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A Genome-Wide Analysis of MADS-box Genes in Peach [Prunus Persica (L.) Batsch]

A Genome-Wide Analysis of MADS-box Genes in Peach [Prunus Persica (L.) Batsch]

Christina E Wells et al. BMC Plant Biol.

Abstract

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 and FLC 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.

Figures

Figure 1
Figure 1
Chromosomal locations of MADS-box genes in peach. MIKC genes are shown in black, Mα genes in purple, Mβ genes in orange, and Mγ genes in fuchsia. Selected molecular markers are shown in gray. Seven major syntenic regions of the peach genome are indicated by colored segments on chromosome bars [25].
Figure 2
Figure 2
Unrooted 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. Mα genes are shown in purple, Mβ genes in orange, and Mγ genes in pink.
Figure 3
Figure 3
Unrooted 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. Established Type II subfamilies are indicated in purple text, MIKC* genes are shown in black, and MIKCc genes are shown in purple. MIKCc subfamilies are named after [18].
Figure 4
Figure 4
Unrooted 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.
Figure 5
Figure 5
Unrooted Bayesian consensus 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.
Figure 6
Figure 6
Expression profiles of Type I (left) and Type II (right) MADS-box genes from six peach tissues: root, expanded leaf (O Leaf), young leaf (Y leaf), fruit, pollen and cotyledon + embryo (Coty_embryo) tissue. FPKM expression values were log-transformed, and genes were grouped by average linkage clustering (see Methods).
Figure 7
Figure 7
Expression profiles of Type I (left) and Type II (right) MADS-box genes from peach apical shoots at 0, 1 and 2 weeks after the transition to short days. FPKM expression values were log-transformed, and genes were grouped by average linkage clustering (see Methods). Asterisks denote genes whose expression level changed significantly over the course of the two-week experiment.

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