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Genome evolution

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https://www.readbyqxmd.com/read/28231417/genetic-and-genomic-evidence-of-niche-partitioning-and-adaptive-radiation-in-mountain-pine-beetle-fungal-symbionts
#1
Dario I Ojeda Alayon, Clement K M Tsui, Nicolas Feau, Arnaud Capron, Braham Dhillon, Yiyuan Zhang, Sepideh Massoumi Alamouti, Celia K Boone, Allan L Carroll, Janice E K Cooke, Amanda D Roe, Felix A H Sperling, Richard C Hamelin
Bark beetles form multipartite symbiotic associations with blue stain fungi (Ophiostomatales, Ascomycota). These symbionts play an important role during the beetle's life cycle by providing nutritional supplementation, overcoming tree defenses and modifying host tissues to favor brood development. The maintenance of stable multipartite symbioses with seemingly less competitive symbionts in similar habitats is of fundamental interest to ecology and evolution. We tested the hypothesis that the coexistence of three fungal species associated with the mountain pine beetle is the result of niche partitioning and adaptive radiation using SNP genotyping coupled with genotype-environment association analysis and phenotypic characterization of growth rate under different temperatures...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28231394/adaptive-divergence-in-wine-yeasts-and-their-wild-relatives-suggests-a-prominent-role-for-introgressions-and-rapid-evolution-at-non-coding-sites
#2
Pedro Almeida, Raquel Barbosa, Douda Bensasson, Paula Gonçalves, José Paulo Sampaio
In Saccharomyces cerevisiae, the main yeast in wine fermentation, the opportunity to examine divergence at the molecular level between a domesticated lineage and its wild counterpart arose recently due to the identification of the closest relatives of wine strains, a wild population associated with Mediterranean oaks. Since genomic data is available for a considerable number of representatives belonging to both groups, we used population genomics to estimate the degree and distribution of nucleotide variation between wine yeasts and their closest wild relatives...
February 23, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28231283/rapid-evolution-of-distinct-helicobacter-pylori-subpopulations-in-the-americas
#3
Kaisa Thorell, Koji Yahara, Elvire Berthenet, Daniel J Lawson, Jane Mikhail, Ikuko Kato, Alfonso Mendez, Cosmeri Rizzato, María Mercedes Bravo, Rumiko Suzuki, Yoshio Yamaoka, Javier Torres, Samuel K Sheppard, Daniel Falush
For the last 500 years, the Americas have been a melting pot both for genetically diverse humans and for the pathogenic and commensal organisms associated with them. One such organism is the stomach-dwelling bacterium Helicobacter pylori, which is highly prevalent in Latin America where it is a major current public health challenge because of its strong association with gastric cancer. By analyzing the genome sequence of H. pylori isolated in North, Central and South America, we found evidence for admixture between H...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28230768/bioinformatic-analysis-reveals-archaeal-trna-tyr-and-trna-trp-identities-in-bacteria
#4
Takahito Mukai, Noah M Reynolds, Ana Crnković, Dieter Söll
The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNA(Tyr) and tRNA(Trp) genes reveal bacterial or archaeal origins...
February 21, 2017: Life
https://www.readbyqxmd.com/read/28230237/parasitism-drives-host-genome-evolution-insights-from-the-pasteuria-ramosa-daphnia-magna-system
#5
Yann Bourgeois, Anne C Roulin, Kristina Müller, Dieter Ebert
Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe...
February 23, 2017: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/28229228/new-strains-of-chickpea-chlorotic-dwarf-virus-discovered-on-diseased-papaya-and-tomato-plants-in-burkina-faso
#6
Alassane Ouattara, Fidèle Tiendrébéogo, Pierre Lefeuvre, Murielle Hoareau, Sohini Claverie, Edgar Valentin Traoré, Nicolas Barro, Oumar Traoré, Arvind Varsani, Jean-Michel Lett
This is the first description of full genome sequences of chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus; family Geminiviridae) identified in papaya and tomato plants sampled in Burkina Faso. The CpCDV full genome sequences from papaya and tomato share the highest pairwise sequence identity (84% and 93.5%) with Sudanese isolates of the CpCDV-K and CpCDV-M strains, respectively. Based on the strain demarcation threshold (>94% identity) for mastreviruses, we propose two new strains, CpCDV-Q and CpCDV-R, identified in papaya and tomato, respectively...
