Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.T he red algae, together with the glaucophytes and the Chloroplastida, are members of the Archaeplastida, the phylogenetic group formed during the primary endosymbiosis event that gave rise to the first photosynthetic eukaryote. Red algal genomes, both plastid and nuclear, also contributed, via secondary endosymbiosis, to several other eukaryotic lineages, including

Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.

Chondrus crispus is a species of red algae that grows on rocks from the middle intertidal into the subtidal zones of the North Atlantic coasts. As such, it has to cope with strongly variable abiotic conditions. Here we studied the response of the photosynthetic apparatus of this red alga to illumination. We found that, as previously described in the case of the unicellular alga Rhodella violacea (E. Delphin et al., Plant Physiol. 118 (1998) 103-113), a single multi-turnover saturating pulse of light is sufficient to induce a strong quenching of fluorescence. To elucidate the mechanisms underlying this fluorescence quenching, we combined room temperature and 77K fluorescence measurements with absorption spectroscopy to monitor the redox state of the different electron carriers in the chain. In addition, we studied the dependence of these various observables upon the excitation wavelength. This led us to identify energy spill-over from Photosystem II to Photosystem I rather than a qE-type non-photochemical quenching as the major source of fluorescence quenching that develops upon a series of 200ms pulses of saturating light results, in line with the conclusion of Ley and Butler (Biochim. Biophys. Acta 592 (1980) 349-363) from their studies of the unicellular red alga Porphyridium cruentum. In addition, we show that the onset of this spill-over is triggered by the reduction of the plastoquinone pool.

Chondrus crispus is a common red macroalga living on the rocky shores of the North Atlantic Ocean. It has a long research history, being a major source of carrageenan, a thickener widely used in the food industry, but also for physiological and ecological studies. To establish it as a model for red algae, its genome has been sequenced, allowing the development of molecular tools such as quantification of gene expression, including RNAseq and RT-qPCR. To determine appropriate genes for RT-qPCR normalization, the expression of 14 genes was monitored in 18 conditions using two sets of algal samples: samples from the sequenced strain, cultured and stressed in laboratory conditions and C. crispus collected on the shore and stressed in situ. The expression stability of the genes between the samples was evaluated by comparing the Ct range and using the programs geNorm and NormFinder. The candidate genes encoded translation related proteins (initiation factors IF4A-1 and IF4A-2, elongation factor EF1α and eRF3, an eukaryotic polypeptide chain release factor), cytoskeleton proteins (two β-tubulins, α-tubulin and actin), enzymes involved in the pentose phosphate pathway (glucose 6-phosphate deshydrogenase), protein recycling process (ubiquitin and ubiquitin-conjugating enzyme) and glycolysis (isocitrate dehydrogenase). The two sets of samples showed different expression patterns. Most of the genes were stable in the algae cultivated in the laboratory, whereas environmental samples showed a more important variation in gene expression. When analyzing the two sets separately, the ranking of the most stables genes were different from one method to another. When considering all samples, the two statistical methods were concordant, revealing translation initiation factor 4A-2 and eukaryotic polypeptide chain release factor 3 as pertinent normalization genes. This study highlights thus the importance of testing reference genes according to the experiments as well as the genetic and physiological background of the organism.

Red algae are the oldest identifiable multicellular eukaryotes, with a fossil record dating back more than a billion years. During that time two major rhodophyte lineages, bangiophytes and florideophytes, have evolved varied levels of morphological complexity. These two groups are distinguished, in part, by different patterns of multicellular development, with florideophytes exhibiting a far greater diversity of morphologies. Interestingly, during their long evolutionary history, there is no record of a rhodophyte achieving the kinds of cellular and tissue‐specific differentiation present in other multicellular algal lineages. To date, the genetic underpinnings of unique aspects of red algal development are largely unexplored; however, they must reflect the complements and patterns of expression of key regulatory genes. Here we report comparative evolutionary and gene expression analyses of core subunits of the SWI/SNF chromatin‐remodeling complex, which is implicated in cell differentiation and developmental regulation in more well studied multicellular groups. Our results suggest that a single, canonical SWI/SNF complex was present in the rhodophyte ancestor, with gene duplications and evolutionary diversification of SWI/SNF subunits accompanying the evolution of multicellularity in the common ancestor of bangiophytes and florideophytes. Differences in how SWI/SNF chromatin remodeling evolved subsequently, in particular gene losses and more rapid divergence of SWI3 and SNF5 in bangiophytes, could help to explain why they exhibit a more limited range of morphological complexity than their florideophyte cousins.

membrane. Our genetic and embryological analyses further indicate that Shh signalling controls Laminin gene expression, a critical step in the formation of the myotomal basement membrane, and that Laminin-111 has specific and essential role in myotomal basement membrane assembly. Together, our data reveal a novel role for Shh signalling in the control of basement membrane assembly and provide a framework for understanding the complex interactions between extra-cellular matrix and intercellular signalling.The hindbrain represents the key relay hub of the central nervous system, linking the bilaterally symmetric half-sides of its lower and upper centers via an extensive network of sensory circuits. The early hindbrain is transiently subdivided into repetitive rhombomeres along its anterior-posterior (AP) axis, that underlies segmental formation of motor nerves and ganglia. It is less clear whether this AP segmentation also contributes to the formation of dorsal interneurons, in addition to dorso-ventral (DV) cues that are known to pattern spinal cord sensory neurons.The aim of this study is to determine the spatial/temporal formation of 3 dorsal interneuron populations (dI1-3) in the chick hindbrain and to delineate their axonal projections during development. In order to characterize dI1-3 distribution along the hindbrain, immunohistochemistry analysis was performed at subsequent stages using antibodies against several Lim-homeodomain proteins (Lhx2/9, Lim1, Islet1). This analysis showed a dynamic DV/AP distribution of these cell subtypes along the hindbrain. Next, we applied a Cre/loxP-based dual-expression system for studying the axonal-trajectories of dI1-2 neurons using mapped enhancer determinants. For dI1 neurons, detected by math1/pouf3 elements, 2 main distinct axonal projections were found, both crossing the ventral midline and turning caudally toward the spinal cord. DI2 axons, mapped with Foxd3 element, showed one main contra-lateral pattern after crossing the floor plate. In addition, both subtypes revealed also ipsilateral routes.Taken together, this study enabled us to construct a comprehensive map of the developmental programming of dI1-3 together with discovering novel trajectories of their axons in the hindbrain. The development of the filamentous brown alga Ectocarpus siliculosus is under the control of intrinsic mechanisms (Le Bail et al., J. Phycol., 2008). Modelling showed that local positional information is determining for the proper development of the very early sporophyte, and that an additional mechanism is further required to ensure a correct organisation of the branching pattern (Billoud et al., Funct. Plant Biol., 2008). Here, we show that the auxin phytohormone Indole-3 Acetic Acid is present in E. siliculosus mainly at the apices of the filaments. Several auxin compounds are able to interfere with both the cell differentiation and the branching pattern in this filamentous alga. Genome-wide survey displays a partial conservation of the auxin biosynthesis pathways and the identificatio...