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Various researches are conducted to study the genome characteristics of three closely related clades of Frankia sp. strains, which are commonly recognized as the facultative symbionts forming nitrogen-fixing root nodules in several plants. The results demonstrate that such soil bacteria can undergo major genome expansions, as well as reductions, as they respond to new environments in the context of their symbioses and hence reflect host range and host plant biogeography.

Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobataand Pocilloporacf. effusa,with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4and modelling5approaches have shown that intra-organismal genetic heterogeneity can be selected for6and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.

Comantheraand Syngonanthus(Eriocaulaceae) are monocotyledonous herbs that occur mainly in neotropical savannas in the Guiana Shield and in southeastern Brazil, with a few species in Africa. Phylogenetic relationships in Syngonanthusand Comantheraare still unresolved and have not yet been assessed using a broad and comprehensive sampling. The present study aimed to test the monophyly of both genera and their putative infrageneric taxa and to evaluate their taxonomy and supporting synapomorphies in the light of a resolved phylogeny. The resulting phylogenetic hypotheses were then used to infer the biogeographical histories of the taxa, especially in Brazil. Molecular analyses based on plastid (trnL-F, psbA-trnH) and nuclear (ITS) markers using parsimony and Bayesian inference were conducted on 62 species belonging to the ingroup. Syngonanthus s.l. (composed of Syngonanthus, Philodiceand Comanthera), Syngonanthuss.str. (including Philodice), Comantheraand both of its subgenera were retrieved as monophyletic, strongly supported by molecular and morphological apomorphies. However Syngonanthussect. Carphocephalusappeared polyphyletic, and its species were embedded within a paraphyletic S. sect. Syngonanthus. Within Comanthera, clades restricted to equatorial savannas appeared to be sisters to clades restricted to southeastern Brazil, especially in the Espinhaço Range, with a disjunct pattern between Bahia and Minas Gerais states. Within Syngonanthuss.str., Andean and African species appeared embedded in Brazilian clades, but resolution and support within the genus must be improved in future research.

Abstract: A cDNA library was constructed from leaves of a cold-acclimated Eucalyptus gunnii elite clone and 13,056 ESTs were sequenced. When the 5,457 unique sequences were compared with Arabidopsis, rice, and poplar datasets, more than 38% of no-hits were found and the best annotation was provided by the woody perennial poplar database. However, among the 62% of sequences that could be annotated, the vast majority (87.5%) was found to be common to the four compared plant species, which shows how highly conserved this gene pool is across the plant kingdom. When the distribution of the annotated sequences was studied according to the Gene Ontology classification, some typical features of the dehydrative stress transcriptome were observed. In particular, genes from sugar metabolism and, above all, those induced by stress or external stimuli were well represented (6% in total). In addition, the library was found to contain a substantial number of ESTs encoding putative transcription factors including CBF (CRT-Binding Factor). The enrichment of this library with stress-related genes was strongly suggested by the high redundancy (up to 300 ESTs) of several genes known to be involved in cell protection such as the PCP (Pollen Coat Protein), Lti6b (Low temperature induced) or metallothionein. It was further confirmed by demonstrating the cold induction of a set of representative genes through Real Time-PCR. All these characteristics make this Eucalyptus EST collection very suitable for investigating the molecular basis of cold tolerance in a woody perennial and for isolating important or new candidate frost tolerance genes.

AbstractRecent investigations in Guinea and Ivory Coast showed that Mus(Nannomys) are hosts of new arenaviruses. However, the taxonomy and biogeography of the western pygmy mice are poorly known, as this genus contains many cryptic species. To improve our taxonomic knowledge on this subgenus and its distribution range in West Africa, we performed a molecular, cytogenetical and morphological study of all Mus(Nannomys) species in this part of Africa. This approach allowed us to detect five species in Guinea (Mus mattheyi, M. minutoides, M. setulosus, M. baoulei, M. musculoides) and four (M. minutoides, M. setulosus, M. baoulei, M. musculoides) in Ivory Coast. Our molecular results confirm the validity of M. baouleiand the extended distribution range of M. mattheyi. We also observed a high degree of genetic differentiation between and within these species, especially within the M. setulosusclade which may be a species complex. The canonical analyses on the craniometrical and external morphological features of the sequenced specimens are insufficient to perfectly separate the studied species. Nevertheless, our results confirm that M. setulosusand M. baouleiare the largest Musspecies that occur in Guinea and Ivory Coast. M. baouleican be distinguished by its short tail and M. setulosusby an enlarged and bilobated lower molar (M3). Among the smaller species, M. musculoidesis difficult to identify using morphological data alone, but differences in tail length proportions, size of tympanic bullae, the length and shape of the upper dental row allow identification of this species with some confidence. Our results allow us to provide some conclusions about the distribution ranges of the studied Mus(Nannomys)spp. in both countries and to discuss their presence in relation to vegetation, habitat and human settlements.

