DOI: 10.5061/dryad.4337n
title: Data from: Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation

description: Apple fruit mealiness is one of the most important textural problems that
 results from an undesirable ripening process during storage. This
 phenotype is characterized by textural deterioration described as soft,
 grainy and dry fruit. Despite several studies, little is known about
 mealiness development and the associated molecular events. In this study,
 we integrated phenotypic, microscopic, transcriptomic and biochemical
 analyses to gain insights into the molecular basis of mealiness
 development.ResultsInstrumental texture characterization allowed the
 refinement of the definition of apple mealiness. In parallel, a new and
 simple quantitative test to assess this phenotype was developed.Six
 individuals with contrasting mealiness were selected among a progeny and
 used to perform a global transcriptome analysis during fruit development
 and cold storage. Potential candidate genes associated with the initiation
 of mealiness were identified. Amongst these, the expression profile of an
 early down-regulated transcript similar to an Arabidopsis thaliana pectin
 methylesterase gene (AtPME2) matched with mealiness development. In silico
 analyses of this Malus x domestica PME gene (MdPME2) confirmed its
 specific pattern compared with all other identified MdPME genes. Protein
 fusion experiments showed that MdPME2 is secreted into the apoplast in
 accordance with a possible activity on pectin structure. Further
 microscopic analysis indicated a progressive loss of cell to cell adhesion
 in mealy apple fruits. Biochemical analysis revealed specific
 modifications of pectin residues associated with mealiness, without global
 changes in the degree of methylesterification of pectins.ConclusionsThese
 data support the role of PME in cell wall remodelling during apple fruit
 development and ripening and suggest a local action of these enzymes.
 Mealiness may partially result from qualitative and spatial variations of
 pectin microarchitecture rather than quantitative pectin differences, and
 these changes may occur early in fruit development. The specific MdPME2
 gene highlighted in this study could be a good early marker of texture
 unfavourable trait in apple.
description: 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