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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula

David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittyla, Bjöern Sundberg, Torgeir R. Hvidsten
doi: https://doi.org/10.1101/094060
David Sundell
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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  • For correspondence: torgeir.hvidsten@umu.se
Nathaniel R. Street
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, Sweden.
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  • For correspondence: torgeir.hvidsten@umu.se
Manoj Kumar
2Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology,Swedish University of Agricultural Sciences, Umeå, Sweden.
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  • For correspondence: torgeir.hvidsten@umu.se
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, Umeå, 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, Umeå, Sweden.
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Edouard Pesquet
1Umeå Plant Science Center, Department of Plant Physiology, Umeå University, Umeå, 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 Niittyla
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, Umeå, Sweden.
4Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, Ås, Norway.
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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, however, efforts to engineer new, elite varieties are constrained by the lack of a comprehensive understanding of the transcriptional network underlying cambial growth and wood formation. We generated RNA Sequencing transcriptome data for four mature, wild-growing aspens (Populus tremula) from high-spatial-resolution tangential cryosection series spanning the secondary phloem, vascular cambium, expanding and secondary cell wall forming xylem cells, cell death zone and the previous year’s annual ring. The transcriptome comprised 28,294 expressed, previously annotated protein-coding genes, 78 novel protein-coding genes and 567 long intergenic non-coding RNAs. Most paralogs originating from the Salicaceae whole genome duplication had diverged expression, with the notable exception of those with high expression during secondary cell wall deposition. We performed coexpression network analysis to identify central transcriptional modules and associated several of these with known biological processes. This revealed previously uncharacterized complexity underlying the regulation of cambial growth and wood formation, with modules forming a continuum of activated processes across the tissues. The high spatial resolution suggested novel roles for known genes involved in xylan and cellulose biosynthesis, regulators of xylem vessel and fiber differentiation and components of lignification. The associated web resource (AspWood, http://aspwood.popgenie.org) integrates the data within a set of interactive tools for exploring the co-expression network of cambial growth and wood formation.

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Posted December 22, 2016.
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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittyla, Bjöern Sundberg, Torgeir R. Hvidsten
bioRxiv 094060; doi: https://doi.org/10.1101/094060
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High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
David Sundell, Nathaniel R. Street, Manoj Kumar, Ewa J. Mellerowicz, Melis Kucukoglu, Christoffer Johnsson, Vikash Kumar, Chanaka Mannapperuma, Ove Nilsson, Hannele Tuominen, Edouard Pesquet, Urs Fischer, Totte Niittyla, Bjöern Sundberg, Torgeir R. Hvidsten
bioRxiv 094060; doi: https://doi.org/10.1101/094060

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