The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

The Pattern of Polymorphism in <i>Arabidopsis thaliana</i>

We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics

The Pattern of Polymorphism in Arabidopsis thaliana

We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics

The pattern of polymorphism in Arabidopsis thaliana.

We resequenced 876 short fragments in a sample of 96 individuals of Arabidopsis thaliana that included stock center accessions as well as a hierarchical sample from natural populations. Although A. thaliana is a selfing weed, the pattern of polymorphism in general agrees with what is expected for a widely distributed, sexually reproducing species. Linkage disequilibrium decays rapidly, within 50 kb. Variation is shared worldwide, although population structure and isolation by distance are evident. The data fail to fit standard neutral models in several ways. There is a genome-wide excess of rare alleles, at least partially due to selection. There is too much variation between genomic regions in the level of polymorphism. The local level of polymorphism is negatively correlated with gene density and positively correlated with segmental duplications. Because the data do not fit theoretical null distributions, attempts to infer natural selection from polymorphism data will require genome-wide surveys of polymorphism in order to identify anomalous regions. Despite this, our data support the utility of A. thaliana as a model for evolutionary functional genomics

Haplotype Sharing on Chromosome 4 among Pairs of Individuals in the Population Samples from Northern Sweden, Central Europe, and the US

<p>The lines indicate regions where the particular pair of accessions share at least five identical adjacent fragments. Within-population comparisons are highlighted in red. The patterns in southern Sweden and in the UK are similar to that in central Europe.</p

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria▿ †

The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria

Population Structure in <i>A. thaliana</i>

<p>Each pie chart represents an accession, and is placed on the map according to origin (some of the population samples were too densely sampled and have been shifted for clarity). Accessions sampled outside Europe have been placed at the correct latitude. The exact origin of the standard lab accession Col-0 is not known. The colors and proportions within each pie chart correspond to the output of Structure in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030196#pbio-0030196-g002" target="_blank">Figure 2</a>. (A) <i>K</i> = 3; (B) <i>K</i> = 8.</p

Characteristics of the Pattern of Polymorphism

<div><p>(A) The allele frequency distribution for synonymous and nonsynonymous SNPs using a sample size of 90 individuals (loci with less than 90 individuals were not used; loci with greater than 90 individuals were randomly culled). For a sample of size <i>n,</i> the expected frequency of SNP loci with a minor allele frequency of <i>i</i> under a standard constant-size population genetics model is . The excess of rare alleles is largely limited to frequencies one and two. </p> <p>(B) The distribution of Tajima's <i>D</i> statistic [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030196#plbi-03-07-01-b27" target="_blank">27</a>] across the sequenced fragments, along with its expected distribution in a constant population (estimated by simulating 1,000 datasets matching the real one in terms of exon/nonexon composition and sample size).</p> <p>(C) The distribution of the level of polymorphism (θ̂<i>_S</i> ) across the sequenced fragments along with its expected distribution (estimated the same way). </p> <p>(D) The level of polymorphism in nonexon sequences as a function of the local gene density (measured in open reading frames per centimorgan).</p> <p>(E) The level of polymorphism in nonexon sequences as a function of the degree of duplication in each fragment (measured as the negative log₁₀ of the BLAST significance for the second-best hit in the genome).</p> <p>The patterns in (D) and (E) are also seen in exons.</p></div

Levels of Polymorphism for Different Classes of Sites

<p>Levels of polymorphism were quantified using two different estimators of the neutral mutation rate <i>θ</i>: θ̂_<i>S</i> , which uses the number of polymorphic sites, and θ̂_P , which uses the average number of pairwise differences [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030196#plbi-03-07-01-b03" target="_blank">3</a>]. </p

Population Structure and Genomic Distributions of Various Statistics

<div><p>(A) Results from Structure under different assumptions about the number of clusters (<i>K</i> = 2,…, 8). Each individual is represented by a line, which is partitioned into <i>K</i> colored segments according to the individual's estimated membership fractions in each of the <i>K</i> clusters. The assignment of each individual is the average across the genome.</p> <p>(B) Results from Structure across Chromosome 1 for <i>K</i> = 3. Each chromosomal segment is colored according to the cluster in which it had the highest probability of membership.</p> <p>(C) A plot showing those fragments that appear to be monophyletic with respect to each of the three clusters identified by Structure.</p> <p>(D) <i>F_ST</i> with respect to the same three clusters (blue solid line) and the lower 95th percentile of <i>F_ST</i> obtained through 1,000 random permutations of the accessions (red dotted line).</p> <p>(E) θ̂<i>_P</i> within each of the three clusters. </p> <p>(F) Tajima's <i>D</i> statistic within each of the three clusters.</p> <p>(G) Results from Structure across Chromosome 1 for <i>K</i> = 8.</p> <p>(H) A plot showing those fragments that appear to be monophyletic with respect to each of these eight clusters.</p> <p>(I) <i>F_ST</i> with respect to these eight clusters.</p></div