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Memorias de investigación
Communications at congresses:
Poplar Promoter Architecture: Genome-wide analysis of poplar promoters and comparative study across seed model plants
Year:2014
Research Areas
  • Computational biology
Information
Abstract
Black cottonwood (Populus trichocarpa) was the first tree genome sequenced (1). Populus has become a model tree for genomics studies thanks to the availability of the sequence and well-developed molecular resources (2). Other characteristics that foster the use of Populus is its fast growth, wide geographical distribution (3), use for raw materials and potential as bioenergy crop (4, 5). Nonetheless, genome-wide analyses of features such as GC-content, gene structures, repeat elements, promoter structures, intron and exon lengths, intergenic distances or any other whole-genome studies are limited. In an attempt to understand the promoter architecture of Populus thrichocarpa and to determine to which extend particularities found in other eukaryotes, especially seed model plants are conserved, we undertook a genome-wide survey aimed to identify oligonucleotides with positional-bias along the promoter. The conceptual proteome comprising up to 73014 proteins was scanned to leave unique promoter sequences. From 41335 gene models a total of 49215 unique promoter sequences were identified. We analysed in silico the distribution profiles of hexamers and octamers along the promoter and identified a set of motifs with clear positional-bias. We compared our results with studies carried-out in the model plants rice and Arabidopsis thaliana (6, 7). The comparison with Arabidopsis and rice revealed conserved elements and some particular features associated to Poplar promoters. We are exploring if attributes observed in Arabidopsis promoters (8, 9) are shared in Populus. To test if the motifs found may have regulatory relevance, expression profiling experiments will be investigated, to access if co-regulated genes share any of the motifs identified by us in their promoter regions. (1) Tuskan et al. (2006). Science 313: 1596-1604 (2) Neale and Kremer (2011). Nature Reviews Genetics 12: 111-122 (3) Slavov et al. (2012). New Phytologist 196: 713-725 (4) Moreno-Cortés et al. (2012). New Phytologist 194: 83-90 (5) Guerra et al. (2013). New Phytologist 197: 162-176 (6) Yamamoto et al. (2007). BMC Genomics 8: 67 (7) Yamamoto et al. (2011). DNA Research 18: 333-342 (8) Walther et al. (2007). PLOS Genetics 3: e11 (9) Bernard et al. (2010). BMC Genomics 11: 166
International
No
Congress
XII Reunión de Biología Molecular de Plantas
960
Place
Reviewers
Si
ISBN/ISSN
0000-0000
Start Date
11/06/2014
End Date
13/06/2014
From page
167
To page
167
XII Reunión de Biología Molecular de Plantas
Participants
  • Autor: Judith Gómez-Porras (UPM)
  • Autor: Isabel Marta Allona Alberich (UPM)
Research Group, Departaments and Institutes related
  • Creador: Grupo de Investigación: Biotecnología Vegetal
  • Departamento: Biotecnología - Biología Vegetal
S2i 2020 Observatorio de investigación @ UPM con la colaboración del Consejo Social UPM
Cofinanciación del MINECO en el marco del Programa INNCIDE 2011 (OTR-2011-0236)
Cofinanciación del MINECO en el marco del Programa INNPACTO (IPT-020000-2010-22)