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© 2018, Filiault et al. The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea 'Goldsmith', complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analyses reveal extensive allele sharing among species and demonstrate that introgression and selection played a role in the Aquilegia radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differs from that of the rest of the genome - a phenomenon that we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

Author(s): Filiault, D; Ballerini, E; Mandakova, T; Akoz, G; Derieg, N; Schmutz, J; Jenkins, J; Grimwood, J; Shu, S; Hayes, R; Hellsten, U; Barry, K; Yan, J; Mihaltcheva, S; Karafiatova, M; Nizhynska, V; Lysak, M; Hodges, S; Nordborg, M | Abstract: The columbine genus Aquilegia is a classic example of an adaptive radiation, involving a wide variety of pollinators and habitats. Here we present the genome assembly of A. coerulea "Goldsmith", complemented by high-coverage sequencing data from 10 wild species covering the world-wide distribution. Our analysis reveals extensive allele sharing among species, and sheds light on the complex process of radiation. We also present the remarkable discovery that the evolutionary history of an entire chromosome differed from that of the rest of the genome --- a phenomenon which we do not fully understand, but which highlights the need to consider chromosomes in an evolutionary context.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.Chromosome inversions play an important role in local adaptation and speciation1,2, and selectively important inversions have been identified in many species3,4. Selection due to different environmental factors or stages in the life cycle1 may favour inversions carrying locally adapted alleles at several loci. In addition, established inversions are predicted to accumulate selectively important genetic differences, which may contribute to reproductive isolation during speciation1.Although few studies have identified the actual loci that influence selection on inversions2,4,5, rearrangements may be favoured due to gene alterations near breakpoints6, chromatin changes7 or combinations of advantageous, co-adapted alleles8. Inversions suppress recombination, so locally advantageous alleles may segregate together, causing higher fitness than recombinant haplotypes9. Most evolutionary studies have focused on widespread, older inversions, so we have little knowledge of the evolutionary processes that guide their initial increase in frequency. For example, do inversions drift to higher frequency, and then acquire new advantageous mutations after they are common? Or are multiple linked, advantageous alleles captured in a new inversion, allowing them to spread together? Analysis of younger inversions may elucidate the evolutionary forces controlling the initial spread of chromosome inversions, which therefore influence their role in adaptation and speciation4,8.Related species often differ for chromosome inversions that carry locally favoured alleles at multiple loci10,11. A key distinction among models for the evolution of inversions is whether early frequency increase is due to genetic drift or natural selection. Genetic drift might predominate initially, with subsequent accumulation of advantageous variants12. Alternatively, the Kirkpatrick–Barton model9 argues that linked, locally adapted alleles exist first, and subsequently are captured within a new, selectively favoured inversion13. In this ‘inversion-late’ evolutionary sequence1,5, linked quantitative trait loci (QTLs), similar to the ancestral haplotype that gave rise to the inversion, may still exist in non-inverted genotypes9. Here, we test these predictions of the Kirkpatrick–Barton model. First, we introduce ecologically diverged subspecies of Boechera stricta. Next, we examine a young inversion to infer the selective forces controlling its early increase in frequency. Finally, we cross collinear, standard genotypes from the hybrid zone to ask whether old, linked QTLs can be found within the inversion region.

Meiotic recombination rates can vary widely across genomes, with hotspots of intense activity interspersed among cold regions. In yeast, hotspots tend to occur in promoter regions of genes, whereas in humans and mice, hotspots are largely defined by binding sites of the positive-regulatory domain zinc finger protein 9. To investigate the detailed recombination pattern in a flowering plant, we use shotgun resequencing of a wild population of the monkeyflower Mimulus guttatus to precisely locate over 400,000 boundaries of historic crossovers or gene conversion tracts. Their distribution defines some 13,000 hotspots of varying strengths, interspersed with cold regions of undetectably low recombination. Average recombination rates peak near starts of genes and fall off sharply, exhibiting polarity. Within genes, recombination tracts are more likely to terminate in exons than in introns. The general pattern is similar to that observed in yeast, as well as in positive-regulatory domain zinc finger protein 9-knockout mice, suggesting that recombination initiation described here in Mimulus may reflect ancient and conserved eukaryotic mechanisms.

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of 'fossil' transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.

