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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Figueroa Corona L, Allen BJ, Puiu D, Wright J, De La Torre AR, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A genome sequence for the threatened whitebark pine. G3 (BETHESDA, MD.) 2024; 14:jkae061. [PMID: 38526344 PMCID: PMC11075562 DOI: 10.1093/g3journal/jkae061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 03/26/2024]
Abstract
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.
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Affiliation(s)
- David B Neale
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Whitebark Pine Ecosystem Foundation, Missoula, MT 59808, USA
| | - Aleksey V Zimin
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Amy Meltzer
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Akriti Bhattarai
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | - Maurice Amee
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
| | | | - Brian J Allen
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- University of California Cooperative Extension, Central Sierra, Jackson, CA 95642, USA
| | - Daniela Puiu
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jessica Wright
- USDA Forest Service, Pacific Southwest Research Station, Davis, CA 95618, USA
| | | | - Patrick E McGuire
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Winston Timp
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Steven L Salzberg
- Department of Biomedical Engineering and Center for Computational Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Computer Science and Biostatistics, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Neale DB, Zimin AV, Meltzer A, Bhattarai A, Amee M, Corona LF, Allen BJ, Puiu D, Wright J, Torre ARDL, McGuire PE, Timp W, Salzberg SL, Wegrzyn JL. A Genome Sequence for the Threatened Whitebark Pine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567420. [PMID: 38014212 PMCID: PMC10680812 DOI: 10.1101/2023.11.16.567420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Whitebark pine (WBP, Pinus albicaulis ) is a white pine of subalpine regions in western contiguous US and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola ) and additional threats from mountain pine beetle ( Dendroctonus ponderosae ), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short-reads of haploid megametophyte tissue and Oxford Nanopore long-reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gbp of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gbp). Approximately 87.2% (24.0 Gbp) of total sequence was placed on the twelve WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich-repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the three subclasses of NLRs (TNL, CNL, RNL). Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo assembled transcriptomes.
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Mesarich CH, Barnes I, Bradley EL, de la Rosa S, de Wit PJGM, Guo Y, Griffiths SA, Hamelin RC, Joosten MHAJ, Lu M, McCarthy HM, Schol CR, Stergiopoulos I, Tarallo M, Zaccaron AZ, Bradshaw RE. Beyond the genomes of Fulvia fulva (syn. Cladosporium fulvum) and Dothistroma septosporum: New insights into how these fungal pathogens interact with their host plants. MOLECULAR PLANT PATHOLOGY 2023; 24:474-494. [PMID: 36790136 PMCID: PMC10098069 DOI: 10.1111/mpp.13309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Fulvia fulva and Dothistroma septosporum are closely related apoplastic pathogens with similar lifestyles but different hosts: F. fulva is a pathogen of tomato, whilst D. septosporum is a pathogen of pine trees. In 2012, the first genome sequences of these pathogens were published, with F. fulva and D. septosporum having highly fragmented and near-complete assemblies, respectively. Since then, significant advances have been made in unravelling their genome architectures. For instance, the genome of F. fulva has now been assembled into 14 chromosomes, 13 of which have synteny with the 14 chromosomes of D. septosporum, suggesting these pathogens are even more closely related than originally thought. Considerable advances have also been made in the identification and functional characterization of virulence factors (e.g., effector proteins and secondary metabolites) from these pathogens, thereby providing new insights into how they promote host colonization or activate plant defence responses. For example, it has now been established that effector proteins from both F. fulva and D. septosporum interact with cell-surface immune receptors and co-receptors to activate the plant immune system. Progress has also been made in understanding how F. fulva and D. septosporum have evolved with their host plants, whilst intensive research into pandemics of Dothistroma needle blight in the Northern Hemisphere has shed light on the origins, migration, and genetic diversity of the global D. septosporum population. In this review, we specifically summarize advances made in our understanding of the F. fulva-tomato and D. septosporum-pine pathosystems over the last 10 years.
