Data from: Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation

MdPME sequence alignmentThe HMM profile of the Pectinesterase proteins (PF01095) was downloaded from the Pfam database (http://pfam.sanger.ac.uk), and used as a query to search the translated Apple genome (http://www.rosaceae.org/) using the HMMER 3.0 program with default parameters (hmmer.org). All sequences collected were checked using the NCBI conserved domain database [65]. Protein coding genes without a complete pectinesterase domain (EC 3.1.1.11) or with extra and incoherent domain were discarded from further analyses. Multiple protein sequence alignments were performed with the online MUSCLE tool (http://www.ebi.ac.uk/Tools/msa/muscle/).Malus_domestica_PMEsequenceAlignementPhylogenic trees of Malus domestica PMEsThe HMM profile of the Pectinesterase proteins (PF01095) was downloaded from the Pfam database (http://pfam.sanger.ac.uk), and used as a query to search the translated Apple genome (http://www.rosaceae.org/) using the HMMER 3.0 program with default parameters (hmmer.org). All sequences collected were checked using the NCBI conserved domain database [65]. Protein coding genes without a complete pectinesterase domain (EC 3.1.1.11) or with extra and incoherent domain were discarded from further analyses. Multiple protein sequence alignments were performed with the online MUSCLE tool (http://www.ebi.ac.uk/Tools/msa/muscle/). Phylogenetic analysis was carried out by the neighbor-joining method using MEGA 5 software [66] using a p-distance model and pairwise deletion for missing data treatment; 1,000 replicates were used for bootstrap analysis.Malus_domestica_PMEs_tree.nwk