The Evolution of HD2 Proteins in Green Plants.

In eukaryotes, protein deacetylation is carried out by two well-conserved histone deacetylase (HDAC) families: RPD3/HDA1 and SIR2. Intriguingly, model plants such as Arabidopsis express an additional plant-specific HDAC family, termed type-2 HDACs (HD2s). Transcriptomic analyses from more than 1300 green plants generated by the 1000 plants (1KP) consortium showed that HD2s appeared early in green plant evolution, the first members being detected in several streptophyte green alga. The HD2 family has expanded via several rounds of successive duplication; members are expressed in all major green plant clades. Interestingly, angiosperm species express new HD2 genes devoid of a zinc-finger domain, one of the main structural features of HD2s. These variants may have been associated with the origin and/or the biology of the ovule/seed.

Nitric oxide production mediates oligogalacturonide-triggered immunity and resistance to Botrytis cinerea in Arabidopsis thaliana.

Nitric oxide (NO) regulates a wide range of plant processes from development to environmental adaptation. In this study, we investigated the production and/or function of NO in Arabidopsis thaliana leaf discs and plants elicited by oligogalacturonides (OGs) and challenged with Botrytis cinerea. We provided evidence that OGs triggered a fast and long lasting NO production which was Ca(2+) dependent and involved nitrate reductase (NR). Accordingly, OGs triggered an increase of both NR activity and transcript accumulation. NO production was also sensitive to the mammalian NO synthase inhibitor L-NAME. Intriguingly, we showed that L-NAME affected NO production by interfering with NR activity, thus questioning the mechanisms of how this compound impairs NO synthesis in plants. We further demonstrated that NO modulates RBOHD-mediated reactive oxygen species (ROS) production and participates in the regulation of OG-responsive genes such as anionic peroxidase (PER4) and a ß-1,3-glucanase. Mutant plants impaired in PER4 and ß-1,3-glucanase, as well as Col-0 plants treated with the NO scavenger cPTIO, were more susceptible to B. cinerea. Taken together, our investigation deciphers part of the mechanisms linking NO production, NO-induced effects and basal resistance to B. cinerea.

Genomic organization of molecular differentiation in Norway spruce (Picea abies).

Diversity and differentiation among three populations representing the geographical domains commonly recognized within the natural distribution area of Picea abies were analysed by using a set of 292 AFLP (amplified fragment length polymorphism), SSR (single sequence repeat) and ESTP (expressed sequence tags polymorphism) markers. As usually observed in forest trees, results showed high within-population diversity (H(S) reaching 0.79) and low among-population differentiation (G(ST) approximately 2%). The genomic organization of differentiation was then investigated on the basis of a subsample of 150 AFLP, SSR and ESTP mapped markers. The number of the loci differentiating the Baltico-Nordic from the central European populations (25 loci) and, within the central European populations, the Alpine from the Hercyno-Carpathian populations (12 loci), were different. These 37 differentiated loci, with individual G(ST) values ranging from 0.008 to 0.20, were evenly distributed on all linkage groups and mostly followed the neutral expectations, suggesting genome-wide effects on differentiation. Nine of them however behave as 'outlier' loci indicating possible locus-specific selective effects. Contribution of ongoing evolutionary forces and historical effects to the geographical differentiation of the species are discussed.

A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers.

Based on an F(1) progeny of 73 individuals, two parental maps were constructed according to the double pseudo-test cross strategy. The paternal map contained 16 linkage groups for a total genetic length of 1,792 cM. The maternal map covered 1,920 cM, and consisted of 12 linkage groups. These parental maps were then integrated using 66 intercross markers. The resulting consensus map covered 2,035 cM and included 755 markers (661 AFLPs, 74 SSRs, 18 ESTPs, the 5S rDNA and the early cone formation trait) on 12 linkage groups, reflecting the haploid number of chromosomes of Picea abies. The average spacing between two adjacent markers was 2.6 cM. The presence of 39 of the SSR and/or ESTP markers from this consensus map on other published maps of different Picea and Pinus species allowed us to establish partial linkage group homologies across three P. abies maps (up to five common markers per linkage group). This first saturated linkage map of P. abies could be therefore used as a support for developing comparative genome mapping in conifers.

Characterization of a mosaic minisatellite locus in the mitochondrial DNA of Norway spruce [Picea abies (L.) Karst.].

