Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
The Plant Genome Integrative Explorer Resource: PlantGenIE.org
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
Show others and affiliations
2015 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, 1149-1156 p.Article in journal (Refereed) Published
Resource type
Text
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.

Place, publisher, year, edition, pages
2015. Vol. 208, no 4, 1149-1156 p.
Keyword [en]
annotation, coexpression, conifer, database, genome browser, Populus, transcriptomics, web source
National Category
Botany
Identifiers
URN: urn:nbn:se:umu:diva-113426DOI: 10.1111/nph.13557ISI: 000365393000016PubMedID: 26192091OAI: oai:DiVA.org:umu-113426DiVA: diva2:885497
Available from: 2015-12-18 Created: 2015-12-18 Last updated: 2017-12-01Bibliographically approved
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

Open Access in DiVA

fulltext(1443 kB)119 downloads
File information
File name FULLTEXT01.pdfFile size 1443 kBChecksum SHA-512
549474f1de49d0d944b1fdf27c04c6d4c69583e7d9ab3d5ef807461bd3ccc20803e379770888d10d41148e8653be65f08ee9031d6b13bc16de328b760986dd65
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Sundell, DavidMannapperuma, ChanakaNetotea, SergiuDelhomme, NicolasSjödin, AndreasJansson, StefanHvidsten, Torgeir R.Street, Nathaniel R.
By organisation
Department of Plant PhysiologyDepartment of Chemistry
In the same journal
New Phytologist
Botany

Search outside of DiVA

GoogleGoogle Scholar
Total: 119 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 249 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf