The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFTlike and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.

The abundance of different simple sequence motifs in plants was accessed through data base searches of DNA sequences and quantitative hybridization with synthetic dinucleotide repeats. Database searches indicated that microsatellites are five times less abundant in the genomes of plants than in mammals. The most common plant repeat motif was AA/TT followed by AT/TA and CT/GA. This group comprised about 75% of all microsatellites with a length of more than 6 repeats. The GT/CA motif being the most abundant dinucleotide repeat in mammals was found to be considerably less frequent in plants. To address the question if plant simple repeat sequences are variable as in mammals, (GT)n and (CT)n microsatellites were isolated from B.napus. Five loci were investigated by PCR-analysis and amplified products were obtained for all microsatellites from B. oleracea, B.napus and B.rapa DNA, but only for one primer pair from B.nigra. Polymorphism was detected for all microsatellites.

Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F ST ¼ 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F ST . The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.L OCAL adaptation is a key process in the evolution of species. Understanding how local adaptation is established and maintained, however, is especially difficult as its establishment is contingent upon historical conditions and its maintenance depends on the balance among conflicting evolutionary forces (e.g., Yeaman and Otto 2011). It is a particularly challenging task in forest trees, because they have long generation times and therefore cannot be easily manipulated experimentally. For instance, transfer experiments are theoretically possible but practically difficult to implement. On the other hand, the analysis of the strong latitudinal clines displayed by forest trees for potentially adaptive traits such as bud set (Dormling 1973;Savolainen et al. 2007;Aitken et al. 2008) can provide crucial information on the forces involved in local adaptation and, in particular, on the relative parts played by demography and selection in the establishment of the cline. Furthermore, phenology in general, and flowering time and bud set in particular, have been extensively studied and strong candidate genes are available, many of which belong to the photoperiodic pathway including the circadian clock (Gyllenstrand et al. 2007;Albani and Coupland 2010;Bergelson and Roux 2010;Fornara et al. 2...

SummaryGynoecia of the Arabidopsis mutant sty1-1 display abnormal style morphology and altered vascular patterning. These phenotypes, which are enhanced in the sty1-1 sty2-1 double mutant, suggest that auxin homeostasis or signalling might be affected by mutations in STY1 and STY2, both members of the SHI gene family. Chemical inhibition of polar auxin transport (PAT) severely affects the apical-basal patterning of the gynoecium, as do mutations in the auxin transport/signalling genes PIN1, PID and ETT. Here we show that the apical-basal patterning of sty1-1 and sty1-1 sty2-1 gynoecia is hypersensitive to reductions in PAT, and that sty1-1 enhances the PAT inhibition-like phenotypes of pin1-5, pid-8 and ett-1 gynoecia. Furthermore, we show that STY1 activates transcription of the flavin monooxygenase-encoding gene THREAD/YUCCA4, involved in auxin biosynthesis, and that changes in expression of STY1 and related genes lead to altered auxin homeostasis. Our results suggest that STY1 and related genes promote normal development of the style and affect apical-basal patterning of the gynoecium through regulation of auxin homeostasis.

This study describes the population structure of Norway spruce (Picea abies) as revealed by protein polymorphisms and morphological variation. Electrophoretically detectable genetic variability was examined at 22 protein loci in 70 populations from the natural range of the species in Europe. Like other conifers, Norway spruce exhibits a relatively large amount of genetic variability and little differentiation among populations. Sixteen polymorphic loci (73%) segregate for a total of 51 alleles, and average heterozygosity per population is 0.115. Approximately 5% of the total genetic diversity is explained by differences between populations (G = 0.052), and Nei's standard genetic distance is less than 0.04 in all cases. We suggest that the population structure largely reflects relatively recent historical events related to the last glaciation and that Norway spruce is still in a process of adaptation and differentiation. There is a clear geographic pattern in the variation of allele frequencies. A major part of the allelefrequency variation can be accounted for by a few synthetic variables (principal components), and 80% of the variation of the first principal component is "explained" by latitude and longitude. The central European populations are consistently depauperate of genetic variability, most likely as an effect of severe restrictions of population size during the last glaciation. The pattern of differentiation at protein loci is very similar to that observed for seven morphological traits examined. This similarity suggests that the same evolutionary forces have acted upon both sets of characters.

Summary While angiosperm clocks can be described as an intricate network of interlocked transcriptional feedback loops, clocks of green algae have been modelled as a loop of only two genes. To investigate the transition from a simple clock in algae to a complex one in angiosperms, we performed an inventory of circadian clock genes in bryophytes and charophytes. Additionally, we performed functional characterization of putative core clock genes in the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis.Phylogenetic construction was combined with studies of spatiotemporal expression patterns and analysis of M. polymorpha clock gene mutants.Homologues to core clock genes identified in Arabidopsis were found not only in bryophytes but also in charophytes, albeit in fewer copies. Circadian rhythms were detected for most identified genes in M. polymorpha and A. agrestis, and mutant analysis supports a role for putative clock genes in M. polymorpha.Our data are in line with a recent hypothesis that adaptation to terrestrial life occurred earlier than previously expected in the evolutionary history of charophyte algae. Both gene duplication and acquisition of new genes was important in the evolution of the plant circadian clock, but gene loss has also contributed to shaping the clock of bryophytes.

Plants are the foundation of terrestrial ecosystems and their colonization of land was likely facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following that founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Through analysis of 271 transcriptomes and 122 plant genomes, we demonstrate that the common symbiosis signalling pathway controlling the association with arbuscular mycorrhizal fungi and with nitrogen-fixing bacteria specifically co-evolved with intracellular endosymbioses, including ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. In contrast, species forming exclusively extracellular symbioses like ectomycorrhizae or associations with cyanobacteria have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million years of plant diversification.