Open Access Research article

Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species

Claudia Voelckel1*, Nicole Gruenheit1, Patrick Biggs2, Oliver Deusch1 and Peter Lockhart1

Author Affiliations

1 Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand

2 Institute of Veterinary, Animal and Biomedical Sciences Massey University, Palmerston North, New Zealand

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BMC Genomics 2012, 13:322  doi:10.1186/1471-2164-13-322

Published: 19 July 2012

Additional files

Additional file 1:

Table S1. Sequences and annotations for 7,128 ESTs from Pachycladon fastigiatum.

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Additional file 2 :

Figure S1. In-silico distribution of GATC positions. The number of GATC positions (DpnII sites) per EST of P. fastigiatum (black bars) and their A. thaliana homologs (grey bars) was determined. For 144 ESTs of P. fastigiatum no GATC restriction site could be found as well as for 301 genes from A. thaliana while there were 19 and six sequences with more than 20 restriction sites.

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Additional file 3 :

Table S2. The number of mapped and filtered reads per lane and dataset. The total number of reads for the three lanes of P. enysii (PE1, PE2, PE3) and P. fastigiatum (PF1, PF2, PF3) was determined as well as the number of reads after trimming. For the different mapping strategies, the number and percentage of reads that mapped to the reference genes and the number of tags used in the differential expression analysis are shown. Percentages are given with respect to the total number of trimmed reads.

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Additional file 4 :

Table S3. Significantly enriched clusters and GO terms of 1,039 and 1,239 loci up-regulated in P. fastigiatum and P. enysii, respectively, identified with DAVID. The 6,428 reference loci were used as population background. Clusters are ordered by enrichment score.

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Additional file 5 :

Table S4. Differential expression statistics Sheet A) Differential expression statistics for 57 and 79 genes identified as commonly up-regulated in microarray and tag profiling analyses (P0) in P. enysii and P. fastigiatum, respectively. Sheet B) Differential expression statistics for 6 and 9 genes identified as oppositely up-regulated in microarray and tag profiling analyses (P0) in P. enysii and P. fastigiatum, respectively. Sheet C) Differential expression statistics of the analysis between homeologous copies. Homeologous gene copies were analysed for differential expression at 773 gene loci. For these genes (i) both homeologous copies were present in the EST reference library and (ii) copy-specific tags could be obtained and exceeded copy-unspecific tags in abundance by at least fivefold. Sheet D) Differential expression statistics for the 1,239 and 1,039 genes up-regulated in P. enysii and P. fastigiatum, respectively in the P0 data set.

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