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NorWood: a gene expression resource for evo-devo studies of conifer wood development
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology,Swedish University of Agricultural Sciences, SE-901 84 Umeå, Sweden.
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1430 Ås, Norway.
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2017 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137Article in journal (Refereed) Epub ahead of print
Abstract [en]

The secondary xylem of conifers is composed mainly of tracheids that differ anatomically and chemically from angiosperm xylem cells. There is currently no high-spatial-resolution data available profiling gene expression during wood formation for any coniferous species, which limits insight into tracheid development.

RNA-sequencing data from replicated, high-spatial-resolution section series throughout the cambial and woody tissues of Picea abies were used to generate the NorWood.conGenIE.org web resource, which facilitates exploration of the associated gene expression profiles and co-expression networks.

Integration within PlantGenIE.org enabled a comparative regulomics analysis, revealing divergent co-expression networks between P. abies and the two angiosperm species Arabidopsis thaliana and Populus tremula for the secondary cell wall (SCW) master regulator NAC Class IIB transcription factors. The SCW cellulose synthase genes (CesAs) were located in the neighbourhoods of the NAC factors in Athaliana and P. tremula, but not in Pabies. The NorWood co-expression network enabled identification of potential SCW CesA regulators in P. abies.

The NorWood web resource represents a powerful community tool for generating evo-devo insights into the divergence of wood formation between angiosperms and gymnosperms and for advancing understanding of the regulation of wood development in P. abies.

Place, publisher, year, edition, pages
2017.
Keyword [en]
co-expression network, comparative genomics, cryosection, evo-devo, growth ring, Norway spruce (Picea abies), RNA-sequencing, secondary cell wall
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-133995DOI: 10.1111/nph.14458OAI: oai:DiVA.org:umu-133995DiVA: diva2:1090640
Available from: 2017-04-25 Created: 2017-04-25 Last updated: 2017-04-26
In thesis
1. Novel resources enabling comparative regulomics in forest tree species
Open this publication in new window or tab >>Novel resources enabling comparative regulomics in forest tree species
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Alternative title[sv]
Nya verktyg för komparativ regulomik i skogsträd
Abstract [en]

Lignocellulosic plants are the most abundant source of terrestrial biomass and are one of the potential sources of renewable energy that can replace the use of fossil fuels. For a country such as Sweden, where the forest industry accounts for 10% of the total export, there would be large economical benefits associated with increased biomass yield. The availability of research on wood development conducted in conifer tree species, which represent the majority of the forestry in Sweden, is limited and the majority of research has been conducted in model angiosperm species such as Arabidopsis thaliana. However, the large evolutionary distance between angiosperms and gymnosperms limits the possibility to identify orthologous genes and regulatory pathways by comparing sequence similarity alone. At such large evolutionary distances, the identification of gene similarity is, in most cases, not sufficient and additional information is required for functional annotation. In this thesis, two high-spatial resolution datasets profiling wood development were processed; one from the angiosperm tree Populus tremula and the other from the conifer species Picea abies. These datasets were each published together with a web resource including tools for the exploration of gene expression, co-expression and functional enrichment of gene sets. One developed resource allows interactive, comparative co-expression analysis between species to identify conserved and diverged co-expression modules. These tools make it possible to identifying conserved regulatory modules that can focus downstream research and provide biologists with a resource to identify regulatory genes for targeted trait improvement.

Abstract [sv]

Lignocellulosa är den vanligast förekommande källan till markburen biomassa och är en av de förnybara energikällor som potentiellt kan ersätta användningen av fossila bränslen. För ett land som Sverige, där skogsindustrin som står för 10 \% av den totala exporten, skulle därför en ökad produktion av biomassa kunna ge stora ekonomiska fördelar. Forskningen på barrträd, som utgör majoriteten av svensk skog är begränsad och den huvudsakliga forskningen som har bedrivits på växter, har skett i modell organismer tillhörande gruppen gömfröiga växter som till exempel i Arabidopsis thaliana. Det evolutionära avståndet mellan gömfröiga (blommor och träd) och nakenfröiga (gran och tall) begränsar dock möjligheten att identifiera regulatoriska system mellan dessa grupper. Vid sådana stora evolutionära avstånd krävs det mer än att bara identifiera en gen i en modellorganism utan ytterligare information krävs som till exempel genuttrycksdata. I denna avhandling har två högupplösta experiment som profilerar vedens utveckling undersökts; ett från gömfröiga träd Populus tremula och det andra från nakenföriga träd (barrträd) Picea abies. Datat som behandlats har publicerats tillsammans med webbsidor med flera olika verktyg för att bland annat visa genuttryck, se korrelationer av genuttryck och test för anrikning av funktionella gener i en grupp. En resurs som utvecklats tillåter interaktiva jämförelser av korrelationer mellan arter för att kunna identifiera moduler (grupper av gener) som bevaras eller skilts åt mellan arter över tid. Identifieringen av sådana bevarade moduler kan hjälpa att fokusera framtida forskning samt ge biologer en möjlighet att identifiera regulatoriska gener för en riktad förbättring av egenskaper hos träd.

Place, publisher, year, edition, pages
Umeå: Umeå university, 2017. 47 p.
Keyword
Comparative genomics, Web resource, Wood development, RNA-Seq, Forestry, Lignocellulose, Regulomics, High-spatial resolution, Populus tremula, Picea abies, Orthology.
National Category
Bioinformatics and Systems Biology
Research subject
biology; Molecular Biotechnology
Identifiers
urn:nbn:se:umu:diva-133984 (URN)978-91-7601-707-4 (ISBN)
Public defence
2017-05-18, KB3A9, KBC-Huset, Umeå university, Umeå, 13:00 (English)
Opponent
Supervisors
Available from: 2017-04-27 Created: 2017-04-24 Last updated: 2017-05-18Bibliographically approved

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Sundell, DavidHvidsten, Torgeir R.Street, Nathaniel R.Tuominen, Hannele
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