The number of sequenced plant genomes and associated genomic resources is growing rapidly with the advent of both an increased focus on plant genomics from funding agencies, and the application of inexpensive next generation sequencing. To interact with this increasing body of data, we have developed Phytozome (http://www.phytozome.net), a comparative hub for plant genome and gene family data and analysis. Phytozome provides a view of the evolutionary history of every plant gene at the level of sequence, gene structure, gene family and genome organization, while at the same time providing access to the sequences and functional annotations of a growing number (currently 25) of complete plant genomes, including all the land plants and selected algae sequenced at the Joint Genome Institute, as well as selected species sequenced elsewhere. Through a comprehensive plant genome database and web portal, these data and analyses are available to the broader plant science research community, providing powerful comparative genomics tools that help to link model systems with other plants of economic and ecological importance.

The freshwater cnidarian Hydra was first described in 17021 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals2. Today, Hydra is an important model for studies of axial patterning3, stem cell biology4 and regeneration5. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis6 and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann–Mangold organizer, pluripotency genes and the neuromuscular junction.

Placozoans are arguably the simplest free-living animals, possibly evoking an early stage in metazoan evolution, yet their biology is poorly understood. Here we report the sequencing and analysis of the {approx}98 million base pair nuclear genome of the placozoan Trichoplax adhaerens. Whole genome phylogenetic analysis suggests that placozoans belong to a 'eumetazoan' clade that includes cnidarians and bilaterians, with sponges as the earliest diverging animals. The compact genome exhibits conserved gene content, gene structure, and synteny relative to the human and other complex eumetazoan genomes. Despite the apparent cellular and organismal simplicity of Trichoplax, its genome encodes a rich array of transcription factor and signaling pathway genes that are typically associated with diverse cell types and developmental processes in eumetazoans, motivating further searches for cryptic cellular complexity and/or as yet unobserved life history stages.

Across a species range, islands of stressful habitats impose similar selection pressures on isolated populations. It is as yet unclear, when populations respond to these selective pressures, the extent to which this results in convergent genetic evolution and whether convergence is due to independent mutations or shared ancestral variation. We address these questions investigating a classic example of adaptation by natural selection - the colonization of plant species to heavy metal contaminated soils. We use field-based reciprocal transplant experiments to demonstrate that mine alleles at a major copper tolerance QTL, Tol1, are strongly selected in the mine environment, but are neutral, or nearly so, in the off-mine environment. We assemble the genome of a mine adapted genotype and identify regions of this genome in tight genetic linkage to Tol1. We discover Tol1 candidate genes that exhibit significantly large differences in expression between tolerant and non-tolerant genotypes or in allele frequency between mine/off-mine population pairs. We identify a single gene, a multicopper oxidase, which exhibits both large differences in expression and allele frequency. Furthermore, patterns of genetic variation at the five loci with the greatest difference in allele frequency between populations, including the multicopper oxidase, are consistent with selection acting upon beneficial haplotypes that predates the existence of the copper mine habitat. We estimate the age of selected Tol1 haplotype to be at least 1700 years old and was at a frequency of 0.4-0.6% in the ancestral population when mining was initiated 150 years ago. These results suggest that adaptation to the mine habitat routinely occurs via selection on ancestral variation, rather than independent de-novo mutations or migration between populations.

The genome-wide heterozygosity at 9590 genes, all heterozygous in a single Eucalyptus grandis parent tree, was examined in a group of 28 S1 offspring. Heterozygosity ranged from 52-79%, averaging 65.5%, much higher than the 50% expected under random segregation, supporting the occurrence of strong (47%) selection against homozygosity. The expected pattern of heterozygosity from theoretical calculations and simulations for recessive detrimentals (pseudo-overdominance) and intrinsic heterozygote advantage was examined and compared with that observed. The observed patterns are consistent with at least several detrimental loci with large effects on both parental chromosomes of the 11 pairs. It is likely that 100 or more genes, many with substantial effects on viability, are contributing to this inbreeding depression. Although our genome-wide analysis of nearly 10 000 genes strongly suggested that pseudo-overdominance was responsible for the observed high inbreeding depression, heterozygote advantage could not be excluded. Finding inconvertible evidence of the cause of inbreeding depression still presents a difficult challenge. This study is the first theoretical examination of the genomic effect of inbreeding in a forest tree and provides an approach to analyze these data to determine the extent and cause of inbreeding depression across other plant genomes.