A major fungal invasion was discovered in the prehistoric painted cave of Lascaux in France in Sep 2001. At least three species of the Fusarium solanicomplex were isolated and identified with a portion of the translation elongation factor 1α gene (EF-1α), a portion of the nuclear large subunit rDNA (LSU) and nuclear ribosomal intergenic spacer region (ITS). This study represents the first time that Fusariumspecies have been reported from a cave containing prehistoric paintings. Significant interspecific molecular variability was observed, suggesting that there might have been repeated introduction of the species, possibly carried by water from soils above the cave.

Due to the presence of genetically well-defined sex chromosomes, with a relatively restricted sex-determination region containing markers identified at the molecular level, the platyfish Xiphophorus maculatus is one of the best models for the positional cloning of a master sex-determining gene in fish. Both male and female heterogametes and three different types of sex chromosomes have been described in the platyfish, with several loci involved in pigmentation, melanoma formation, and sexual maturity closely linked to the master sex-determining locus. Using the melanoma-inducing oncogene Xmrk, its protooncogenic counterpart egfrb, as well as other X- and Y-linked molecular markers, bacterial artificial chromosome (BAC) contigs have been assembled for the sex-determining region of X. maculatus, which was mapped by fluorescent in situ hybridization to the subtelomeric region of the sex chromosomes. Initial sequence analysis of these contigs revealed several gene candidates and uncovered syntenies with different mammalian and chicken autosomes, supporting an independent origin of sex chromosomes in platyfish and tetrapods. Strikingly, the sex determination region of the platyfish is very instable and frequently undergoes duplications, deletions, and transpositions. This instability might be linked to the high genetic variability affecting sex determination and other sex-linked traits in Xiphophorus.

Monitor lizards are emblematic reptiles that are widely distributed in the Old World. Although relatively well studied in vertebrate research, their biogeographic history is still controversial. We constructed a molecular dataset for 54 anguimorph species, including representatives of all families with detailed sampling of the Varanidae (38 species). Our results are consistent with an Asian origin of the Varanidae followed by a dispersal to Africa 41 (49–33) Ma, possibly via an Iranian route. Another major event was the dispersal of monitors to Australia in the Late Eocene–Oligocene 32 (39–26) Ma. This divergence estimate adds to the suggestion that Australia was colonized by several squamate lineages prior to the collision of the Australian plate with the Asian plate starting 25 Ma.

Bathycoccus prasinos is an extremely small cosmopolitan marine green alga whose cells are covered with intricate spider's web patterned scales that develop within the Golgi cisternae before their transport to the cell surface. The objective of this work is to sequence and analyze its genome, and to present a comparative analysis with other known genomes of the green lineage.

Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease.

Phlebotomus chabaudi Croset, Abonnenc & Rioux, 1970 and Phlebotomus riouxi Depaquit, Killick-Kendrick & Léger, 1998 (Diptera: Psychodidae) are closely related species of phlebotomine sand flies, the females of which are suspected of transmitting Leishmania killicki Rioux, Lanotte, and Pratlong 1986 in Tunisia. Although males of these species are distinguishable by the number and size of setae on the basal lobe of the coxite, morphologically differential characters between the females are blurred. A molecular study, based on 40 Algerian and Tunisian specimens, was conducted to distinguish females of these two species. Alignment of the cytochrome c oxidase I (COI) sequences and their analysis by using neighbor-joining and maximum likelihood showed the separation of P. chabaudi and P. riouxi, irrespective of intraspecific variability. Both COI and cytochrome b have been tested as molecular identification tools. Single strand conformation polymorphism analysis did not distinguish these two species, whereas restriction fragment length polymorphism can be applied to identify P. chabaudi and P. riouxi for surveillance purposes.

Background The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions and sexual development.Results We present a 10X draft sequence of P. anserina genome, linked to the sequences of a large expressed sequence tag collection. Similar to higher eukaryotes, the P. anserina transcription/splicing machinery generates numerous non-conventional transcripts. Comparison of the P. anserina genome and orthologous gene set with the one of its close relatives, Neurospora crassa, shows that synteny is poorly conserved, the main result of evolution being gene shuffling in the same chromosome. The P. anserina genome contains fewer repeated sequences and has evolved new genes by duplication since its separation from N. crassa, despite the presence of the repeat induced point mutation mechanism that mutates duplicated sequences. We also provide evidence that frequent gene loss took place in the lineages leading to P. anserina and N. crassa. P. anserina contains a large and highly specialized set of genes involved in utilization of natural carbon sources commonly found in its natural biotope. It includes genes potentially involved in lignin degradation and efficient cellulose breakdown.Conclusion The features of the P. anserina genome indicate a highly dynamic evolution since the divergence of P. anserina and N. crassa, leading to the ability of the former to use specific complex carbon sources that match its needs in its natural biotope.