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Affiliation(s)
- Carl H. Mesarich
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology InstituteUniversity of PretoriaPretoriaSouth Africa
| | - Ellie L. Bradley
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | - Silvia de la Rosa
- Laboratory of Molecular Plant Pathology, School of Agriculture and EnvironmentMassey UniversityPalmerston NorthNew Zealand
| | | | - Yanan Guo
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | | | - Richard C. Hamelin
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | | | - Mengmeng Lu
- Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | - Hannah M. McCarthy
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Christiaan R. Schol
- Laboratory of PhytopathologyWageningen UniversityWageningenNetherlands
- Plant BreedingWageningen University & ResearchWageningenNetherlands
| | | | - Mariana Tarallo
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Alex Z. Zaccaron
- Department of Plant PathologyUniversity of California DavisDavisCaliforniaUSA
| | - Rosie E. Bradshaw
- Bioprotection AotearoaMassey UniversityPalmerston NorthNew Zealand
- Laboratory of Molecular Plant Pathology, School of Natural SciencesMassey UniversityPalmerston NorthNew Zealand
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Liu JJ, Zamany A, Cartwright C, Xiang Y, Shamoun SF, Rancourt B. Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease. FRONTIERS IN PLANT SCIENCE 2022; 13:908680. [PMID: 35845706 PMCID: PMC9279933 DOI: 10.3389/fpls.2022.908680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Western hemlock (Tsuga heterophylla) is highly susceptible to Annosus root and butt rot disease, caused by Heterobasidion occidentale across its native range in western North America. Understanding molecular mechanisms of tree defense and dissecting genetic components underlying disease resistance will facilitate forest breeding and disease control management. The aim of this study was to profile host transcriptome reprogramming in response to pathogen infection using RNA-seq analysis. Inoculated seedlings were clearly grouped into three types: quantitative resistant (QR), susceptible (Sus), and un-infected (Uif), based on profiles of H. occidentale genes expressed in host tissues. Following de novo assembly of a western hemlock reference transcriptome with more than 33,000 expressed genes, the defensive transcriptome reprogramming was characterized and a set of differentially expressed genes (DEGs) were identified with gene ontology (GO) annotation. The QR seedlings showed controlled and coordinated molecular defenses against biotic stressors with enhanced biosynthesis of terpenoids, cinnamic acids, and other secondary metabolites. The Sus seedlings showed defense responses to abiotic stimuli with a few biological processes enhanced (such as DNA replication and cell wall organization), while others were suppressed (such as killing of cells of other organism). Furthermore, non-synonymous single nucleotide polymorphisms (ns-SNPs) of the defense- and resistance-related genes were characterized with high genetic variability. Both phylogenetic analysis and principal coordinate analysis (PCoA) revealed distinct evolutionary distances among the samples. The QR and Sus seedlings were well separated and grouped into different phylogenetic clades. This study provides initial insight into molecular defense and genetic components of western hemlock resistance against the Annosus root and butt rot disease. Identification of a large number of genes and their DNA variations with annotated functions in plant resistance and defense promotes the development of genomics-based breeding strategies for improved western hemlock resistance to H. occidentale.
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Affiliation(s)
- Jun-Jun Liu
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Arezoo Zamany
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Charlie Cartwright
- British Columbia Ministry of Forests, Cowichan Lake Research Station, Mesachie Lake, BC, Canada
| | - Yu Xiang
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Simon F. Shamoun
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
| | - Benjamin Rancourt
- Natural Resources Canada, Canadian Forest Service, Victoria, BC, Canada
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Liu JJ, Schoettle AW, Sniezko RA, Waring KM, Williams H, Zamany A, Johnson JS, Kegley A. Comparative Association Mapping Reveals Conservation of Major Gene Resistance to White Pine Blister Rust in Southwestern White Pine ( Pinus strobiformis) and Limber Pine ( P. flexilis). PHYTOPATHOLOGY 2022; 112:1093-1102. [PMID: 34732078 DOI: 10.1094/phyto-09-21-0382-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
All native North American white pines are highly susceptible to white pine blister rust (WPBR) caused by Cronartium ribicola. Understanding genomic diversity and molecular mechanisms underlying genetic resistance to WPBR remains one of the great challenges in improvement of white pines. To compare major gene resistance (MGR) present in two species, southwestern white pine (Pinus strobiformis) Cr3 and limber pine (P. flexilis) Cr4, we performed association analyses of Cr3-controlled resistant traits using single nucleotide polymorphism (SNP) assays designed with Cr4-linked polymorphic genes. We found that ∼70% of P. flexilis SNPs were transferable to P. strobiformis. Furthermore, several Cr4-linked SNPs were significantly associated with the Cr3-controlled traits in P. strobiformis families. The most significantly associated SNP (M326511_1126R) almost colocalized with Cr4 on the Pinus consensus linkage group 8, suggesting that Cr3 and Cr4 might be the same R locus, or have localizations very close to each other in the syntenic region of the P. strobiformis and P. flexilis genomes. M326511_1126R was identified as a nonsynonymous SNP, causing amino acid change (Val376Ile) in a putative pectin acetylesterase, with coding sequences identical between the two species. Moreover, top Cr3-associated SNPs were further developed as TaqMan genotyping assays, suggesting their usefulness as marker-assisted selection (MAS) tools to distinguish genotypes between quantitative resistance and MGR. This work demonstrates the successful transferability of SNP markers between two closely related white pine species in the hybrid zone, and the possibility for deployment of MAS tools to facilitate long-term WPBR management in P. strobiformis breeding and conservation.
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Affiliation(s)
- Jun-Jun Liu
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Anna W Schoettle
- Rocky Mountain Research Station, Forest Service, U.S. Department of Agriculture, Fort Collins, CO 80526, U.S.A
| | - Richard A Sniezko
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
| | - Kristen M Waring
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011-5018, U.S.A
| | - Holly Williams
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Arezoo Zamany
- Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia V8Z 1M5, Canada
| | - Jeremy S Johnson
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
- School of Forestry, Northern Arizona University, Flagstaff, AZ 86011-5018, U.S.A
| | - Angelia Kegley
- Dorena Genetic Resource Center, Forest Service, U.S. Department of Agriculture, Cottage Grove, OR 97424, U.S.A
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