Chromosome 5 is one of the largest human chromosomes and contains numerous intrachromosomal duplications, yet it has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding conservation with non-mammalian vertebrates, suggesting that they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-coding genes including the protocadherin and interleukin gene families. We also completely sequenced versions of the large chromosome-5-specific internal duplications. These duplications are very recent evolutionary events and probably have a mechanistic role in human physiological variation, as deletions in these regions are the cause of debilitating disorders including spinal muscular atrophy.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favored alleles at multiple loci. However, it is unknown whether favored mutations slowly accumulate on older inversions or if young inversions spread because they capture preexisting adaptive Quantitative Trait Loci (QTLs). By genetic mapping, chromosome painting and genome sequencing we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation.

Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes-a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes- and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement., 栽培されている柑橘類は、野生祖先種から選択されたもの、またはその交雑種であるが、その祖先種の正体、および柑橘類栽培化に対する寄与には依然として議論がある。今回、柑橘類ゲノム（クレメンタインの高精度標準ハプロイドゲノム、ならびにマンダリン、パメロ、スイートオレンジ、およびサワーオレンジのゲノム）の配列解読および比較を行ったところ、栽培種が2つの祖先種に由来することが明らかにされた。栽培パメロは単一祖先種 Citrus maxima から選択されたことがわかったが、栽培マンダリンは祖先マンダリン種 Citrus reticulata に C. maxima から遺伝子移入が行われたものであった。最も広く栽培されている柑橘類であるスイートオレンジは過去に混種した個体の子孫であるが、サワーオレンジは純粋な C. maxima と C. reticulata とのF1雑種であり、このことは、野生のマンダリンが初期の育種生殖系列の要素であったことを意味している。中国の野生「マンダリン」は C. reticulata とは大きく異なっており、別の未確認の野生柑橘種である可能性が示唆される。ゲノム解析で柑橘類の系統発生を理解することにより、分類学的な関係が解明され、配列本位の遺伝的改良が促進される。

International audience; Eucalypts are the world's most widely planted hardwood trees. Their outstanding diversity, adaptability and growth have made them a global renewable resource of fibre and energy. We sequenced and assembled >94% of the 640-megabase genome of Eucalyptus grandis. Of 36,376 predicted protein-coding genes, 34% occur in tandem duplications, the largest proportion thus far in plant genomes. Eucalyptus also shows the highest diversity of genes for specialized metabolites such as terpenes that act as chemical defence and provide unique pharmaceutical oils. Genome sequencing of the E. grandis sister species E. globulus and a set of inbred E. grandis tree genomes reveals dynamic genome evolution and hotspots of inbreeding depression. The E. grandis genome is the first reference for the eudicot order Myrtales and is placed here sister to the eurosids. This resource expands our understanding of the unique biology of large woody perennials and provides a powerful tool to accelerate comparative biology, breeding and biotechnology.

Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users., Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users.

We search for OVI absorption in a Keck HIRES spectrum of the z=3.62 quasar Q1422+231. Comparison of CIV measurements to cosmological simulations shows that \lya forest absorbers with N_HI > 10^{14.5} have [C/H]~=-2.5, for the UV background spectrum of Haardt & Madau (HM). Lower column density absorption arises in lower density gas, where OVI is the most sensitive metal tracer. Since OVI lines lie at wavelengths contaminated by Lyman series absorption, we interpret our Q1422 results by comparing to artificial spectra drawn from an SPH simulation of a Lambda-dominated CDM model. A search for deep, narrow features in Q1422 yields only a few candidate OVI lines, statistically consistent with the number in artificial spectra with no metals; spectra generated with the HM background and [O/H] >= -2.5 predict too many narrow lines. However, applying the optical depth ratio technique of Songaila (1998), we DO find significant OVI associated with CIV systems; matching Q1422 requires [O/C]~=+0.5, implying [O/H]~=-2.0. Taken together these results imply that (a) the metallicity in the low density IGM is at least a factor of three below that in the overdense regions where CIV absorption is detectable, and (b) oxygen is overabundant in these regions, consistent with the enrichment pattern of old halo stars. If the UV background is heavily truncated above 4 Ry, an implausibly high oxygen overabundance ([O/C]>+2) is required by the data; thus a majority of the volume of the universe must have undergone helium reionization by z=3.(Abridged)

