The quest for epigenetic regulation underlying unisexual flower development in Cucumis melo

Abstract

BackgroundMelon (Cucumis melo) is an important vegetable crop from the Cucurbitaceae family and a reference model specie for sex determination, fruit ripening and vascular fluxes studies. Nevertheless, the nature and role of its epigenome in gene expression regulation and more specifically in sex determination remains largely unknown.ResultsWe have investigated genome wide H3K27me3 and H3K9ac histone modifications and gene expression dynamics, in five melon organs. H3K9ac and H3K27me3 were mainly distributed along gene-rich regions and constrained to gene bodies. H3K9ac was preferentially located at the TSS, whereas H3K27me3 distributed uniformly from TSS to TES. As observed in other species, H3K9ac and H3K27me3 correlated with high and low gene expression levels, respectively. Comparative analyses of unisexual flowers pointed out sex-specific epigenetic states of TFs involved in ethylene response and flower development. Chip-qPCR analysis of laser dissected carpel and stamina primordia, revealed sex-specific histone modification of MADS-box genes. Using sex transition mutants, we demonstrated that the female promoting gene, CmACS11, represses the expression of the male promoting gene CmWIP1 via deposition of H3K27me3.ConclusionsOur findings reveal the organ-specific landscapes of H3K9ac and H3K27me3 in melon. Our results also provide evidence that the sex determination genes recruit histone modifiers to orchestrate unisexual flower development in monoecious species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-017-0132-6) contains supplementary material, which is available to authorized users.

Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce

“…2A ). These observations are consistent with previous studies in angiosperms, moss, and unicellular algae ( Zhang et al , 2007 ; Makarevitch et al , 2013 ; Widiez et al , 2014 ; Baker et al , 2015 ; Hussey et al , 2017 ; Latrasse et al , 2017 ; Mikulski et al , 2017 ; Chica et al , 2017 ; Lü et al , 2018 ; Qi et al , 2018 ; Li et al , 2019 ). This shows that (i) the CUT&RUN method can be successfully applied to large genomes, such as that of Norway spruce, and (ii) despite the significant differences in genome size between angiosperms and gymnosperms, deposition of H3K27me3 is detected in similar genomic features across different plant species.…”

“…So far, most studies in chromatin profiling in plants have been limited to relatively small genomes (e.g. different angiosperms, a moss, and a liverwort) ( Zhang et al , 2007 ; Widiez et al , 2014 ; Hussey et al , 2017 ; Latrasse et al , 2017 ; Chica et al , 2017 ; Lü et al , 2018 ; Montgomery et al , 2020 ). However, genome-wide analysis in gymnosperms has remained a challenge due to the large genome sizes of these species ( Pellicer et al , 2018 ).…”

“…Here, we surveyed the differences of H3K27me3 deposition in EC and NEC of Norway spruce. Most genome-wide analyses of histone modifications in plants have been accomplished in species with relatively small genomes, with the exception of maize, barley, and wheat ( Zhang et al , 2007 ; Makarevitch et al , 2013 ; Widiez et al , 2014 ; Baker et al , 2015 ; Hussey et al , 2017 ; Latrasse et al , 2017 ; Chica et al , 2017 ; Lü et al , 2018 ; Qi et al , 2018 ; Li et al , 2019 ; Montgomery et al , 2020 ). In contrast to many angiosperm studies, genome-wide chromatin profiling in other plant species has been limited to moss, liverwort, and unicellular algae ( Widiez et al , 2014 ; Mikulski et al , 2017 ; Montgomery et al , 2020 ).…”

Quantitative Trait Loci (QTL) Analysis of Fruit and Agronomic Traits of Tropical Pumpkin (Cucurbita moschata) in an Organic Production System

“…We took the sequence of these gene models and compared them to the Melon genome [25] by sequence analysis (Tables S1 and S2; [23,24]). We decided to analyze our data against the melon genome, because there have been several QTL and genomic studies on melon fruit quality that are similar to our study [26][27][28]. Markers associated with fruit flesh color intensity Pumpkin_282381, Pumpkin_93626, Pumpkin_164349, Pumpkin_46427, Pumpkin_210956, and Pumpkin_221779 aligned with pumpkin gene models whose orthologs in melon have been measured to be differentially regulated in green versus orange fruit color [26] and fruit flesh tissue [27].…”

“…We decided to analyze our data against the melon genome, because there have been several QTL and genomic studies on melon fruit quality that are similar to our study [26][27][28]. Markers associated with fruit flesh color intensity Pumpkin_282381, Pumpkin_93626, Pumpkin_164349, Pumpkin_46427, Pumpkin_210956, and Pumpkin_221779 aligned with pumpkin gene models whose orthologs in melon have been measured to be differentially regulated in green versus orange fruit color [26] and fruit flesh tissue [27]. In parallel, Pumpkin_164349, which our study showed to be associated with pickleworm tolerance, aligns with CmoCh15G001520, a clathrin heavy chain protein encoding gene orthologous to MELO3C008306 that has been observed to be upregulated in Fusarium infections [28].…”