BackgroundThe terrestrial habitat was colonized by the ancestors of modern land plants about 500 to 470 million years ago. Today it is widely accepted that land plants (embryophytes) evolved from streptophyte algae, also referred to as charophycean algae. The streptophyte algae are a paraphyletic group of green algae, ranging from unicellular flagellates to morphologically complex forms such as the stoneworts (Charales). For a better understanding of the evolution of land plants, it is of prime importance to identify the streptophyte algae that are the sister-group to the embryophytes. The Charales, the Coleochaetales or more recently the Zygnematales have been considered to be the sister group of the embryophytes However, despite many years of phylogenetic studies, this question has not been resolved and remains controversial.ResultsHere, we use a large data set of nuclear-encoded genes (129 proteins) from 40 green plant taxa (Viridiplantae) including 21 embryophytes and six streptophyte algae, representing all major streptophyte algal lineages, to investigate the phylogenetic relationships of streptophyte algae and embryophytes. Our phylogenetic analyses indicate that either the Zygnematales or a clade consisting of the Zygnematales and the Coleochaetales are the sister group to embryophytes.ConclusionsOur analyses support the notion that the Charales are not the closest living relatives of embryophytes. Instead, the Zygnematales or a clade consisting of Zygnematales and Coleochaetales are most likely the sister group of embryophytes. Although this result is in agreement with a previously published phylogenetic study of chloroplast genomes, additional data are needed to confirm this conclusion. A Zygnematales/embryophyte sister group relationship has important implications for early land plant evolution. If substantiated, it should allow us to address important questions regarding the primary adaptations of viridiplants during the conquest of land. Clearly, the biology of the Zygnematales will receive renewed interest in the future.

Resistance to herbivore attack is elicited by damage-and herbivore-specific signals. To understand the role of salicylic acid (SA) and jasmonic acid (JA) signalling in the herbivore-induced transcriptional responses of the native tobacco Nicotiana attenuata , a comparison was made of the responses in undamaged systemic leaves after attack by five herbivore species ( Manduca sexta , Spodoptera littoralis , Trichoplusia ni , Tupiocoris notatus and Myzus nicotianae ) from three feeding guilds and to elicitation by SA, BTH and methyl-JA with a 789-gene oligo-microarray and measured endogenous SA and JA levels. Systemic responses to M. sexta attack were similar to the responses in locally attacked tissues; however, the up-regulation of genes (such as proteinase inhibitor, PI) was more attenuated and resembled the responses to attack from the other Lepidopteran, S. littoralis, and to methyl-JA elicitation. Responses to attack from the puncture-feeding T. notatus repressed some JA-elicited genes (PI) elicited by the leafchewing Lepidopterans and most closely resembled SA elicitation. Attack from the phloem-feeding M. nicotianae aphids elicited few responses. Treatment with the SAmimic BTH induced both SA-and JA-elicited genes and most closely resembled the aphid response. SA concentrations were uniformly increased by herbivore attack and correlated with the down-regulation of photosynthetic genes in all treatments.

BackgroundMillions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.Results97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species.ConclusionsOur results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.

Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced the genomes of Dictyostelium fasciculatum (DF ) and Polysphondylium pallidum (PP), which represent the early diverging groups 1 and 2, respectively. In contrast to DD, PP and DF have conventional telomere organization and strongly reduced numbers of transposable elements. The number of proteincoding genes is similar between species, but only half of them comprise an identifiable set of orthologous genes. In general, genes involved in primary metabolism, cytoskeletal functions and signal transduction are conserved, while genes involved in secondary metabolism, export, and signal perception underwent large differential gene family expansions. This most likely signifies involvement of the conserved set in core cell and developmental mechanisms, and of the diverged set in niche-and species-specific adaptations for defense and food, mate, and kin selection. Phylogenetic dating using a concatenated data set and extensive loss of synteny indicate that DF, PP, and DD split from their last common ancestor at least 0.6 billion years ago.[Supplemental material is available for this article.]The central and most fascinating problem in biology is how natural selection has acted on random changes in the genomes of individuals to generate the immense range and complexity of extinct and extant living forms. However, understanding the relationship between genotypic and phenotypic change on a genomewide scale is complicated by the large number of loci involved and the range of phenotypic change. Comparative genomics is the tool of choice to define common gene sets and the first occurrence of genetic changes that may have caused phenotypic innovation. Genetic manipulation of altered genes can then reveal whether the genomic change was causal to the phenotypic alteration.The social amoeba Dictyostelium discoideum (DD) is a widely used model system for studying a range of problems in cell and developmental biology and more recently the evolution of social behavior and multicellularity.

This study investigated the fitness effects of four mutations (npr1, cpr1, cpr5, and cpr6) and two transgenic genotypes (NPR1-L and NPR1-H) affecting different points of the systemic acquired resistance (SAR) signaling pathway associated with pathogen defense in Arabidopsis thaliana. The npr1 mutation, which resulted in a failure to express SAR, had no effect on fitness under growth chamber conditions, but decreased fitness in the field. The expression of NPR1 positively correlated with the fitness in the field. Constitutive activation of SAR by cpr1, cpr5, and cpr6 generally decreased fitness in the field and under two nutrient levels in two growth chamber conditions. At low-nutrient levels, fitness differences between wild type and the constitutive mutants were unchanged or reduced (especially in cpr5). The reduced fitness of the constitutive mutants suggests that this pathway is costly, with the precise fitness consequences highly dependent on the environmental context.