A theory for the structure of isothermal, self-gravitating gas spheres in pressure equilibrium in a softened gravitational field is developed. The one parameter spline softening proposed by Hernquist & Katz (1989) is used. We show that the addition of this extra scale parameter implies that the set of equilibrium solutions constitute a one-parameter family, rather than the one and only one isothermal sphere solution for Newtonian gravity. We demonstrate the perhaps somewhat surprising result that for any finite choice of softening length and temperature, it is possible to deposit an arbitrarily large mass of gas in pressure equilibrium and with a non-singular density distribution inside of r_0 for any r_0 > 0. The theoretical predictions of our models are compared with the properties of the small, massive, quasi-isothermal gas clumps which typically form in numerical Tree-SPH simulations of 'passive' galaxy formation of Milky Way sized galaxies. We find reasonable agreement despite the neglect of rotational support in the models. We comment on whether the hydrodynamical resolution in our numerical simulation of galaxy formation is sufficient, and finally we conclude that one should be cautious, when comparing results of numerical simulations involving gravitational softening and hydrodynamical smoothing, with reality.

We develop a prescription for characterizing the strengths of metal lines associated with Lyman-alpha forest absorbers (LYFAs) of a given neutral hydrogen column density N_HI and metallicity [Fe/H]. This Line Observability Index (LOX) is line-specific and translates, for weak lines, into a measure of the equivalent width. It can be evaluated quickly for thousands of transitions within the framework of a given model of the Lyman-alpha forest, providing a ranking of the lines in terms of their strengths and enabling model builders to select the lines that should be detectable in observed spectra of a given resolution and signal-to-noise ratio. We compute the LOX for a large number of elements and transitions in two cosmological models of the Lyman-alpha forest at z=3 derived from a hydrodynamic simulation of structure formation, and we discuss how the LOX depends on redshift and on model parameters such as the mean baryonic density and radiation field. We find that the OVI (1032,1038) doublet is the best probe of the metallicity in low column density LYFAs N_{HI} \approx 10^{14.5} cm^{-2}). Metallicities down to [O/H] \sim -3 ([Fe/H] \sim -3.5 with the assumed [O/Fe] ratio) yield OVI absorption features that should be detectable in current high-quality spectra, provided that the expected position of the OVI feature is not contaminated by HI absorption. The strongest transitions in lower ionisation states of oxygen are OV(630), OIV(788), and OIII(833), and are likely to be detected with next generation UV instruments. Of the lines with rest wavelengths \lambda_r > 1216, which can potentially be observed redwards of the \lya forest, the CIV(1548,1551) doublet is expected to dominate in all LYFAs, regardless of the value of N_HI.

Summary • Plant population genomics informs evolutionary biology, breeding, conservation and bioenergy feedstock development. For example, the detection of reliable phenotype–genotype associations and molecular signatures of selection requires a detailed knowledge about genome-wide patterns of allele frequency variation, linkage disequilibrium and recombination. • We resequenced 16 genomes of the model tree Populus trichocarpa and genotyped 120 trees from 10 subpopulations using 29 213 single-nucleotide polymorphisms. • Significant geographic differentiation was present at multiple spatial scales, and range-wide latitudinal allele frequency gradients were strikingly common across the genome. The decay of linkage disequilibrium with physical distance was slower than expected from previous studies in Populus, with r 2 dropping below 0.2 within 3–6 kb. Consistent with this, estimates of recent effective population size from linkage disequilibrium (Ne 4000–6000) were remarkably low relative to the large census sizes of P. trichocarpa stands. Fine-scale rates of recombination varied widely across the genome, but were largely predictable on the basis of DNA sequence and methylation features. • Our results suggest that genetic drift has played a significant role in the recent evolutionary history of P. trichocarpa. Most importantly, the extensive linkage disequilibrium detected suggests that genome-wide association studies and genomic selection in undomesticated populations may be more feasible in Populus than previously assumed.

We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

International audience; Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.

International audience; Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

Going Multicellular The volvocine algae include both the unicellular Chlamydomonas and the multicellular Volvox , which diverged from one another 50 to 200 million years ago. Prochnik et al. (p. 223 ) compared the Volvox genome with that of Chlamydomonas to identify any genomic innovations that might have been associated with the transition to multicellularity. Size changes were observed in several protein families in Volvox , but, overall, the Volvox genome and predicted proteome were highly similar to those of Chlamydomonas . Thus, biological complexity can arise without major changes in genome content or protein domains.

Frog Genome The African clawed frog Xenopus tropicalis is the first amphibian to have its genome sequenced. Hellsten et al. (p. 633 , see the cover) present an analysis of a draft assembly of the genome. The genome of the frog, which is an important model system for developmental biology, encodes over 20,000 protein-coding genes, of which more than 1700 genes have identified human disease associations. Detailed comparison of the content of protein-coding genes with other tetrapods—human and chicken—reveals extensive shared synteny, occasionally spanning entire chromosomes.

