Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts

Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt) in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae

Robustness and evolvability in the B-system of flower development

BACKGROUND: Gene duplication has often been invoked as a key mechanism responsible for evolution of new morphologies. The floral homeotic B-group gene family has undergone a number of gene duplication events, and yet the functions of these genes appear to be largely conserved. However, detailed comparative analysis has indicated that such duplicate genes have considerable cryptic variability in their functions. In the Solanaceae, two duplicate B-group gene lineages have been retained in three subfamilies. Comparisons of orthologous genes across members of the Solanaceae have demonstrated that the combined function of all four B-gene members is to establish petal and stamen identity, but that this function was partitioned differently in each species. These observations emphasize both the robustness and the evolvability of the B-system. SCOPE: We provide an overview of how the B-function genes can robustly specify petal and stamen identity and at the same time evolve through changes in protein-protein interaction, gene expression patterns, copy number variation or alterations in the downstream genes they control. By using mathematical models we explore regulatory differences between species and how these impose constraints on downstream gene regulation. CONCLUSIONS: Evolvability of the B-genes can be understood through the multiple ways in which the B-system can be robust. Quantitative approaches should allow for the incorporation of more biological realism in the representations of these regulatory systems and this should contribute to understanding the constraints under which different B-systems can function and evolve. This, in turn, can provide a better understanding of the ways in which B-genes have contributed to flower diversity.status: publishe

FLOWERING LOCUS C in monocots and the tandem origin of angiosperm specific MADS-box genes

MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC-like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described

Phylogenetic relationships in Nartheciaceae (Dioscoreales), with focus on pollen and orbicule morphology

Amolecular phylogenetic analysis of Nartheciaceae is presented, with nine species of the family’s five genera. The main phylogenetic findings are: (a) Nietneria and Narthecium are placed in a clade sister to Lophiola; (b) sister to the L

FLOWERING LOCUS C in monocots and the tandem origin of angiosperm specific MADS-box genes

MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-) -like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC-like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described

Gomphocalyx and Phylohydrax (Rubiaceae): sister taxa excluded from Spermacoceae s.s., featuring a remarkable case of convergent evolution

The genera Gomphocalyx and Phylohydrax (Rubiaceae) have been invariably placed in the tribe Spermacoceae s.s. based on the uni-ovulate ovary locules and pluri-aperturate pollen grains. Sequence data from the rps16 intron and the rbcL gene here presented exclude Gomphocalyx and Phylohydrax from Spermacoceae s.s. The two genera are closely related and their nearest relatives are found among members of the former tribe Hedyotideae. This position may be surprising at first, because the growth form of Phylohydrax is similar to some observed in Sper

Phylogenetic relationships in Nartheciaceae (Dioscoreales), with focus on pollen and orbicule morphology

Amolecular phylogenetic analysis of Nartheciaceae is presented, with nine species of the family’s five genera. The main phylogenetic findings are: (a) Nietneria and Narthecium are placed in a clade sister to Lophiola; (b) sister to the Lophiola-Narthecium- Nietneria clade is a clade formed by Aletris and the monospecific Metanarthecium; (c) the inclusion of Metanarthecium luteo-viride in Aletris, as proposed by several authors, is well supported. The pollen and orbicule morphology of representatives of five genera is described. The results underline a close relationship between Nietneria, Narthecium, and Lophiola and confirm the previously reported observations of Metanarthecium pollen and the types of sexine ornamentation in Aletris. Pollen grains of Nietneria are monosulcate with a microreticulate sexine, confirming a close relationship with Lophiola and Narthecium. Spherical smoothsurfaced orbicules were observed in all genera of Nartheciaceae and the presence of a circular perforation on the orbicule surface is potentially synapomorphic for the family