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Novel resources enabling comparative regulomics in forest tree species
Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). (Fysiologisk botanik)ORCID iD: 0000-0003-0903-4509
2017 (English)Doctoral thesis, comprehensive summary (Other academic)Alternative title
Nya verktyg för komparativ regulomik i skogsträd (Swedish)
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 [en]
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: urn:nbn:se:umu:diva-133984ISBN: 978-91-7601-707-4 (print)OAI: oai:DiVA.org:umu-133984DiVA: diva2:1090499
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
List of papers
1. ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
Open this publication in new window or tab >>ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa
2014 (English)In: BMC Genomics, ISSN 1471-2164, Vol. 15, 106- p.Article in journal (Refereed) Published
Abstract [en]

Background: Divergence in gene regulation has emerged as a key mechanism underlying species differentiation. Comparative analysis of co-expression networks across species can reveal conservation and divergence in the regulation of genes. Results: We inferred co-expression networks of A. thaliana, Populus spp. and O. sativa using state-of-the-art methods based on mutual information and context likelihood of relatedness, and conducted a comprehensive comparison of these networks across a range of co-expression thresholds. In addition to quantifying gene-gene link and network neighbourhood conservation, we also applied recent advancements in network analysis to do cross-species comparisons of network properties such as scale free characteristics and gene centrality as well as network motifs. We found that in all species the networks emerged as scale free only above a certain co-expression threshold, and that the high-centrality genes upholding this organization tended to be conserved. Network motifs, in particular the feed-forward loop, were found to be significantly enriched in specific functional subnetworks but where much less conserved across species than gene centrality. Although individual gene-gene co-expression had massively diverged, up to similar to 80% of the genes still had a significantly conserved network neighbourhood. For genes with multiple predicted orthologs, about half had one ortholog with conserved regulation and another ortholog with diverged or non-conserved regulation. Furthermore, the most sequence similar ortholog was not the one with the most conserved gene regulation in over half of the cases. Conclusions: We have provided a comprehensive analysis of gene regulation evolution in plants and built a web tool for Comparative analysis of Plant co-Expression networks (ComPlEx, http:// complex. plantgenie. org/). The tool can be particularly useful for identifying the ortholog with the most conserved regulation among several sequence-similar alternatives and can thus be of practical importance in e. g. finding candidate genes for perturbation experiments.

National Category
Genetics
Identifiers
urn:nbn:se:umu:diva-88337 (URN)10.1186/1471-2164-15-106 (DOI)000332597700001 ()
Available from: 2014-06-10 Created: 2014-04-30 Last updated: 2017-04-25Bibliographically approved
2. The Plant Genome Integrative Explorer Resource: PlantGenIE.org
Open this publication in new window or tab >>The Plant Genome Integrative Explorer Resource: PlantGenIE.org
Show others...
2015 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, 1149-1156 p.Article in journal (Refereed) Published
Abstract [en]

Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, BLAST homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the COMPLEX resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.

Keyword
annotation, coexpression, conifer, database, genome browser, Populus, transcriptomics, web source
National Category
Botany
Identifiers
urn:nbn:se:umu:diva-113426 (URN)10.1111/nph.13557 (DOI)000365393000016 ()26192091 (PubMedID)
Available from: 2015-12-18 Created: 2015-12-18 Last updated: 2017-04-25Bibliographically approved
3. NorWood: a gene expression resource for evo-devo studies of conifer wood development
Open this publication in new window or tab >>NorWood: a gene expression resource for evo-devo studies of conifer wood development
Show others...
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.

Keyword
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:nbn:se:umu:diva-133995 (URN)10.1111/nph.14458 (DOI)
Available from: 2017-04-25 Created: 2017-04-25 Last updated: 2017-04-26
4. High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
Open this publication in new window or tab >>High-spatial-resolution transcriptome profiling reveals uncharacterized regulatory complexity underlying cambial growth and wood formation in Populus tremula
Show others...
2016 (English)Manuscript (preprint) (Other academic)
Abstract [en]

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 years 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 co-expression 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.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-133999 (URN)10.1101/094060 (DOI)
Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2017-04-26

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