February 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28228978/population-and-clinical-genetics-of-human-transposable-elements-in-the-post-genomic-era
#7
REVIEW
Lavanya Rishishwar, Lu Wang, Evan A Clayton, Leonardo Mariño-Ramírez, John F McDonald, I King Jordan
Recent technological developments-in genomics, bioinformatics and high-throughput experimental techniques-are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity...
2017: Mobile Genetic Elements
https://www.readbyqxmd.com/read/28228773/import-of-soluble-proteins-into-chloroplasts-and-potential-regulatory-mechanisms
#8
REVIEW
Inga Sjuts, Jürgen Soll, Bettina Bölter
Chloroplasts originated from an endosymbiotic event in which a free-living cyanobacterium was engulfed by an ancestral eukaryotic host. During evolution the majority of the chloroplast genetic information was transferred to the host cell nucleus. As a consequence, proteins formerly encoded by the chloroplast genome are now translated in the cytosol and must be subsequently imported into the chloroplast. This process involves three steps: (i) cytosolic sorting procedures, (ii) binding to the designated receptor-equipped target organelle and (iii) the consecutive translocation process...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28228535/genome-wide-prediction-of-metabolic-enzymes-pathways-and-gene-clusters-in-plants
#9
Pascal Schlapfer, Peifen Zhang, Chuan Wang, Taehyong Kim, Michael Banf, Lee Chae, Kate Dreher, Arvind K Chavali, Ricardo Nilo-Poyanco, Thomas Bernard, Daniel Kahn, Seung Y Rhee
Plant metabolism underpins many traits of ecological and agronomic importance. Plants produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have not yet been elucidated. To engineer and improve metabolic traits, we need comprehensive and accurate knowledge of the organization and regulation of plant metabolism at the genome scale. Here, we present a computational pipeline to identify metabolic enzymes, pathways and gene clusters from a sequenced genome...
February 22, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28228515/intrafamily-and-intragenomic-conflicts-in-human-warfare
#10
Alberto J C Micheletti, Graeme D Ruxton, Andy Gardner
Recent years have seen an explosion of multidisciplinary interest in ancient human warfare. Theory has emphasized a key role for kin-selected cooperation, modulated by sex-specific demography, in explaining intergroup violence. However, conflicts of interest remain a relatively underexplored factor in the evolutionary-ecological study of warfare, with little consideration given to which parties influence the decision to go to war and how their motivations may differ. We develop a mathematical model to investigate the interplay between sex-specific demography and human warfare, showing that: the ecology of warfare drives the evolution of sex-biased dispersal; sex-biased dispersal modulates intrafamily and intragenomic conflicts in relation to warfare; intragenomic conflict drives parent-of-origin-specific patterns of gene expression-i...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28228384/impact-of-disseminated-neuroblastoma-cells-on-the-identification-of-the-relapse-seeding-clone
#11
M Reza Abbasi, Fikret Rifatbegovic, Clemens Brunner, Georg Mann, Andrea Ziegler, Ulrike Pötschger, Roman Crazzolara, Marek Ussowicz, Martin Benesch, Georg Ebetsberger-Dachs, Godfrey Chi-Fung Chan, Neil Jones, Ruth Ladenstein, Inge M Ambros, Peter F Ambros
PURPOSE: Tumor relapse is the most frequent cause of death in stage 4 neuroblastomas. Since genomic information on the relapse precursor cells could guide targeted therapy, our aim was to find the most appropriate tissue for identifying relapse-seeding clones. EXPERIMENTAL DESIGN: We analyzed 10 geographically and temporally separated samples of a single patient by SNP array and validated the data in 154 stage 4 patients. RESULTS: In the case study, aberrations unique to certain tissues and time points were evident besides concordant aberrations shared by all samples...
