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G3 (Bethesda). 2017 Feb 9;7(2):361-376. doi: 10.1534/g3.116.032797.

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.

Author information

1
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.
2
Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.
3
Agriculture and Agri-Food Canada, Summerland Research and Development Centre, British Columbia V0H 1Z0, Canada.
4
Agriculture and Agri-Food Canada, Morden Research and Development Centre, Manitoba R6M 1Y5, Canada.
5
Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142.
6
The Institute for Cereal Crops Improvement, Tel Aviv University, Ramat Aviv 69978, Israel.
7
Department of Plant Pathology, Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas 66506.
8
Department of Plant Pathology, Washington State University, Pullman, Washington 99164.
9
Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108.
10
Wheat Health, Genetics, and Quality Research Unit, United States Department of Agriculture-Agricultural Research Service, Pullman, Washington 99164.
11
Department of Plant Pathology, Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Manhattan, Kansas 66506 cuomo@broadinstitute.org Guus.Bakkeren@agr.gc.ca john.fellers@ars.usda.gov.

Abstract

Three members of the Puccinia genus, Pucciniatriticina (Pt), Pstriiformis f.sp. tritici (Pst), and Pgraminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi, and basidiomycetes, and to identify genes of significance for infection. Pt had the largest genome of the three, estimated at 135 Mb with expansion due to mobile elements and repeats encompassing 50.9% of contig bases; in comparison, repeats occupy 31.5% for Pst and 36.5% for Pgt We find all three genomes are highly heterozygous, with Pst [5.97 single nucleotide polymorphisms (SNPs)/kb] nearly twice the level detected in Pt (2.57 SNPs/kb) and that previously reported for Pgt Of 1358 predicted effectors in Pt, 784 were found expressed across diverse life cycle stages including the sexual stage. Comparison to related fungi highlighted the expansion of gene families involved in transcriptional regulation and nucleotide binding, protein modification, and carbohydrate degradation enzymes. Two allelic homeodomain pairs, HD1 and HD2, were identified in each dikaryotic Puccinia species along with three pheromone receptor (STE3) mating-type genes, two of which are likely representing allelic specificities. The HD proteins were active in a heterologous Ustilago maydis mating assay and host-induced gene silencing (HIGS) of the HD and STE3 alleles reduced wheat host infection.

KEYWORDS:

Puccinia; effectors; genome comparisons; mating-type genes; sexual stage

PMID:
27913634
PMCID:
PMC5295586
DOI:
10.1534/g3.116.032797
[Indexed for MEDLINE]
Free PMC Article

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