiliation: Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.|Current address: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
authors.forename: Muhammad Adil
authors.initials: MA
authors.lastname: Khan
authors.affiliation: Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
authors.forename: Ann-Maree
authors.initials: AM
authors.lastname: Catanzariti
authors.affiliation: ANU Bioinformatics Consulting Unit, The John Curtin School of Medical Research, The Australian National University, 131 Garran Road, Acton, ACT, 2601, Australia.
authors.forename: Cameron A
authors.initials: CA
authors.lastname: Jack
authors.affiliation: CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia.|Current address: KWS SAAT SE, Grimsehlstraße 31, Einbeck, 37574, Germany.
authors.forename: Adnane
authors.initials: A
authors.lastname: Nemri
authors.affiliation: CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Lawrence
authors.affiliation: CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Narayana M
authors.initials: NM
authors.lastname: Upadhyaya
authors.affiliation: Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
authors.forename: Adrienne R
authors.initials: AR
authors.lastname: Hardham
authors.affiliation: CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Jeffrey G
authors.initials: JG
authors.lastname: Ellis
authors.affiliation: CSIRO Agriculture, GPO Box 1600, Canberra, ACT, 2601, Australia.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Dodds
authors.affiliation: Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia. david.jones@anu.edu.au.
authors.forename: David A
authors.initials: DA
authors.lastname: Jones
mesh_terms: D000595:Amino Acid Sequence; D001487:Basidiomycota / Q000235:genetics* / Q000472:pathogenicity; D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods; D005787:Gene Frequency; D056426:Genetic Loci; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D019656:Loss of Heterozygosity; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D011995:Recombination, Genetic; D014774:Virulence / Q000235:genetics*
keywords: Avirulence gene; Genetic linkage map; Loss of heterozygosity (LOH); Map-based cloning; Melampsora lini; Recombination; Restriction-site associated DNA sequencing (RADseq); Rust fungus; Scaffold anchoring