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1 a Link Between LEAFY and B-Gene Homologs in Welwitschia Mirabilis

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1 a Link Between LEAFY and B-Gene Homologs in Welwitschia Mirabilis A link between LEAFY and B-gene homologs in Welwitschia mirabilis sheds light on 2 ancestral mechanisms prefiguring floral development Edwige Moyroud1, Marie Monniaux1, Emmanuel Thévenon1, Renaud Dumas1, Charles P. 4 Scutt2, Michael W.Frohlich2,3, François Parcy1 1 LPCV, CEA, CNRS, INRA, Université Grenoble-Alpes, BIG, 38000, Grenoble, France 6 2 Laboratoire de Reproduction et Développement des Plantes, UMR5667, CNRS, INRA, Université de Lyon, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon Cedex 8 07, France. 3 Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK. 10 CORRESPONDING AUTHORS: François Parcy; [email protected] 33 (0)4 38784978 @Francois_Parcy 12 and Michael Frohlich; [email protected] 44 (0)79 5223 2864 Twitter heading: 14 Paving the way for flowers: a piece of the floral network predates flower origin 16 Twitter account: @Francois_Parcy WORD COUNT 18 Total: 6197 words Summary: 199 words 20 Introduction: 1415 words Materials and Methods: 733 words 22 Results: 2000 words Discussion: 1879 words 24 Acknowledgements: 170 words This manuscript also contains 5 Main Figures (all in colour except Fig. 4), 4 Supplementary 26 Figures, 5 Supplementary Tables, Supplementary Methods and Supplementary References. 1 28 SUMMARY • Flowering plants evolved from an unidentified gymnosperm ancestor. Comparing the 30 mechanisms controlling development in angiosperm flowers and gymnosperm cones may help elucidate the mysterious origin of the flower. 32 • We combined gene expression studies with protein behaviour characterisation in Welwitschia mirabilis to test whether the known regulatory links between LEAFY and 34 its MADS-box gene targets, central to flower development, might also contribute to gymnosperm reproductive development. 36 • We found that WelLFY, one of two LEAFY-like genes in Welwitschia, could be an upstream regulator of the MADS box genes APETALA3/PISTILLATA-like (B-genes). 38 We demonstrated that even though their DNA binding domains are extremely similar, WelLFY and its paralog WelNDLY exhibit distinct DNA binding specificities and 40 that, unlike WelNDLY, WelLFY shares with its angiosperm ortholog the capacity to bind promoters of Welwitschia B-genes. Finally, we identified several cis-elements 42 mediating these interactions in Welwitschia and obtained evidence that the link between LFY homologs and B-genes is also conserved in two other gymnosperms, 44 Pinus and Picea. • Although functional approaches to investigate cone development in gymnosperms are 46 limited, our state-of-the-art biophysical techniques, coupled with expression studies, provide evidence that crucial links, central to the control of floral development, may 48 already have existed before the appearance of flowers. 50 KEY WORDS: Angiosperms, bisexual structure, flower development, flower origin, gymnosperms, 52 LEAFY, MADS-box, transcription factors 54 2 INTRODUCTION 56 One of the most important developmental changes in the evolutionary origin of the flower was the combining of male and female reproductive organs onto a single axis (Frohlich 58 & Parker, 2000; Baum, D.A., and Hileman, 2006; Theissen & Melzer, 2007; Rudall & Bateman, 2010). However, the origin of bisexuality in the angiosperms remains enigmatic 60 (Bateman et al., 2006; Frohlich & Chase, 2007; Doyle, 2008; Mathews & Kramer, 2012). By comparing the genetic circuits that control the development of bisexual flowers versus 62 unisexual gymnosperm reproductive structures (GRS), we aim to generate evidence regarding the developmental network that functioned in the last common ancestor of the living seed 64 plants (angiosperms and extant gymnosperms). An understanding of this ancestral seed plant network should help to identify the subsequent molecular changes which led to the 66 appearance of the first flowers in the angiosperm lineage. 68 In angiosperms, male and female reproductive organ identity is controlled by the combinatorial expression of B- and C-class MADS-box genes: C-gene expression confers 70 female (carpel) identity in primordia arising from the centre of the floral meristem, while combined B- and C-gene expression confers male (stamen) identity in primordia that form in 72 the surrounding zone (Becker & Theißen, 2003). B- and C-class genes belong to the APETALATA3/PISTILLATA (AP3/PI in Arabidopsis) and AGAMOUS (AG in Arabidopsis) 74 clades of MADS-box genes, respectively. Gymnosperms also possess MADS-box genes within these two lineages (Theißen & Becker, 2004): AG-like genes are expressed in both 76 male and female GRS, while AP3/PI-like genes are only expressed in male GRS (Sundström & Engström, 2002; Winter et al., 2002; Zhang et al., 2004). The expression of gymnosperm 78 AP3/PI- or AG-like transgenes in flowering plants whose native B or C genes are inactivated by mutation, is sufficient to restore near wild-type flower development, suggesting that the 80 biochemical properties of B and C homologs are widely conserved between seed