February 22, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28228136/circulating-tumor-cells-capture-disease-evolution-in-advanced-prostate-cancer
#12
Justin Lack, Marc Gillard, Maggie Cam, Gladell P Paner, David J VanderWeele
BACKGROUND: Genetic analysis of advanced cancer is limited by availability of representative tissue. Biopsies of prostate cancer metastasized to bone are invasive with low quantity of tumor tissue. The prostate cancer genome is dynamic, however, with temporal heterogeneity requiring repeated evaluation as the disease evolves. Circulating tumor cells (CTCs) offer an alternative, "liquid biopsy", though single CTC sequencing efforts are laborious with high failure rates. METHODS: We performed exome sequencing of matched treatment-naïve tumor tissue, castrate resistant tumor tissue, and pooled CTC samples, and compared mutations identified in each...
February 23, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28226421/opening-plenary-speaker-human-genomics-precision-medicine-and-advancing-human-health
#13
Eric D Green
Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226237/novel-insights-into-tree-biology-and-genome-evolution-as-revealed-through-genomics
#14
David B Neale, Pedro J Martínez-García, Amanda R De La Torre, Sara Montanari, Xiao-Xin Wei
Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226236/new-strategies-and-tools-in-quantitative-genetics-how-to-go-from-the-phenotype-to-the-genotype
#15
C Bazakos, M Hanemian, C Trontin, J M Jiménez-Gómez, O Loudet
Quantitative genetics has a long history in plants: It has been used to study specific biological processes, identify the factors important for trait evolution, and breed new crop varieties. These classical approaches to quantitative trait locus mapping have naturally improved with technology. In this review, we show how quantitative genetics has evolved recently in plants and how new developments in phenotyping, population generation, sequencing, gene manipulation, and statistics are rejuvenating both the classical linkage mapping approaches (for example, through nested association mapping) as well as the more recently developed genome-wide association studies...
February 6, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28226235/plant-mitochondrial-genomes-dynamics-and-mechanisms-of-mutation
#16
José M Gualberto, Kathleen J Newton
The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified...
February 9, 2017: Annual Review of Plant Biology
https://www.readbyqxmd.com/read/28225773/whole-genome-duplication-and-molecular-evolution-in-cornus-l-cornaceae-insights-from-transcriptome-sequences
#17
Yan Yu, Qiuyun Xiang, Paul S Manos, Douglas E Soltis, Pamela S Soltis, Bao-Hua Song, Shifeng Cheng, Xin Liu, Gane Wong
The pattern and rate of genome evolution have profound consequences in organismal evolution. Whole-genome duplication (WGD), or polyploidy, has been recognized as an important evolutionary mechanism of plant diversification. However, in non-model plants the molecular signals of genome duplications have remained largely unexplored. High-throughput transcriptome data from next-generation sequencing have set the stage for novel investigations of genome evolution using new bioinformatic and methodological tools in a phylogenetic framework...
2017: PloS One
https://www.readbyqxmd.com/read/28224497/hidden-markov-models-in-population-genomics
#18
Julien Y Dutheil
With the advent of sequencing techniques population genomics took a major shift. The structure of data sets has evolved from a sample of a few loci in the genome, sequenced in dozens of individuals, to collections of complete genomes, virtually comprising all available loci. Initially sequenced in a few individuals, such genomic data sets are now reaching and even exceeding the size of traditional data sets in the number of haplotypes sequenced. Because all loci in a genome are not independent, this evolution of data sets is mirrored by a methodological change...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28224054/variant-profiling-of-evolving-prokaryotic-populations
#19
Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Genomic heterogeneity of bacterial species is observed and studied in experimental evolution experiments and clinical diagnostics, and occurs as micro-diversity of natural habitats. The challenge for genome research is to accurately capture this heterogeneity with the currently used short sequencing reads. Recent advances in NGS technologies improved the speed and coverage and thus allowed for deep sequencing of bacterial populations. This facilitates the quantitative assessment of genomic heterogeneity, including low frequency alleles or haplotypes...
2017: PeerJ
https://www.readbyqxmd.com/read/28224003/darwinism-for-the-genomic-age-connecting-mutation-to-diversification
#20
Xia Hua, Lindell Bromham
A growing body of evidence suggests that rates of diversification of biological lineages are correlated with differences in genome-wide mutation rate. Given that most research into differential patterns of diversification rate have focused on species traits or ecological parameters, a connection to the biochemical processes of genome change is an unexpected observation. While the empirical evidence for a significant association between mutation rate and diversification rate is mounting, there has been less effort in explaining the factors that mediate this connection between genetic change and species richness...
2017: Frontiers in Genetics
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