Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation 1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Mya). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species 2. Medicago truncatula (Mt) is a long-established model for the study of legume biology. Here we describe the draft sequence of the Mt euchromatin based on a recently completed BAC-assembly supplemented with Illumina-shotgun sequence, together capturing ~94% of all Mt genes. A whole-genome duplication (WGD) approximately 58 Mya played a major role in shaping the Mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the Mt genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max (Gm) and Lotus japonicus (Lj). Mt is a close relative of alfalfa (M. sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the Mt genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox.

Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them are sorely needed. We report the draft genome sequence of the root-knot nematode Meloidogyne incognita, a biotrophic parasite of many crops, including tomato, cotton and coffee. Most of the assembled sequence of this asexually reproducing nematode, totaling 86 Mb, exists in pairs of homologous but divergent segments. This suggests that ancient allelic regions in M. incognita are evolving toward effective haploidy, permitting new mechanisms of adaptation. The number and diversity of plant cell wall-degrading enzymes in M. incognita is unprecedented in any animal for which a genome sequence is available, and may derive from multiple horizontal gene transfers from bacterial sources. Our results provide insights into the adaptations required by metazoans to successfully parasitize immunocompetent plants, and open the way for discovering new antiparasitic strategies.Plant-parasitic nematodes are responsible for global agricultural losses amounting to an estimated $157 billion annually. Although chemical nematicides are the most reliable means of controlling root-knot nematodes, they are increasingly being withdrawn owing to their toxicity to humans and the environment. Novel and specific targets are thus needed to develop new strategies against these pests.The Southern root-knot nematode Meloidogyne incognita is able to infect the roots of almost all cultivated plants, making it perhaps the

Ralstonia solanacearum is a devastating, soil-borne plant pathogen with a global distribution and an unusually wide host range. It is a model system for the dissection of molecular determinants governing pathogenicity. We present here the complete genome sequence and its analysis of strain GMI1000. The 5.8-megabase (Mb) genome is organized into two replicons: a 3.7-Mb chromosome and a 2.1-Mb megaplasmid. Both replicons have a mosaic structure providing evidence for the acquisition of genes through horizontal gene transfer. Regions containing genetically mobile elements associated with the percentage of G+C bias may have an important function in genome evolution. The genome encodes many proteins potentially associated with a role in pathogenicity. In particular, many putative attachment factors were identified. The complete repertoire of type III secreted effector proteins can be studied. Over 40 candidates were identified. Comparison with other genomes suggests that bacterial plant pathogens and animal pathogens harbour distinct arrays of specialized type III-dependent effectors.

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought 1 . Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives 2,3 , including numerous extremophile species 4 . Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences 5 and required single-molecule realtime sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade 6 and a sunflowerspecific whole-genome duplication around 29 million years ago 7 . An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs 8,9 .As the only major crop domesticated in North America, with its sunlike inflorescence that inspired artists, the sunflower is both a social icon and a major research focus for scientists. In evolutionary biology, the Helianthus genus is a long-time model for hybrid speciation and adaptive introgression 10 . In plant science, the sunflower is a model for understanding solar tracking 11 and inflorescence development 12 .Despite this large interest, assembling its genome has been extremely difficult as it mainly consists of long and highly similar repeats. This complexity has challenged leading-edge assembly protocols for close to a decade 13 .To finally overcome this challenge, we generated a 102× sequencing coverage of the genome of the inbred line XRQ using 407 singlemolecule real-time (SMRT) cells on the PacBio RS II platform. Production of 32 million very long reads allowed us to generate a genome assembly that captures 3 gigabases (Gb) (80% of the estimated genome size) in 13,957 sequence contigs. Four high-density genetic maps were combined with a sequence-based physical map to build the sequences of the 17 pseudo-chromosomes that anchor 97% of the gene content (Fig.

A r t i c l e s Theobroma cacao L. is a diploid tree fruit species (2n = 2x = 20 (ref. 1)) endemic to the South American rainforests. Cocoa was domesticated approximately 3,000 years ago 2 in Central America 3. The Criollo cocoa variety, having a nearly unique and homozygous genotype, was among the first to be cultivated 4. Criollo is now one of the two cocoa varieties providing fine flavor chocolate. However, due to its poor agronomic performance and disease susceptibility, more vigorous hybrids created with foreign (Forastero) genotypes have been introduced. These hybrids, named Trinitario, are now widely cultivated 5. Here we report the sequence of a Belizean Criollo plant 6. Consumers have shown an increased interest for high-quality chocolate, and for dark chocolate, containing a higher percentage of cocoa 7. Fine-cocoa production is nevertheless estimated to be less than 5% of the world cocoa production due to the low productivity and disease susceptibility of the traditional fine-flavor cocoa varieties. Therefore, breeding of improved Criollo varieties is important for sustainable production of fine-flavor cocoa. 3.7 million tons of cocoa are produced annually (see URLs). However, fungal, oomycete and viral diseases, as well as insect pests, are responsible for an estimated 30% of harvest losses (see URLs). Like many other tropical crops, knowledge of T. cacao genetics and genomics is limited. To accelerate progress in cocoa breeding and the understanding of its biochemistry, we sequenced and analyzed the genome

Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction. We show that the genomes of ameiotic asexual Meloidogyne are large, polyploid and made of duplicated regions with a high within-species average nucleotide divergence of ~8%. Phylogenomic analysis of the genes present in these duplicated regions suggests that they originated from multiple hybridization events and are thus homoeologs. We found that up to 22% of homoeologous gene pairs were under positive selection and these genes covered a wide spectrum of predicted functional categories. To biologically assess functional divergence, we compared expression patterns of homoeologous gene pairs across developmental life stages using an RNAseq approach in the most economically important asexually-reproducing nematode. We showed that >60% of homoeologous gene pairs display diverged expression patterns. These results suggest a substantial functional impact of the genome structure. Contrasting with high within-species nuclear genome divergence, mitochondrial genome divergence between the three ameiotic asexuals was very low, signifying that these putative hybrids share a recent common maternal ancestor. Transposable elements (TE) cover a ~1.7 times higher proportion of the genomes of the ameiotic asexual Meloidogyne compared to the sexual relative and might also participate in their plasticity. The intriguing parasitic success of asexually-reproducing Meloidogyne species could be partly explained by their TE-rich composite genomes, resulting from allopolyploidization events, and promoting plasticity and functional divergence between gene copies in the absence of sex and meiosis.

Genome sequencing of the model legumes, Medicago truncatula and Lotus japonicus , provides an opportunity for large-scale sequence-based comparison of two genomes in the same plant family. Here we report synteny comparisons between these species, including details about chromosome relationships, large-scale synteny blocks, microsynteny within blocks, and genome regions lacking clear correspondence. The Lotus and Medicago genomes share a minimum of 10 large-scale synteny blocks, each with substantial collinearity and frequently extending the length of whole chromosome arms. The proportion of genes syntenic and collinear within each synteny block is relatively homogeneous. Medicago–Lotus comparisons also indicate similar and largely homogeneous gene densities, although gene-containing regions in Mt occupy 20–30% more space than Lj counterparts, primarily because of larger numbers of Mt retrotransposons. Because the interpretation of genome comparisons is complicated by large-scale genome duplications, we describe synteny, synonymous substitutions and phylogenetic analyses to identify and date a probable whole-genome duplication event. There is no direct evidence for any recent large-scale genome duplication in either Medicago or Lotus but instead a duplication predating speciation. Phylogenetic comparisons place this duplication within the Rosid I clade, clearly after the split between legumes and Salicaceae (poplar).

tschiex@toulouse.inra.fr.