Rust fungi are among the most
devastating fungal pathogens world-wide. They are basidiomycete
fungi, belong to the order Uredinales and
encompass approximately 5,000 species which can be ordered into 140-150
different genera. They infect many plant species and families and cause many
known diseases such as coffee rust, bean rust and rust of pine trees. Probably
the most economically damaging diseases are the rusts
on cereal crops. Several rust fungi have a major economic impact on the
farming community in Western Canada. In particular stem and leaf rust of wheat
and barley, and crown rust on oats can cause up to 20% loss in yield. This translates
into hundreds of millions of dollars in annual lost revenue and cost for
preventive fungicide treatments. A conservative estimate puts losses in 1999
due to the wheat leaf rust alone at 90M in Western Canada.
Rust
fungi have been known since biblical times and have been studied for over a
century. However, because they are obligate biotrophs it is very difficult to culture these in the
laboratory. Progress on molecular genetic studies has therefore been very slow.
Recently, however, "Genomics technologies” have been applied on several of
the economically most important rusts, the wheat stem rust fungus, Puccinia graminis f. sp. tritici, and the wheat leaf rust
fungus Puccinia triticina (formerly, Puccinia recondita
f.sp. tritici). Exemplary research has also
been done on the bean rust (Voegele (2006). "Uromyces fabae: development,
metabolism, and interactions with its host Vicia faba." FEMS Microbiol
Lett 259,
165-73) and flax rust, Melampsora lini (Ellis, Dodds and Lawrence (2007). "The
role of secreted proteins in diseases of plants caused by rust, powdery mildew
and smut fungi." Current Opinion in Microbiology 10, 326-331). The generation of
genomic resources is already accelerating the pace of research in this field.
Rust fungi have without doubt
the most complicated life cycles of all fungi. Some of them, the macrocyclic forms such as P. triticina,
have five life-cycle stages and require two different,
completely unrelated host plants. Diploid teliospores
(2n) form on senescing wheat plants in the fall (see stage III in diagram
below) and are resilient survival structures which, upon germination and
meiosis under the right conditions, give rise to haploid basidiospores
(n, stage IV). These very ephemeral basidiospores will
enter a sexual cycle which takes place on the alternate host plant.
"Fertilization" requires the mixing of pycnidiospores
of different mating types (n, stage 0) embedded in the nectar of the pycnidia, often by insects. This produces aecia from which
aeciospores, dikaryotic (n + n) dispersal structures
(stage I), are released. Aeciospores will start the infection cycle on the
primary host which results in the production of masses of dikaryotic
(n + n) urediniospores (stage II) in brown-coloured,
"rusty" pustules. The urediniospores can
re-infect the same or fresh host plants several times during the growing season
resulting in exponential increases of inoculum. Wind currents and proper
weather conditions can result in heavily infected wheat producing areas, or
even epidemics.
P.
triticina life cycle
(cartoon from "Introductory Mycology", used
by permission of John Wiley &
Sons, Inc.)
HIGHER FUNGI
Subdivision: BASIDIOMYCOTINA
Class: HEMIBASIDIOMYCETES (TELIOMYCETIDAE)
Order: Uredinales
Genus: Puccinia
Species: triticina
Disease |
Host |
Pathogen |
Alternate Host |
wheat leaf rust(brown rust) |
Triticum aestivum |
Puccinia triticina, formerly P. recondita
f. sp. tritici |
meadow rue (Thalictrum speciosissimum) |
Genome
size of P. triticina is estimated at approx. 100 – 120 Mbp.
For comparison:
Genome size of P. graminis f. sp. tritici
(Pgt) was estimated to be approx. 67 Mbp ( 64% unique, 30% repetitive sequences; 45.3% G + C (Backlund, J. E. and L.J. Szabo.
1993. Current Genetics 24:89-93).
Pgt genome sequencing to approx. 8x coverage has recently been
achieved (Jan.
2007; Broad Institute), including 40,000+ ESTs. Based on the genome
sequence, the current Pgt genome size is estimated at
approx. 80 Mbp.
Having
generated large data sets of Expressed Sequence Tags (ESTs) covering all life
cycle stages (Hu
et al., 2007; Xu et al., 2011), and a Bacterial Artificial Chromosome
(BAC) library, we have contributed to sequencing of complete P. triticina genomes (Puccinia Group
Sequencing Project, Broad Institute of Harvard and MIT; collaboration with Dr.
C. Cuomo, Broad Institute, Cambridge, MA, Dr. L. Szabo,
ARS-USDA, CDL-St. Paul MN and Dr. J. Fellers, ARS-USDA, Manhattan KS), funded through the NSF/USDA CSREES Microbial Genome
Sequencing Program. BAC end-sequencing was performed by Scientists at the Michael Smith Genome Sciences
Centre, Vancouver, BC, Canada.
Large-scale,
next-gen genome re-sequencing of many isolates and races, and RNA-seq to generate transcriptome
profiles is conducted at the Michael Smith
Genome Sciences Centre, Vancouver, BC, Canada to investigate gene and
race/isolate diversity as found in agriculture settings and upon environmental
selection bottlenecks (e.g., resistance gene introductions), and to study fungal
and host responses during various interaction types (Wang
et al, 2012). Research is part of two projects: "Genomics Approaches
to Mitigate Fungal Threats to Crops" with B. Saville, Trent University, ON, an Ontario Ministry of
Research and Innovation-funded project on large-scale transcriptome
analyses of cereal rust and other fungi during host infections, and "Poplar
and cereal rust comparative genomics: identification of pathogen determinants
to prevent and predict epidemics” with R. Hamelin, Dept. of Forest Sciences,
UBC & Canadian Forest Service, Laurentian Forestry Centre in Quebec (funded
through the Genome British Columbia Strategic Opportunities Fund, round 3). Collaboration with AAFC researchers, B. McCallum and T. Fetch (AAFC
Cereal Research Centre in Winnipeg, MB), and Visiting Scientists, Drs. D.
Joly and X. Wang.