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AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula

David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Nicolas Delhomme, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittylä, Bjöern Sundberg, Torgeir R. Hvidsten
doi: https://doi.org/10.1101/094060
David Sundell
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
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Nathaniel R. Street
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
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Manoj Kumar
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Ewa J. Mellerowicz
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Melis Kucukoglu
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Christoffer Johnsson
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Vikash Kumar
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Chanaka Mannapperuma
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
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Nicolas Delhomme
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
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Ove Nilsson
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Hannele Tuominen
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
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Edouard Pesquet
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
3Department of Ecology, Environment and Plant Sciences, Stockholm University, Sweden
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Urs Fischer
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Totte Niittylä
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Bjöern Sundberg
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Torgeir R. Hvidsten
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umea, Sweden
4Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway
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  • For correspondence: torgeir.hvidsten@umu.se
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Abstract

Trees represent the largest terrestrial carbon sink and a renewable source of ligno-cellulose. There is significant scope for yield and quality improvement in these largely undomesticated species, and efforts to engineer new, elite varieties will benefit from an improved understanding of the transcriptional network underlying cambial growth and wood formation. We generated high-spatial-resolution RNA Sequencing data spanning the secondary phloem, vascular cambium and wood forming tissues. The transcriptome comprised 28,294 expressed, previously annotated genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication were found to have diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. Co-expression network analysis revealed that the regulation of the transcriptome underlying cambial growth and wood formation comprises numerous modules forming a continuum of active processes across the tissues. The high spatial resolution enabled identification of novel roles for characterised genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the expression profiles and co-expression network.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 23, 2017.
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AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Nicolas Delhomme, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittylä, Bjöern Sundberg, Torgeir R. Hvidsten
bioRxiv 094060; doi: https://doi.org/10.1101/094060
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AspWood: High-spatial-resolution transcriptome profiles reveal uncharacterized modularity of wood formation in Populus tremula
David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Nicolas Delhomme, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittylä, Bjöern Sundberg, Torgeir R. Hvidsten
bioRxiv 094060; doi: https://doi.org/10.1101/094060

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