BackgroundThe size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination.ResultsWe develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome.ConclusionsIn addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.

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BackgroundGenome evolution in the gymnosperm lineage of seed plants has given rise to many of the most complex and largest plant genomes, however the elements involved are poorly understood.Methodology/Principal Findings Gymny is a previously undescribed retrotransposon family in Pinus that is related to Athila elements in Arabidopsis. Gymny elements are dispersed throughout the modern Pinus genome and occupy a physical space at least the size of the Arabidopsis thaliana genome. In contrast to previously described retroelements in Pinus, the Gymny family was amplified or introduced after the divergence of pine and spruce (Picea). If retrotransposon expansions are responsible for genome size differences within the Pinaceae, as they are in angiosperms, then they have yet to be identified. In contrast, molecular divergence of Gymny retrotransposons together with other families of retrotransposons can account for the large genome complexity of pines along with protein-coding genic DNA, as revealed by massively parallel DNA sequence analysis of Cot fractionated genomic DNA.Conclusions/SignificanceMost of the enormous genome complexity of pines can be explained by divergence of retrotransposons, however the elements responsible for genome size variation are yet to be identified. Genomic resources for Pinus including those reported here should assist in further defining whether and how the roles of retrotransposons differ in the evolution of angiosperm and gymnosperm genomes.

Mutation of PIK3CA, the gene coding for the p110a catalytic subunit of phosphoinositide 3-kinase (PI3K), has been reported in a limited range of human tumors. We now report that PIK3CA is also mutated in esophageal tumors. Single-strand conformational polymorphism (SSCP) and denaturing high-performance liquid chromatography (DHPLC) were used to screen all 20 exons of PIK3CA in 101 samples from 95 individuals with esophageal cancer and/or Barrett's esophagus. Somatic mutation of PIK3CA was detected in 4 of 35 (11.8%) of esophageal squamous cell carcinomas (SCC) and 3 of 50 (6%) adenocarcinomas. No mutations were detected in any of 17 samples of Barrett's esophagus. For PIK3CB, we screened exons 11 and 22, which code for the regions corresponding to the exon 9 and 20 mutational ÔhotspotsÕ of PIK3CA. No somatic changes were detected in PIK3CB This study extends previous observations in other tumor types by demonstrating the presence of somatic PIK3CA mutations in both SCC and adenocarcinoma of the esophagus, thus implicating the PI3K pathway in the initiation and/or progression of esophageal cancers. ' 2005 Wiley-Liss, Inc.Key words: phosphatidylinositide 3 0 -kinase; mutation; oncogene; esophageal cancer; Barrett's esophagus Phosphatidylinositide 3-kinases (PI3K) are a ubiquitous family of lipid kinases that catalyse the phosphorylation of phosphatidylinositol (PI), PI(4)P and PI(4,5)P 2 forming PI(3)P, PI(3,4)P 2 and PI(3,4,5)P 3 , respectively. 1 These lipid products are then able to activate a variety of downstream targets that regulate a wide range of important cellular processes, including cell proliferation, migration and survival, oncogenic transformation and intracellular trafficking of proteins. Of the PI3Ks, the most extensively studied are the class 1A sub-group, which exist as heterodimers consisting of a unique catalytic subunit (p110a, b, and d) along with one of a number of shared regulatory subunits (p85a, p85b and p55g). 1,2 Numerous genetic and functional studies have clearly established a fundamental role for the PI3K pathway in the development of neoplasia. Amplification of the PIK3CA gene (which codes for the p110a catalytic subunit of PI3K) has been reported in a number of different tumor types. 3,4 We have previously reported activating somatic mutations in the p85a regulatory subunit of PI3K (PIK3R1) in primary ovarian and colon tumors, 5 while more recently we, and others, have demonstrated a high frequency of somatic mutations in PIK3CA in a limited selection of tumor types. [6][7][8][9][10][11] Therapeutic strategies that target PI3K or its downstream targets such as Akt and mTOR are beginning to show considerable promise as potential new anticancer treatments. [12][13][14] In addition, there is increasing evidence that PI3K inhibitors can enhance the efficacy of conventional chemotherapeutic agents in both in vitro and in vivo models. 13,14 Since tumors harbouring mutations in PI3K are likely to be more susceptible to the therapeutic actions of agents that target the PI3K pathway, it i...

This accessible, yet authoritative book shows how the pandemic is a syndemic of disease and inequality. Drawing on international data and accounts, it argues that these inequalities are a political choice and we need to learn quickly to prevent growing inequality and to reduce health inequalities in the future.

Studies of symbioses have traditionally focused on explaining one-to-one interactions between organisms. In reality, symbioses are often much more dynamic. They can involve many interacting members, and change depending on context. In studies of the ambrosia symbiosis-the mutualism between wood borer beetles and fungi-two variables have introduced uncertainty when explaining interactions: imprecise symbiont identification, and disregard for anatomical complexity of the insects. The black twig borer, Xylosandrus compactus Eichhoff, is a globally invasive ambrosia beetle that infests >200 plant species. Despite many studies on this beetle, reports of its primary symbionts are conflicting. We sampled adult X. compactus and infested plant material in central Florida to characterize the fungal symbiont community using dilution series, beetle partitioning, and DNA-based identification. X. compactus was consistently associated with two fungal taxa, Fusarium spp. and Ambrosiella xylebori Multivariate analyses revealed that A. xylebori was strongly associated with the beetle mycangium while Fusarium spp. were associated with the abdomen and external surfaces. The Fusarium spp. carried by X. compactus are not members of the Ambrosia Fusarium Clade, and are probably not mutualists. Fungal community composition of the mycangium was less variable than external body surfaces, thus providing a more consistent fungal inoculum. This is the first report of spatial partitioning as a mechanism for maintenance of a multimember ambrosia fungus community. Our results provide an explanation for discrepancies among previous reports, and suggest that conflicting results are not due to differences in symbiont communities, but due to inconsistent and incomplete sampling.

Rust fungi are a group of fungal pathogens that cause some of the world's most destructive diseases of trees and crops. A shared characteristic among rust fungi is obligate biotrophy, the inability to complete a lifecycle without a host. This dependence on a host species likely affects patterns of gene expansion, contraction, and innovation within rust pathogen genomes. The establishment of disease by biotrophic pathogens is reliant upon effector proteins that are encoded in the fungal genome and secreted from the pathogen into the host's cell apoplast or within the cells. This study uses a comparative genomic approach to elucidate putative effectors and determine their evolutionary histories. We used OrthoMCL to identify nearly 20,000 gene families in proteomes of 16 diverse fungal species, which include 15 basidiomycetes and one ascomycete. We inferred patterns of duplication and loss for each gene family and identified families with distinctive patterns of expansion/contraction associated with the evolution of rust fungal genomes. To recognize potential contributors for the unique features of rust pathogens, we identified families harboring secreted proteins that: (i) arose or expanded in rust pathogens relative to other fungi, or (ii) contracted or were lost in rust fungal genomes. While the origin of rust fungi appears to be associated with considerable gene loss, there are many gene duplications associated with each sampled rust fungal genome. We also highlight two putative effector gene families that have expanded in Cqf that we hypothesize have roles in pathogenicity.

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