Summary 24• The genome of the filamentous brown alga Ectocarpus was the first to be completely 25 sequenced from within the brown algal group and has served as a key reference genome both 26 for this lineage and for the stramenopiles. 27• We present a complete structural and functional reannotation of the Ectocarpus genome. 28• The large-scale assembly of the Ectocarpus genome was significantly improved and genome-29 wide gene re-annotation using extensive RNA-seq data improved the structure of 11,108 30 existing protein-coding genes and added 2,030 new loci. A genome-wide analysis of splicing 31 isoforms identified an average of 1.6 transcripts per locus. A large number of previously 32

Understanding the genetic underpinnings of adaptive traits in microalgae is important for the study of evolution and for applied uses. We used long-term selection under a regime of serial transfers with haploid populations of the green alga Chlamydomonas reinhardtii raised in liquid TAP medium containing 200 mM NaCl. After 1255 generations, evolved salt (ES) populations could grow as rapidly in high salt medium as progenitor cells (progenitor light [PL]). Transcriptome data were analysed to elucidate the basis of salt tolerance in ES cells when compared with PL cells and to cells incubated for 48 h in high salt medium (progenitor salt [PS], the short-term acclimation response). These data demonstrate that evolved and short-term acclimation responses to salt stress differ fundamentally from each other. Progenitor salt cells exhibit well-known responses to salt stress such as reduction in photosynthesis, upregulation of glycerophospholipid signaling, and upregulation of the transcription and translation machinery. In contrast, ES cells show downregulation of genes involved in the stress response and in transcription/translation. Our results suggest that gene-rich mixotrophic lineages such as C. reinhardtii may be able to adapt rapidly to abiotic stress engendered either by a rapidly changing climate or physical vicariance events that isolate populations in stressful environments.

We investigated the genetic diversity and symbiotic efficiency of 223 Sinorhizobium sp. isolates sampled from a single Mediterranean soil and trapped with four Medicago truncatula lines. DNA molecular polymorphism was estimated by capillary electrophoresis-single-stranded conformation polymorphism and restriction fragment length polymorphism on five loci (IGS NOD , typA, virB11, avhB11, and the 16S rRNA gene). More than 90% of the rhizobia isolated belonged to the Sinorhizobium medicae species (others belonged to Sinorhizobium meliloti), with different proportions of the two species among the four M. truncatula lines. The S. meliloti population was more diverse than that of S. medicae, and significant genetic differentiation among bacterial populations was detected. Single inoculations performed in tubes with each bacterial genotype and each plant line showed significant bacterium-plant line interactions for nodulation and N 2 fixation levels. Competition experiments within each species highlighted either strong or weak competition among genotypes within S. medicae and S. meliloti, respectively. Interspecies competition experiments showed S. meliloti to be more competitive than S. medicae for nodulation. Although not highly divergent at a nucleotide level, isolates collected from this single soil sample displayed wide polymorphism for both nodulation and N 2 fixation. Each M. truncatula line might influence Sinorhizobium soil population diversity differently via its symbiotic preferences. Our data suggested that the two species did not evolve similarly, with S. meliloti showing polymorphism and variable selective pressures and S. medicae showing traces of a recent demographic expansion. Strain effectiveness might have played a role in the species and genotype proportions, but in conjunction with strain adaptation to environmental factors.The rhizobium-legume nitrogen-fixing association is a good model for studying symbiosis and coevolution between organisms. In this mutualistic association, bacteria form nodules on plant roots (more rarely on the stem), where atmospheric nitrogen is reduced to ammonium available for the plant. Among the various plant-bacterium couples studied so far, the Medicago truncatula association with Sinorhizobium meliloti is particularly interesting (8) and has often been studied as a model system for genetic description of the molecular pathways involved in the establishment of the symbiosis (16). M. truncatula has the ability to form an efficient symbiosis with two bacterial species, S. meliloti (9) and its sister species, Sinorhizobium medicae (29).The genetic diversity of these two bacterial species, especially S. meliloti, has usually been described as quite important (2,7,11,40). This bacterial diversity, assessed by phenotypic or genotypic analyses, has been reported to be influenced by several factors, including geographical location (32), soil factors (14), and plant species (19,37). Furthermore, at an interspecies level, several studies on S. meliloti and S. medicae natural pop...