DOI: 10.5061/dryad.65k7t
title: Data from: A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]

description: BACKGROUND: MADS-box genes encode a family of eukaryotic transcription
 factors distinguished by the presence of a highly-conserved ~58 amino acid
 DNA-binding and dimerization domain (the MADS-box). The central role
 played by MADS-box genes in peach endodormancy regulation led us to
 examine this large gene family in more detail. We identified the locations
 and sequences of 79 MADS-box genes in peach, separated them into
 established subfamilies, and broadly surveyed their tissue-specific and
 dormancy-induced expression patterns using next-generation sequencing. We
 then focused on the dormancy-related SVP/AGL24 and FLC subfamilies,
 comparing their numbers and phylogenetic relationships with those of other
 sequenced woody perennial genomes. RESULTS: We identified 79 MADS-box
 genes distributed across all eight peach chromosomes and frequently
 located in clusters of two or more genes. They encode proteins with a mean
 length of 248 ± 72 amino acids and include representatives from most of
 the thirteen Type II (MIKC) subfamilies, as well as members of the Type I
 Mα, Mβ, and Mγ subfamilies. Most Type I genes were present in
 species-specific monophyletic lineages, and their expression in the peach
 sporophyte was low or absent. Most Type II genes had Arabidopsis orthologs
 and were expressed at much higher levels throughout vegetative and fruit
 tissues. During short-day-induced growth cessation, seven Type II genes
 from the SVP/AGL24, AGL17, and SEP subfamilies showed significant changes
 in expression. Phylogenetic analyses indicated that multiple, independent
 expansions have taken place within the SVP/AGL24 andFLC lineages in woody
 perennial species. CONCLUSIONS: Most Type I genes appear to have arisen
 through tandem duplications after the divergence of the Arabidopsis and
 peach lineages, whereas Type II genes appear to have increased following
 whole genome duplication events. An exception to the latter rule occurs in
 the FLC and SVP/AGL24 Type II subfamilies, in which species-specific
 tandem duplicates have been retained in a number of perennial species.
 These subfamilies comprise part of a genetic toolkit that regulates
 endodormancy transitions, but phylogenetic and expression data suggest
 that individual orthologs may not function identically across all species.
description: Fig_2_Type_I_MADS_genes_peachUnrooted Bayesian consensus tree of Type I MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes.Fig_3_Type_II_MADS_genes_peachUnrooted Bayesian consensus tree of Type II MADS-box proteins from peach and Arabidopsis. Bayesian posterior probabilities for all clades are given at their respective nodes.Fig_4_SVP_AGL24_genesUnrooted Bayesian consensus tree of MADS-box proteins from the SVP/AGL24 subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes.Fig_5_FLC_genesUnrooted maximum likelihood phylogenetic tree of MADS-box proteins from the FLC subfamily in peach, Arabidopsis, grapevine, poplar, maize, sorghum, and rice. Bayesian posterior probabilities for all clades are given at their respective nodes.