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

Mikol Segonne S, Bruneau M, Celton J, Le Gall S, Francin-Allami M, Juchaux M, Laurens F, Orsel M, Renou J

Date Published: January 27, 2015

DOI: http://dx.doi.org/10.5061/dryad.4337n

 

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Title MdPME sequence alignment
Downloaded 4 times
Description The 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/).
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Title Phylogenic trees of Malus domestica PMEs
Downloaded 3 times
Description The 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.
Download Malus_domestica_PMEs_tree.nwk (2.601 Kb)
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When using this data, please cite the original publication:

Mikol Segonne S, Bruneau M, Celton J, Le Gall S, Francin-Allami M, Juchaux M, Laurens F, Orsel M, Renou J (2014) Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation. BMC Plant Biology 14: 375. http://dx.doi.org/10.1186/s12870-014-0375-3

Additionally, please cite the Dryad data package:

Mikol Segonne S, Bruneau M, Celton J, Le Gall S, Francin-Allami M, Juchaux M, Laurens F, Orsel M, Renou J (2014) Data from: Multiscale investigation of mealiness in apple: an atypical role for a pectin methylesterase during fruit maturation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.4337n
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