Models of the formation and subsequent viscous evolution of galactic discs are examined. The discs are assumed to form as described by the cooling flow solutions of Sommer-Larsen. The star formation rate is assumed to be given by the prescription of Wyse & Silk, thereby relaxing the requirement of proportionality between t * ant t v used in previous works. The resulting stellar and gas profiles are found to resemble well the observed profiles of disc galaxies. Gradients in gas and star metallicities are also calculated. Values around -0.05 dex/kpc are obtained for the gas metallicity, in fine agreement with the observed [O/H] gradient in our Galaxy. The exact magnitude of these gradients depends only weakly on the model parameters

Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create achromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70percent more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78percent of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75percent of the genes present in multiple copies. The two duplication events were followed by genediversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approximately 520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution.

Choanoflagellates are the closest known relatives of metazoans. To discover potential molecular mechanisms underlying the evolution of metazoan multicellularity, we sequenced and analysed the genome of the unicellular choanoflagellate Monosiga brevicollis. The genome contains approximately 9,200 intron-rich genes, including a number that encode cell adhesion and signalling protein domains that are otherwise restricted to metazoans. Here we show that the physical linkages among protein domains often differ between M. brevicollis and metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellate and metazoan lineages. The completion of the M. brevicollis genome allows us to reconstruct with increasing resolution the genomic changes that accompanied the origin of metazoans.

Sea anemones are seemingly primitive animals that, along with corals, jellyfish, and hydras, constitute the oldest eumetazoan phylum, the Cnidaria. Here, we report a comparative analysis of the draft genome of an emerging cnidarian model, the starlet sea anemone Nematostella vectensis . The sea anemone genome is complex, with a gene repertoire, exon-intron structure, and large-scale gene linkage more similar to vertebrates than to flies or nematodes, implying that the genome of the eumetazoan ancestor was similarly complex. Nearly one-fifth of the inferred genes of the ancestor are eumetazoan novelties, which are enriched for animal functions like cell signaling, adhesion, and synaptic transmission. Analysis of diverse pathways suggests that these gene “inventions” along the lineage leading to animals were likely already well integrated with preexisting eukaryotic genes in the eumetazoan progenitor.

We report the draft genome of the black cottonwood tree, Populus trichocarpa . Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs of duplicated genes from that event survived in the Populus genome. A second, older duplication event is indistinguishably coincident with the divergence of the Populus and Arabidopsis lineages. Nucleotide substitution, tandem gene duplication, and gross chromosomal rearrangement appear to proceed substantially more slowly in Populus than in Arabidopsis. Populus has more protein-coding genes than Arabidopsis , ranging on average from 1.4 to 1.6 putative Populus homologs for each Arabidopsis gene. However, the relative frequency of protein domains in the two genomes is similar. Overrepresented exceptions in Populus include genes associated with lignocellulosic wall biosynthesis, meristem development, disease resistance, and metabolite transport.

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for ∼20% of global carbon fixation. We report the 34 million–base pair draft nuclear genome of the marine diatom Thalassiosira pseudonana and its 129 thousand–base pair plastid and 44 thousand–base pair mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, use of a range of nitrogenous compounds, and a complete urea cycle, all attributes that allow diatoms to prosper in aquatic environments.

Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu.

We use numerical simulations of structure formation in a Cold Dark Matter model to predict the absorption lines in the soft X-rays produced by heavy elements in the shock-heated intergalactic medium at low redshift. The simulation incorporates a model for metal production in galaxies and the subsequent dispersion of the metals to the intergalactic medium. We analyze in particular absorption lines produced by oxygen, and calculate the ionization stage taking into account the observed X-ray background at the present time. We find that oxygen is fully ionized by the X-ray background in low-density voids, and is mostly in the form of OVII and OVIII in the sheets and filamentary regions. Strong absorption lines of OVII and OVIII with equivalent widths W ~ 100 km/s are produced in filamentary regions of overdensities ~ 100 and temperatures ~ 10^6 K, located in the outskirts of groups and clusters of galaxies. The OVII line at E = 574 eV is generally the strongest one in these systems. Our model predicts that any X-ray source (such as a quasar) should typically show about one OVII absorption line with W > 100 km/s in the interval from z=0 to z=0.3. These lines could be detected with the upcoming generation of X-ray telescopes, and their origin in intervening systems could be confirmed by the association with groups of galaxies and X-ray emitting halos near the line-of-sight at the same redshift. The hot intergalactic medium may be one of the main reservoirs of baryons in the present universe, and the heavy element X-ray absorption lines offer a promising possibility of detecting this new component in the near future., Accepted by ApJ. The full resolution color GIF version of Fig.2 is included

