Title and abstract updated.

README.md

-# Cell layer-specific expression of the B-class MADS-box gene PhDEF drives petal tube or limb development in petunia flowers
+# Cell layer-specific expression of the homeotic MADS-box transcription factor PhDEF contributes to modular petunia petal morphogenesis
 
 Scripts written for RNA-seq analysis used in https://hal.science/hal-03405575
 
@@ -74,19 +74,21 @@ which are organized in different cell layers deriving from the meristematic L1,
 How cells from these distinct layers acquire their respective identity and coordinate their growth
 to ensure normal floral organ morphogenesis is unresolved. Here, we study petunia petals
 that form a limb and tube through congenital fusion, a complex morphology that coevolved with pollinators.
-We have identified petunia mutants expressing the B-class MADS-box gene *PhDEF* in the epidermis
-or in the mesophyll of the petal only, called wico and star respectively. Strikingly, wico flowers form
-a strongly reduced tube while their limbs are almost normal, while star flowers form a normal tube
-but very reduced and unpigmented limbs, showing that petunia petal morphogenesis is highly modular.
-Comparative transcriptome analysis of star, wico and wild-type petals revealed a strong down-regulation
-of the anthocyanin production pathway in star petals including its major regulator *ANTHOCYANIN2* (*AN2*).
-We found that PhDEF directly binds to *AN2* regulatory sequence *in vitro* by gel shift assay, and in vivo
-by chromatin immunoprecipitation, suggesting that *PhDEF* directly activates the petal pigmentation pathway
-by activating *AN2*. Altogether, we show that cell-layer specific homeotic activity in petunia petals
-differently impacts tube and limb development, revealing the relative importance of the different cell layers
+We have identified petunia mutants (periclinal chimeras) expressing the B-class MADS-box gene *PhDEF*
+in the petal epidermis or in the petal mesophyll, called *wico* and *star* respectively.
+Strikingly, *wico* flowers form a strongly reduced tube while their limbs are almost normal,
+while *star* flowers form a normal tube but very reduced and unpigmented limbs,
+showing that petunia petal morphogenesis is highly modular. These periclinal chimeras revealed
+layer-specific roles of PhDEF during petal development, and we further explored the link
+between PhDEF and petal pigmentation, as a well characterized limb epidermal trait.
+The anthocyanin production pathway was strongly down-regulated in *star* petals including
+its major regulator *ANTHOCYANIN2* (*AN2*). We found that PhDEF directly binds to *AN2* regulatory sequence
+*in vitro* by gel shift assay, and *in vivo* by chromatin immunoprecipitation, suggesting that PhDEF
+might regulate *AN2* expression and therefore the pigmentation pathway in the petal epidermis.
+Altogether, we show that cell-layer specific homeotic activity in petunia petals differently impacts
+tube and limb development, revealing the relative importance of the different cell layers
 in the modular architecture of petunia petals.
 
-
 ## URLs
 
 https://gitbio.ens-lyon.fr/rdp/petunia_star_wico_rnaseq