PoplarDB : Publications
- Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Hellsten U, DiFazio S, Boerjan W & Martin F (2005) Genome-wide identification of NBS Resistance Genes in Populus trichocarpa. The Plant Journal, submitted.
- Supplemental data: Table S1: List of gene models encoding NBS protein in Populus trichocarpa.
- Supplemental data: Table S2: Summary table of MEME and MAST analyses for CN/CNL (A), TN/TNL/TNLT/TNLN (B), BN/BNL (C) and N/NL (D) proteins. Motifs from the MEME analyses in the supplemental files were combined and manually aligned in a spreadsheet to allow the comparisons of motif composition and configuration. Because motif analyses were performed for each domain separately for each of the protein families, motif numbers are specific only to that domain. The MEME "score" for the overall match of the protein to the motif models is given as a P value.
- Supplemental data: Table S3: Number of clusters and the total number of corresponding NBS genes for each type of clusters in Populus trichocarpa 'Nisqually-1' genome sequence. Consecutive NBS-genes separated by 8 -or less- other genes were considered as clusters, as reported in Richly et al. (2002) and Meyers et al. (2003). The number of clusters and NBS-genes which were found on linkage groups are in brackets. Singletons are also indicated.
- Supplemental data: Figure S1 A, B, C and D: Neighbor-joining analysis of the different familes of NBS-LRR proteins in Populus trichocarpa Nisqually-1. (A) CN & CNL proteins; (B) BN & BNL proteins; (C) TN & TNL proteins; and (D) N & NL proteins. The NJ trees were constructed using the full-length sequence from the R proteins belonging to the different classes.
- Supplemental data: Figure S2: Multiple alignment of the poplar BNL proteins containing the zinc-finger BED/DUF1544 domains (IPRO003656/IPR011523) with the BED domains found in proteins from other plants and animals.
- Supplemental data: Figure S3: Alignment of the deduced amino acid sequences from the Populus tremula EST UB48DPF09 and five predicted TNL proteins from P. trichocarpa. The conserved nuclear localisation sequence is shown by a bar.
- Kohler A, Delaruelle C, Martin D, Encelot E & Martin F (2003) The poplar root transcriptome: analysis of 7,000 expressed sequence tags. FEBS Letters 542: 37-41 (the pdf file).
- Supplemental data: Table 1: ESTs from Populus trichocarpa X P. deltoides not found in the Umea Plant Science Center Populus database.
- Supplemental data: Table 2: ESTs coding for water channels, transporters and assimilating enzymes expressed in Populus trichocarpa X P. deltoides roots.
- Supplemental data: Figure 2: Pictures showing the different developmental stages of adventitious root development of rooted cuttings (1Mo pdf file).
- Software: MacESTtools: a series of MacOSX-compatible scripts for sequence processing and analysis. (Contact D. Martin (firstname.lastname@example.org) for further information)
- Kohler A, Blaudez D, Chalot M, & Martin F (2004) Cloning and expression of multiple metallothioneins from hybrid poplar. New Phytologist 164: 83-93 (the pdf file).
- Supplemental data: Table 1: Specific primers used for RT-PCR of PtdMTs and Table 2: Primers used for yeast complementation.
- Supplemental data: cDNAs, coding sequences and genomic sequences of MTs from Populus trichocarpa X P. deltoides.
- Supplemental data: Figure S1: Multiple alignment of genomic, cDNA and coding nucleotide sequences of the metallothioneins PtdMT1ab, PtdMT2ab, and PtdMT3ab from the hybrid poplar, Populus trichocarpa x P. deltoides cv. Beaupre. Alignment was carried out using MULTALIN
- Supplemental data: Array data set used in Fig. 4 (PtdMT expression in roots and leaves) and Array data set used in Figure 5 (Adventitious root development).
- Gupta P, Duplessis S, White H, Karnosky, DF, Martin F and Podila G.K. (2004) Gene expression patterns of trembling aspen trees following long-term exposure to interacting elevated CO2 and tropospheric O3. New Phytologist, submitted.
- Supplemental data: Table S1: List of the 238 significantly regulated ESTs analyzed in our expression analysis. The columns comes as follow: Clone-ID of poplar ESTs spotted on nylon arrays; accession n° in GenBank (Kohler et al., 2003); gene function as determined by homology search; mean ratios calculated from ratios measured in 2001 and 2002 for the three treatments (elevated [CO2], elevated [O3] and combined elevated [CO2] & [O3]) compared to the control conditions; lnP-value of regulation levels calculated for the three treatments as measured by the statistical program available on the Cyber-T website; SOMs clusters correspondence (see Figure 2); ratios calculated in 2001 and 2002 for the three treatments (elevated [CO2], elevated [O3] and combined elevated [CO2] & [O3]) compared to the control conditions. Rows of the table comes in two parts. The first part comprises genes which were significantly regulated in at least one treatment of the FACE experiment at a level higher than 1.5-fold regulation. The second part corresponds to genes which were regulated at a level lower than 1.5-fold regulation. Mean ratios highlighted in grey in the table indicate that the regulation pattern was similar in year 2001 and 2002 (up-regulated or down-regulated both year-replicates).
- Supplemental data: Table S2, Table S3, and Table S4, Microsoft Excel spreadsheets with raw datas and associated statistical results obtained with the Cyber-T website
(Table S2, CO2 vs control; Table S3, O3 vs control; Table S4, CO2 & O3 vs control).
- Kohler A & Martin F (2004) Transcript Patterns Associated with Adventitious Root Development in Poplar (submitted)
- Supplemental data: Figure S1: Photos showing the different developmental stages of adventitious root development of rooted cuttings.
- Supplemental data: Figure S2: Environmental/low pressure micrographs of tranverse sections of rooted cuttings at the the different developmental stages (photos: Dr. D Le Thiec, INRA-Nancy).
- Supplemental data: Table S1:
- Rouhier N, Gelhaye E, Gualberto JM, Jordy MN, De Fay E, Hirasawa M, Duplessis S, Lemaire SD, Frey P, Martin F, Manieri W, Knaff DB, Jacquot JP (2004) Poplar peroxiredoxin Q. A thioredoxin-linked chloroplast antioxidant functional in pathogen defense. Plant Physiology 134: 1027–1038 (the pdf file).
- Rouhier N, Gelhaye E, Corbier C, Jacquot JP (2004) Active site mutagenesis and phospholipid hydroperoxide reductase activity of poplar type II peroxiredoxin. Physiologia Plantarum 120: 57–62 (the pdf file).
- Lammers P, Tuskan GA, DiFazio SP, Podila GK, Martin F (2004) Mycorrhizal symbionts of Populus to be sequenced
by the United States Department of Energy's Joint Genome Institute. Mycorrhiza 14: 63–64 (the pdf file).
- Martin F, Tuskan GA, DiFazio SP, Lammers P, Newcombe G, Podila GK (2004) Symbiotic sequencing for the
Populus mesocosm. Mycorrhiza 14: 63–64 (the pdf file).
- Blaudez D, Kohler A, Martin F, Sanders D, Chalot M (2003)Poplar Metal Tolerance Protein 1 confers zinc tolerance
and is an oligomeric vacuolar zinc transporter with an essential Leucine Zipper motif. Plant Cell 15: 2911–2928. (the pdf file).
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