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Memorias de investigación
Ponencias en congresos:
Poplar Promoter Architecture: Genome-wide analysis of poplar promoters and comparative study across seed model plants
Año:2014
Áreas de investigación
  • Bioinformática
Datos
Descripción
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
Internacional
No
Nombre congreso
XII Reunión de Biología Molecular de Plantas
Tipo de participación
960
Lugar del congreso
Revisores
Si
ISBN o ISSN
0000-0000
DOI
Fecha inicio congreso
11/06/2014
Fecha fin congreso
13/06/2014
Desde la página
167
Hasta la página
167
Título de las actas
XII Reunión de Biología Molecular de Plantas
Esta actividad pertenece a memorias de investigación
Participantes
  • Autor: Judith Gómez-Porras (UPM)
  • Autor: Isabel Marta Allona Alberich (UPM)
Grupos de investigación, Departamentos, Centros e Institutos de I+D+i relacionados
  • Creador: Grupo de Investigación: Biotecnología Vegetal
  • Departamento: Biotecnología - Biología Vegetal
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