Computational protocol: Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants

Similar protocols

Protocol publication

[…] Nucleotide sequences of RPD3/HDA1 histone deacetylases were sequenced and reconfirmed using the TAIR database . Amino acid and nucleotide sequences in fasta formats retrieved from the plant Chromatin Database (ChromDB) were also used for multiple sequence alignment using ClustalW2 . Highly conserved regions were highlighted in black. Generated phylograms based on the sequence alignments from ClustalW2 were compared with phylogenetic trees inferred from MEGA4. [...] Amino acid sequences in fasta formats were analyzed using different databases such as Pfam , InterPro Scan , Automatic Domain Decomposition Algorithm , and UniProtKB/TrEMBL to further explore the conserved domains of Class II histone deacetylases. In addition, subcellular localization of each of the 6 proteins was predicted using TAIR , SLP-L , and WoLF PSORT . Nuclear export signals were detected using NetNES [] while nuclear localization signals were inferred using PSORTII []. [...] Amino acid as well as nucleotide sequences in fasta format were retrieved from ChromDB. These were further configured into a fasta format based on its conserved domain using the MAFFT program at EMBL-EBI [] prior to analysis. MAFFT fasta formatted sequences were keyed in for phylogenetic analyses using the Molecular Evolutionary Genetic Analysis 4 (MEGA4) program []. Tree reconstruction was inferred using the Neighbor Joining method with a Poisson correction model and a bootstrap test of 1000 replicates. [...] RPD3/HDA1 genes were individually queried for their expression patterns using Genevestigator []. Only highly pertinent expression levels in different anatomical parts, hormone inducers, as well as biotic and abiotic stresses were included. However, the expression levels of all the RPD3/HDA1 in all the developmental stages were considered in the study. […]

Pipeline specifications

Software tools Clustal W, MEGA, ADDA, WoLF PSORT, NetNES, MAFFT
Databases TAIR UniProtKB ChromDB
Applications Phylogenetics, Protein sequence analysis
Organisms Arabidopsis thaliana, Populus trichocarpa, Pinus taeda, Oryza sativa, Zea mays
Diseases Plant Poisoning