Computational protocol: PPP1, a plant-specific regulator of transcription controls Arabidopsis development and PIN expression

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Protocol publication

[…] For phylogenetic analysis we used the following sequence accessions compiled at Pubmed, MIPS, and JGI: M. truncatula, ABE86175; O. sativa, BAF13748; P. patens, XM_001783694; V. vinifera, XP_002273364; O. tauri, XP_003074385; O. lucimarinus, XP_001415547; S. bicolor, XP_002466133; R. communis, XP_002522916; P. trichocarpa, XP_002307063; S. lycopersicum, gene:scaffold00395_179.1; Chlorella sp. NC64A, ChlNC64A_1|57236|estExt_fgenesh3_pg.C_50136; M. guttatus, mgv1a002542m; C. papaya, supercontig 37.46; C. sativus, Cucsa 357500; G. max, Glyma04g38450, Glyma05g32950, Glyma06g16600, Glyma08g00580; S. moellendorfi, Selmo1|117904|e_gw1.57.486.1; B. distachyon, Bradi1g02450.2; A. lyrata, XP_002873379; A. thaliana, NP_680157. Multiple sequence alignments were performed with ClustalX by using default settings. The resulting alignment was used for generation of a neighborhood-joining tree, corrected for multiple substitutions in the alignment and an exclusion of gapped positions. Statistical support for branches was calculated with bootstrap replicas (n = 100).For the in silico analyses the genome sequence was obtained from the Bioconductor annotation package BSgenome.Athaliana.TAIR.TAIR9. Motif occurrence in the genome was determined in R using the BioStrings package. The promoter sequences 3000 kb upstream of the transcription start site were obtained from the Bioconductor annotation package TxDb.Athaliana.BioMart.plantsmart25. Using pairwise alignment the 16-bp promoter fragment was aligned to the PIN promoters. With package SeqLogo the sequence logo of the aligned promoter regions was created. The 7 bp DNA fragment was matched against promoter sequences. The hypergeometric test was performed to assess the significance of enrichment of the 7-mer in a subset of the promoter sequences. […]

Pipeline specifications

Software tools FGENESH, Clustal W, Biostrings, seqLogo
Databases TAIR
Applications Phylogenetics, Genome data visualization
Organisms Arabidopsis thaliana