A mosaic minisatellite region has been identified in the mitochondrial genome of Norway spruce (Picea abies). The array was composed of three tandem repeats PaTR1 (32 bp), PaTR2a (26 bp) and PaTR2b (26 bp). PaTR2a and PaTR2b differed by one base substitution. The analysis of 92 trees covering the whole natural distribution area of the species allowed detection of 11 length variants ranging from 131 bp to 447 bp. This high intra-specific polymorphism relies on variation in the number of the tandem repeats. Population genetic parameters estimated among 14 populations suggested high population differentiation (Gst=0.749). The phylogenetic analysis of the 11 sequenced length variants has been performed using a parsimony approach. The topology of the tree showed a good association of groups with geographical origin and a low level of size homoplasy. The phylogenetic reconstruction also suggests that this minisatellite locus has mainly evolved by an increase in the repeat copy number.

Haplotype variation in a mitochondrial tandem repeat of Norway spruce (Picea abies) populations suggests a serious founder effect during postglacial re-colonization of the western Alps.

Populations from 13 elevational transects of Norway spruce [Picea abies (L.) Karst] across the Alpine range were sampled to elucidate the geographical pattern of genetic variation in relation to postglacial re-colonization and to study elevational effects on haplotypic diversity. We assessed fragment length variation in a tandem repeat region of the mitochondrial (mt) nad1 intron 2. This maternally inherited genetic marker is suited to infer migration as it is dispersed by seed only. A total of 10 haplotypes was found, most of which were due to repeat copy number variation. An analysis of molecular variance (amova) showed that overall population differentiation was high (F(ST)=0.41), and it revealed a significant differentiation between monomorphic western and moderately to highly variable eastern Alpine populations. This phylogeographic pattern may be explained by a founder effect during postglacial re-colonization. An early arriving haplotype, assumed to originate from a western Carpathian refugium, could expand into suitable habitats, reducing the chances for establishment of subsequently arriving haplotypes. On the other hand, the high variation in populations within an Italian transect of the south-eastern Alps may be the consequence of merging migration pathways from and close distance to putative glacial refugia, most likely those assumed in the Carpathian mountains and on the Balkan peninsula or possibly in the central plains of Italy. An effect of elevation on haplotypic diversity was not evident, though a low, but significant, partition of total genetic variation was attributed to among-population variation in one Italian transect. Various factors, such as vertical seed dispersal and forest management, may account for blurring an otherwise established pattern of genetic variation on a small geographical scale.

Phylogeny and phylogeography of the circumpolar genus Fraxinus (Oleaceae) based on internal transcribed spacer sequences of nuclear ribosomal DNA.

The DNA sequences of the nuclear internal transcribed spacers (1 and 2) of nuclear ribosomal DNA were determined for 27 taxa of Fraxinus in an attempt to reconstruct the phylogeny of the genus and interpret its biogeographic history in a phylogenetic context. Minimal intra-individual and intraspecific polymorphisms were observed and infrageneric taxa were all recovered in phylogenetic analyses. The tree topologies estimated from parsimony and neighbor-joining analyses of one- and two-parameter substitution rates were congruent and supported by high bootstrap estimates. Indels were also found to be phylogenetically informative. The phylogenetic trees obtained were in quite good agreement with the current taxonomy of the genus but homoplasy was observed in the evolution of floral characters. Polyploidy also appeared to have evolved several times in the genus. Fraxinus nigra was more closely related to European and Asian taxa than to the other American ashes. The Asian F. platypoda had a closer relationship to Asian and European ashes in section Bumelioides than to its presumed North American allies of section Melioides. With respect to the position of F. quadrangulata as sister group to the remainder to the remaining species, the subgenus Fraxinus appeared paraphyletic. Phylogeographical analysis indicated that Fraxinus likely originated in North America, with two subsequent events of intercontinental migration from North America to Asia.

Cloning and analysis of a 6.8-kb rDNA intergenic spacer region of the European ash (Fraxinus excelsior L.).

The 6.8-kb rDNA intergenic spacer region of F. excelsior was isolated from a CsCl/actinomycin-D gradient and cloned into pUC18 for further characterization. We observed the presence of subrepeats delimited by HaeIII enzyme sites. These subrepeats were sub-cloned and 11 clones were sequenced. These corresponded to subrepeated elements of either 32 bp or 41 bp that shared a 23-bp common sequence in the 5' end. Within each family of subrepeats, the percentage of common nucleotides was 84.4% for the 5 32-bp subrepeats and 67.4% for the 640-bp subrepeats. Non-repeated HaeIII fragments of 450 bp and 650 bp were also sub-cloned. To compare homology at the IGS region between the rDNA spacers of F. excelsior and the three related species (F. oxyphylla, F. americana, F. ornus), we conducted Southern hybridization analyses using each member of the 32-bp and 40-bp subrepeat families and the unique 450-bp and 650-bp fragments as probes. These analyses indicated that (1) the American ash is more genetically distant from the other three species that the latter are from each other and (2) F. oxyphylla and F. excelsior are more closely related to each other than to F. ornus.