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Paasela T, Lim KJ, Pavicic M, Harju A, Venäläinen M, Paulin L, Auvinen P, Kärkkäinen K, Teeri TH. Transcriptomic Analysis Reveals Novel Regulators of the Scots Pine Stilbene Pathway. PLANT & CELL PHYSIOLOGY 2023; 64:1204-1219. [PMID: 37674261 PMCID: PMC10579783 DOI: 10.1093/pcp/pcad089] [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: 02/28/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Stilbenes accumulate in Scots pine heartwood where they have important roles in protecting wood from decaying fungi. They are also part of active defense responses, and their production is induced by different (a)biotic stressors. The specific transcriptional regulators as well as the enzyme responsible for activating the stilbene precursor cinnamate in the pathway are still unknown. UV-C radiation was the first discovered artificial stress activator of the pathway. Here, we describe a large-scale transcriptomic analysis of pine needles in response to UV-C and treatment with translational inhibitors, both activating the transcription of stilbene pathway genes. We used the data to identify putative candidates for the missing CoA ligase and for pathway regulators. We further showed that the pathway is transcriptionally activated by phosphatase inhibitor, ethylene and jasmonate treatments, as in grapevine, and that the stilbene synthase promoter retains its inducibility in some of the tested conditions in Arabidopsis, a species that normally does not synthesize stilbenes. Shared features between gymnosperm and angiosperm regulation and partially retained inducibility in Arabidopsis suggest that pathway regulation occurs not only via ancient stress-response pathway(s) but also via species-specific regulators. Understanding which genes control the biosynthesis of stilbenes in Scots pine aids breeding of more resistant trees.
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Affiliation(s)
| | - Kean-Jin Lim
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, Helsinki 00014, Finland
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Lin’an District, Hangzhou, Zhejiang 311300, China
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, 1 Bethel Valley Rd, Oak Ridge, TN 37830, USA
| | - Anni Harju
- Production Systems Unit, Natural Resources Institute Finland (Luke), Vipusenkuja 5, Savonlinna 57200, Finland
| | - Martti Venäläinen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Vipusenkuja 5, Savonlinna 57200, Finland
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, PO Box 56, Helsinki 00014, Finland
| | - Katri Kärkkäinen
- Production Systems Unit, Natural Resources Institute Finland (Luke), Paavo Havaksentie 3, Oulu 90570, Finland
| | - Teemu H Teeri
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, PO Box 27, Helsinki 00014, Finland
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Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJM, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:189-212. [PMID: 26017574 DOI: 10.1111/tpj.12886] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/15/2015] [Indexed: 05/21/2023]
Abstract
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Affiliation(s)
- René L Warren
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anthony Raymond
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Greg A Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Benjamin P Vandervalk
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Hamid Mohamadi
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Daniel Paulino
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Gordon Robertson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Margarete Hoffmann
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Alvin Yanchuk
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Jean Bousquet
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - John MacKay
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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