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Henningsen EC, Hewitt T, Dugyala S, Nazareno ES, Gilbert E, Li F, Kianian SF, Steffenson BJ, Dodds PN, Sperschneider J, Figueroa M. 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. G3 (BETHESDA, MD.) 2022; 12:6613142. [PMID: 35731221 PMCID: PMC9339303 DOI: 10.1093/g3journal/jkac149] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022]
Abstract
Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
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Affiliation(s)
- Eva C Henningsen
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Tim Hewitt
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Sheshanka Dugyala
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Feng Li
- eGenesis Inc., Cambridge, MA 02139, USA
| | - Shahryar F Kianian
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA.,USDA-ARS Cereal Disease Laboratory, St. Paul, MN 55108, USA
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Peter N Dodds
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Jana Sperschneider
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT 2601, Australia
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Arends D, Kärst S, Heise S, Korkuc P, Hesse D, Brockmann GA. Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. Genetics 2022; 220:iyab192. [PMID: 34791189 PMCID: PMC8733443 DOI: 10.1093/genetics/iyab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022] Open
Abstract
While direct additive and dominance effects on complex traits have been mapped repeatedly, additional genetic factors contributing to the heterogeneity of complex traits have been scarcely investigated. To assess genetic background effects, we investigated transmission ratio distortions (TRDs) of alleles from parent to offspring using an advanced intercross line (AIL) of an initial cross between the mouse inbred strains C57BL/6NCrl (B6N) and BFMI860-12 [Berlin Fat Mouse Inbred (BFMI)]. A total of 341 males of generation 28 and their respective 61 parents and 66 grandparents were genotyped using Mega Mouse Universal Genotyping Arrays. TRDs were investigated using allele transmission asymmetry tests, and pathway overrepresentation analysis was performed. Sequencing data were used to test for overrepresentation of nonsynonymous SNPs (nsSNPs) in TRD regions. Genetic incompatibilities were tested using the Bateson-Dobzhansky-Muller two-locus model. A total of 62 TRD regions were detected, many in close proximity to the telocentric centromere. TRD regions contained 44.5% more nsSNPs than randomly selected regions (182 vs 125.9 ± 17.0, P < 1 × 10-4). Testing for genetic incompatibilities between TRD regions identified 29 genome-wide significant incompatibilities between TRD regions [P(BF) < 0.05]. Pathway overrepresentation analysis of genes in TRD regions showed that DNA methylation, epigenetic regulation of RNA, and meiotic/meiosis regulation pathways were affected independent of the parental origin of the TRD. Paternal BFMI TRD regions showed overrepresentation in the small interfering RNA biogenesis and in the metabolism of lipids and lipoproteins. Maternal B6N TRD regions harbored genes involved in meiotic recombination, cell death, and apoptosis pathways. The analysis of genes in TRD regions suggests the potential distortion of protein-protein interactions influencing obesity and diabetic retinopathy as a result of disadvantageous combinations of allelic variants in Aass, Pgx6, and Nme8. Using an AIL significantly improves the resolution at which we can investigate TRD. Our analysis implicates distortion of protein-protein interactions as well as meiotic drive as the underlying mechanisms leading to the observed TRD in our AIL. Furthermore, genes with large amounts of nsSNPs located in TRD regions are more likely to be involved in pathways that are related to the phenotypic differences between the parental strains. Genes in these TRD regions provide new targets for investigating genetic adaptation, protein-protein interactions, and determinants of complex traits such as obesity.
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Affiliation(s)
- Danny Arends
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Stefan Kärst
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Sebastian Heise
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Paula Korkuc
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Deike Hesse
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
| | - Gudrun A Brockmann
- Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Berlin D-10115, Germany
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