Effects of gravitational softening on the global structure of self-gravitating disks in centrifugal equillibrium are examined in relation to hydrodynamical/gravitational simulations. The one-parameter spline softening proposed by Hernquist & Katz is used. It is found that if the characteristic size of a disk, r, is comparable or less than the gravitational softening length, epsilon, then the cross section of the simulated disk is significantly larger than that of a no-softening (Newtonian) disk with the same mass and angular momentum. We furthermore demonstrate that if r is less than or about epsilon/2 then the scaling relation r proportional to epsilon^3/4 holds for a given mass and specific angular momentum distribution with mass. Finally we compare some of the theoretical results obtained in this and a previous paper with the results of numerical Tree-SPH simulations and find qualitative agreement., 9 pages, 3 figures

We study metal line absorption of CIV, CII, SiIV, and NV at redshifts z=3.5 to z=2 within the framework of a cosmological model for the Lyman alpha forest, comparing the results of numerical simulations to recent observations by Songaila & Cowie (1996, SC). In agreement with Rauch, Haehnelt & Steinmetz (1996), we find that the observed mean value of the CIV/HI ratio around z=3 is reproduced if a uniform metallicity of [C/H] = -2.5 is assumed in our model, but that the observed scatter in this ratio is larger than predicted, implying a scatter in the metallicity of the absorbing systems of roughly an order of magnitude. We further argue that absorbers with relatively low column densities (log(N_HI) < 15) likely have a mean metallicity [C/H] less than -2.5, a result which is basically independent of the model considered, and similar to what is predicted in the simulations by Gnedin & Ostriker (1997). Our model predicts no significant evolution in the mean values of metal line column densities between z=3.5 and z=2. Comparison of the predicted and observed numbers of SiIV and NV systems suggests that the photoionizing background radiation field around z=3 is somewhat softer than that proposed by Haardt & Madau (1996). Our model does not account for the increase in the SiIV/CIV ratio at z=3.2 found by SC. While SC suggested that the increase could be explained by a softening of the radiation field due to HeII absorption at z > 3, such a modification does not raise the mean value of SiIV/CIV in our simulation because it shifts numerous weak SiIV systems to just above the detection limit, thus keeping the mean column density of observable SiIV systems low., 14 pages Latex + 5 figures

An intron is an extended genomic feature whose function requires multiple constrained positions—donor and acceptor splice sites, a branch point, a polypyrimidine tract and suitable splicing enhancers—that may be distributed over hundreds or thousands of nucleotides. New introns are therefore unlikely to emerge by incremental accumulation of functional sub-elements. Here we demonstrate that a functional intron can be created de novo in a single step by a segmental genomic duplication. This experiment recapitulates in vivo the birth of an intron that arose in the ancestral jawed vertebrate lineage nearly half-a-billion years ago., The appearance of a new intron that splits an exon without disrupting the corresponding peptide sequence is a rare event in vertebrate genomes. Hellsten et al. demonstrate that, under certain circumstances, a functional intron can be produced in a single step by segmental genomic duplication.

Nature 463, 178–183 (2010) During resubmission of this work, a paper was published1 that used a comparative genomics approach between soybean and maize to show that a single-base mutation in chromosome 19 accounts for the duplicate recessive epistasis needed to greatly reduce phytate production in soybean seed.

Background Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication. Results We identified 2218 gene triplets in which a single gene in X. tropicalis corresponds to precisely two co-orthologous genes in X. laevis – the largest such collection published from any duplication event in animals. Analysis of these triplets reveals accelerated evolution or relaxation of constraint in the peptides of the X. laevis pairs compared with the orthologous sequences in X. tropicalis and other vertebrates. In contrast, single-copy X. laevis genes do not show this acceleration. Duplicated genes can differ substantially in expression levels and patterns. We find no significant difference in gene content in the duplicated set, versus the single-copy set based on molecular and biological function ontologies. Conclusion These results support a scenario in which duplicate genes are retained through a process of subfunctionalization and/or relaxation of constraint on both copies of an ancestral gene.