plants (Winter et al., 2002; Zhang et al., 2004). To generate the bisexual structure of the first 82 flowers, a C-class expression domain must have arisen next to a B+C-class domain on the same growing axis. Accordingly, several authors have proposed a change in the regulation of 84 AP3/PI and/or AG homologs as a crucial event on the lineage leading to the angiosperms and candidate genes potentially responsible for this regulatory shift have been suggested (Albert et 86 al., 2002; Becker & Theißen, 2003; Theißen & Becker, 2004; Baum, D.A., and Hileman, 3 2006). However, regulators of AP3/PI and/or AG homologs in extant gymnosperms, the sister 88 group to flowering plants, remain to be identified. The LEAFY/FLORICAULA (LFY/FLO) gene encodes a unique plant transcription 90 factor, which, in angiosperms, patterns the floral meristem by regulating B- and C- class genes (Moyroud et al., 2009a, 2010). In Arabidopsis for instance, LFY is a direct activator of 92 both APETALA3 (AP3) and AGAMOUS (AG) (Parcy et al., 1998; Busch et al., 1999; Lohmann et al., 2001; Lamb et al., 2002). All major groups of extant gymnosperms possess 94 two paralogous LFY-like genes (Frohlich & Parker, 2000; Vazquez-Lobo et al., 2007), first identified in Monterey pine as PRFLL (Mellerowicz et al., 1998) and NEEDLY (NDLY) 96 (Mouradov et al., 1998a). The only known exception to the maintenance of two LFY-like paralogs in gymnosperms is in the genus Gnetum, at least some species of which seem to 98 possess a single LFY-like gene (Frohlich & Meyerowitz, 1997; Shindo et al., 2001; Frohlich, 2003). Phylogenetic analyses indicate that both LFY and NDLY homologs were probably 100 present in the last common ancestor of the living seed plants and that the NDLY gene, retained in most gymnosperms, was subsequently lost in the angiosperm lineage before the radiation 102 of the extant flowering plants (Frohlich & Parker, 2000). 104 LFY-like genes are expressed in the developing GRS of all gymnosperms studied to date, consistent with a role for these genes in reproductive development (Mellerowicz et al., 106 1998; Mouradov et al., 1998a; Shindo et al., 2001; Carlsbecker et al., 2004; Dornelas & Rodriguez, 2005; Guo, C.L., Chen, L.G., He, X.H., Dai, Z., and Yuan, 2005; Shiokawa et al., 108 2008). A recent study in Norway spruce brings further supports for a role of LFY-like proteins in reproductive initiation: in the acrocona mutant, vegetative shoots can develop into 110 female cones and this vegetative-to-reproductive transition correlates with an upregulation of LFY-like genes (Carlsbecker et al., 2013). A comprehensive study performed in three conifer 112 genera also demonstrated that LFY and NDLY homologs are both expressed within male and female GRS, sometimes in overlapping territories, but that their expression patterns often 114 diverge so that the two paralogs are expressed in mutually exclusive domains, especially in late developmental stages (Vazquez-Lobo et al., 2007). These observations suggest that LFY 116 and NDLY make distinct contributions to GRS formation, though the identity of the genes they regulate in gymnosperms and the molecular basis accounting for their hypothetical 118 functional divergence remain to be established. 4 120 A link between LFY-like genes and homologs of floral homeotic genes in gymnosperms has been a central postulate of many hypotheses of flower origin (Albert et al., 122 2002; Becker & Theißen, 2003; Theißen & Becker, 2004; Baum, D.A., and Hileman, 2006), though the existence of this link has never been demonstrated. In particular, it is not known 124 whether gymnosperm LFY-like genes perform a similar function to their angiosperm counterparts by regulating AP3/PI- and AG-like genes as the regulatory potential of LFY-like 126 proteins has never been analysed in any gymnosperm species. To investigate the role(s) of LFY-like genes in gymnosperms, i.e. a non-flowering seed plant lineage, we used a 128 combination of gene expression and biophysical analyses to test for the existence of a minimal network involving LFY-like proteins and AP3/PI- and AG-like MADS-box genes in 130 the gymnosperm Welwitschia mirabilis. 132 Welwitschia presents numerous advantages as a gymnosperm for molecular- developmental studies: plants can make male reproductive structures (cones) in as little as two 134 years from seed (Van Jaarsveld, 1992) and are small enough to be isolated in controlled environments. Although the plant body is famously bizarre, the reproductive structures are 136 generalized; they have not lost numerous parts, as have their relatives Gnetum and Ephedra, nor do they have extensive fusions, with the resulting morphological ambiguity of conifer 138 cones (Mundry & Stützel, 2004). Welwitschia cones show long gradate development in which all stages are simultaneously available. The cones are borne on thin, branching stems that 140 emerge from the “scaly body” between the leaves (Fig. 1A). Each cone bears a series of opposite-decussate axillary fertile units subtended by sterile bracts (Fig. 1B-C), such that 142 newly formed units emerge at the cone tip and become progressively older towards the base.
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