Gene map of the plastid chromosome of <i>Lathraea squamaria</i>.

<p>Genes shown inside the circle are transcribed clockwise; those outside the circle are transcribed counterclockwise. The large single copy region (LSC) and the small single copy region (SSC) are separated by two inverted repeats (IRa and IRb). Pseudogenes are marked by Ψ.</p

Estimates of divergence time of 17 taxa on the ML tree.

<p>The values at the nodes represent mean ages in million years, and the 95% highest posterior density (HPD) interval is indicated by a blue bar. At terminal branches, substitution rates (per site per year) are provided. Nodes where parasitism and holoparasitism evolved are indicated by blue and yellow arrows, respectively. Age constraints were applied to nodes marked by red dots.</p

Comparison of estimated here divergence ages for four nodes and the Orobanchaceae crown group age (CGA) with reported ages from other studies and with the Orobanchaceae stem group age (SGA).

<p>Mean and 95% HPD interval of each estimation (when provided) is shown with a reference given in brackets. Asterisks mean this study.</p

Characteristics of <i>Lathraea squamaria</i> plastid genome.

<p>Characteristics of <i>Lathraea squamaria</i> plastid genome.</p

Complete Plastid Genome of the Recent Holoparasite <i>Lathraea squamaria</i> Reveals Earliest Stages of Plastome Reduction in Orobanchaceae

<div><p>Plants from the family Orobanchaceae are widely used as a model to study different aspects of parasitic lifestyle including host–parasite interactions and physiological and genomic adaptations. Among the latter, the most prominent are those that occurred due to the loss of photosynthesis; they include the reduction of the photosynthesis-related gene set in both nuclear and plastid genomes. In Orobanchaceae, the transition to non-photosynthetic lifestyle occurred several times independently, but only one lineage has been in the focus of evolutionary studies. These studies included analysis of plastid genomes and transcriptomes and allowed the inference of patterns and mechanisms of genome reduction that are thought to be general for parasitic plants. Here we report the plastid genome of <i>Lathraea squamaria</i>, a holoparasitic plant from Orobanchaceae, clade Rhinantheae. We found that in this plant the degree of plastome reduction is the least among non-photosynthetic plants. Like other parasites, <i>Lathraea</i> possess a plastome with elevated absolute rate of nucleotide substitution. The only gene lost is <i>petL</i>, all other genes typical for the plastid genome are present, but some of them–those encoding photosystem components (22 genes), cytochrome b₆/f complex proteins (4 genes), plastid-encoded RNA polymerase subunits (2 genes), ribosomal proteins (2 genes), <i>ccsA</i> and <i>cemA</i>–are pseudogenized. Genes for cytochrome b₆/f complex and photosystems I and II that do not carry nonsense or frameshift mutations have an increased ratio of non-synonymous to synonymous substitution rates, indicating the relaxation of purifying selection. Our divergence time estimates showed that transition to holoparasitism in <i>Lathraea</i> lineage occurred relatively recently, whereas the holoparasitic lineage Orobancheae is about two times older.</p></div

Phylogenetic tree of the 17 taxa inferred by the maximum likelihood approach.

<p>Bootstrap support values are provided at the nodes. The scale bar corresponds to 0.1 substitution per site.</p

Table_1_Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia.xlsx

<p>While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the newly sequenced genome of Holospora curviuscula, a macronuclear symbiont of Paramecium bursaria, and known genomes of other Holospora species shows that even though all Holospora spp. can persist outside the host, they cannot synthesize most of the essential small molecules, such as amino acids, and lack some central energy metabolic pathways, including glycolysis and the citric acid cycle. As the main energy source, Holospora spp. likely rely on nucleotides pirated from the host. Holospora-specific genes absent from other Rickettsiales are possibly involved in the lifestyle switch from the infectious to the reproductive form and in cell invasion.</p

Fast Evolution from Precast Bricks: Genomics of Young Freshwater Populations of Threespine Stickleback <i>Gasterosteus aculeatus</i>

<div><p>Adaptation is driven by natural selection; however, many adaptations are caused by weak selection acting over large timescales, complicating its study. Therefore, it is rarely possible to study selection comprehensively in natural environments. The threespine stickleback (<i>Gasterosteus aculeatus</i>) is a well-studied model organism with a short generation time, small genome size, and many genetic and genomic tools available. Within this originally marine species, populations have recurrently adapted to freshwater all over its range. This evolution involved extensive parallelism: pre-existing alleles that adapt sticklebacks to freshwater habitats, but are also present at low frequencies in marine populations, have been recruited repeatedly. While a number of genomic regions responsible for this adaptation have been identified, the details of selection remain poorly understood. Using whole-genome resequencing, we compare pooled genomic samples from marine and freshwater populations of the White Sea basin, and identify 19 short genomic regions that are highly divergent between them, including three known inversions. 17 of these regions overlap protein-coding genes, including a number of genes with predicted functions that are relevant for adaptation to the freshwater environment. We then analyze four additional independently derived young freshwater populations of known ages, two natural and two artificially established, and use the observed shifts of allelic frequencies to estimate the strength of positive selection. Adaptation turns out to be quite rapid, indicating strong selection acting simultaneously at multiple regions of the genome, with selection coefficients of up to 0.27. High divergence between marine and freshwater genotypes, lack of reduction in polymorphism in regions responsible for adaptation, and high frequencies of freshwater alleles observed even in young freshwater populations are all consistent with rapid assembly of <i>G. aculeatus</i> freshwater genotypes from pre-existing genomic regions of adaptive variation, with strong selection that favors this assembly acting simultaneously at multiple loci.</p></div

Map showing the locations of populations studied.

<p>Please see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004696#pgen-1004696-t001" target="_blank">Table 1</a> for description of sampling sites.</p

Biliary Microbiota, Gallstone Disease and Infection with <i>Opisthorchis felineus</i>

<div><p>Background</p><p>There is increasing interest in the microbiome of the hepatobiliary system. This study investigated the influence of infection with the fish-borne liver fluke, <i>Opisthorchis felineus</i> on the biliary microbiome of residents of the Tomsk region of western Siberia.</p><p>Methodology/Principal Findings</p><p>Samples of bile were provided by 56 study participants, half of who were infected with <i>O</i>. <i>felineus</i>, and all of who were diagnosed with gallstone disease. The microbiota of the bile was investigated using high throughput, Illumina-based sequencing targeting the prokaryotic 16S rRNA gene. About 2,797, discrete phylotypes of prokaryotes were detected. At the level of phylum, bile from participants with opisthorchiasis showed greater numbers of Synergistetes, Spirochaetes, Planctomycetes, TM7 and Verrucomicrobia. Numbers of > 20 phylotypes differed in bile of the <i>O</i>. <i>felineus</i>-infected compared to non-infected participants, including presence of species of the genera <i>Mycoplana</i>, <i>Cellulosimicrobium</i>, <i>Microlunatus</i> and <i>Phycicoccus</i>, and the Archaeans genus, <i>Halogeometricum</i>, and increased numbers of <i>Selenomonas</i>, <i>Bacteroides</i>, <i>Rothia</i>, <i>Leptotrichia</i>, <i>Lactobacillus</i>, <i>Treponema</i> and <i>Klebsiella</i>.</p><p>Conclusions/Significance</p><p>Overall, infection with the liver fluke <i>O</i>. <i>felineus</i> modified the biliary microbiome, increasing abundance of bacterial and archaeal phylotypes.</p></div