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https://www.readbyqxmd.com/read/29330451/tracheophyte-genomes-keep-track-of-the-deep-evolution-of-the-caulimoviridae
#1
Seydina Issa Diop, Andrew D W Geering, Françoise Alfama-Depauw, Mikaël Loaec, Pierre-Yves Teycheney, Florian Maumus
Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29329426/a-practical-guide-to-estimating-the-heritability-of-pathogen-traits
#2
Venelin Mitov, Tanja Stadler
Pathogen traits, such as the virulence of an infection, can vary significantly between patients. A major challenge is to measure the extent to which genetic differences between infecting strains explain the observed variation of the trait. This is quantified by the trait's broad-sense heritability, H2. A recent discrepancy between estimates of the heritability of HIV-virulence has opened a debate on the estimators' accuracy. Here, we show that the discrepancy originates from model limitations and important lifecycle differences between sexually reproducing organisms and transmittable pathogens...
January 9, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#3
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29321538/sweep-dynamics-sd-plots-computational-identification-of-selective-sweeps-to-monitor-the-adaptation-of-influenza-a-viruses
#4
Thorsten R Klingen, Susanne Reimering, Jens Loers, Kyra Mooren, Frank Klawonn, Thomas Krey, Gülsah Gabriel, Alice C McHardy
Monitoring changes in influenza A virus genomes is crucial to understand its rapid evolution and adaptation to changing conditions e.g. establishment within novel host species. Selective sweeps represent a rapid mode of adaptation and are typically observed in human influenza A viruses. We describe Sweep Dynamics (SD) plots, a computational method combining phylogenetic algorithms with statistical techniques to characterize the molecular adaptation of rapidly evolving viruses from longitudinal sequence data...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29321239/comparative-genomic-analysis-of-the-pseudofungus-hyphochytrium-catenoides
#5
Guy Leonard, Aurélie Labarre, David S Milner, Adam Monier, Darren Soanes, Jeremy G Wideman, Finlay Maguire, Sam Stevens, Divya Sain, Xavier Grau-Bové, Arnau Sebé-Pedrós, Jason E Stajich, Konrad Paszkiewicz, Matthew W Brown, Neil Hall, Bill Wickstead, Thomas A Richards
Eukaryotic microbes have three primary mechanisms for obtaining nutrients and energy: phagotrophy, photosynthesis and osmotrophy. Traits associated with the latter two functions arose independently multiple times in the eukaryotes. The Fungi successfully coupled osmotrophy with filamentous growth, and similar traits are also manifested in the Pseudofungi (oomycetes and hyphochytriomycetes). Both the Fungi and the Pseudofungi encompass a diversity of plant and animal parasites. Genome-sequencing efforts have focused on host-associated microbes (mutualistic symbionts or parasites), providing limited comparisons with free-living relatives...
January 2018: Open Biology
https://www.readbyqxmd.com/read/29317064/comparison-of-geographic-distributions-of-irritable-bowel-syndrome-with-inflammatory-bowel-disease-fail-to-support-common-evolutionary-roots-irritable-bowel-syndrome-and-inflammatory-bowel-diseases-are-not-related-by-evolution
#6
Andrew Szilagyi, Xiaoqing Xue
Irritable Bowel Syndrome (IBS) shares overlapping symptoms and some features of pathogenesis with Inflammatory Bowel Diseases (IBD: Crohn's disease [CD], and Ulcerative Colitis [UC]). Geographic markers such as latitude/sunshine and more recently lactase population distributions are found to be correlated with IBD. As a result of clinical and pathogenic similarities between the 2 conditions, some authorities questioned whether a connection exists between them. We compare IBS directly with IBD, and indirectly with geographic markers associated with IBD, in order to evaluate possible evolutionary links between IBS and IBD...
January 2018: Medical Hypotheses
https://www.readbyqxmd.com/read/29311232/context-dependent-requirements-for-fimh-and-other-canonical-virulence-factors-in-gut-colonization-by-extraintestinal-pathogenic-escherichia-coli
#7
Colin W Russell, Brittany A Fleming, Courtney A Jost, Alexander Tran, Alan T Stenquist, Morgan A Wambaugh, Mary P Bronner, Matthew A Mulvey
Extraintestinal pathogenic Escherichia coli (ExPEC) act as commensals within the mammalian gut, but can induce pathology upon dissemination to other host environments such as the urinary tract and bloodstream. ExPEC genomes are likely shaped by evolutionary forces encountered within the gut where the bacteria spend much of their time, provoking the question of how their extraintestinal virulence traits arose. The principle of coincidental evolution, in which a gene that evolved in one niche happens to be advantageous in another, has been used to argue that ExPEC virulence factors originated in response to selective pressures within the gut ecosystem...
January 8, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29310713/an-imd-like-pathway-mediates-both-endosymbiont-control-and-host-immunity-in-the-cereal-weevil-sitophilus-spp
#8
Justin Maire, Carole Vincent-Monégat, Florent Masson, Anna Zaidman-Rémy, Abdelaziz Heddi
Many insects developing on nutritionally unbalanced diets have evolved symbiotic associations with vertically transmitted intracellular bacteria (endosymbionts) that provide them with metabolic components, thereby improving the host's abilities to thrive on such poor ecological niches. While host-endosymbiont coevolutionary constraints are known to entail massive genomic changes in the microbial partner, host's genomic evolution remains elusive, particularly with regard to the immune system. In the cereal weevil Sitophilus spp...
January 8, 2018: Microbiome
https://www.readbyqxmd.com/read/29306353/vibrio-cholerae-genomic-diversity-within-and-between-patients
#9
Inès Levade, Yves Terrat, Jean-Baptiste Leducq, Ana A Weil, Leslie M Mayo-Smith, Fahima Chowdhury, Ashraful I Khan, Jacques Boncy, Josiane Buteau, Louise C Ivers, Edward T Ryan, Richelle C Charles, Stephen B Calderwood, Firdausi Qadri, Jason B Harris, Regina C LaRocque, B Jesse Shapiro
Cholera is a severe, water-borne diarrhoeal disease caused by toxin-producing strains of the bacterium Vibrio cholerae. Comparative genomics has revealed 'waves' of cholera transmission and evolution, in which clones are successively replaced over decades and centuries. However, the extent of V. cholerae genetic diversity within an epidemic or even within an individual patient is poorly understood. Here, we characterized V. cholerae genomic diversity at a micro-epidemiological level within and between individual patients from Bangladesh and Haiti...
December 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29304222/quentin-reconstruction-of-disease-transmissions-from-viral-quasispecies-genomic-data
#10
Pavel Skums, Alex Zelikovsky, Rahul Singh, Walker Gussler, Zoya Dimitrova, Sergey Knyazev, Igor Mandric, Sumathi Ramachandran, David Campo, Deeptanshu Jha, Leonid Bunimovich, Elizabeth Costenbader, Connie Sexton, Siobhan O'Connor, Guo-Liang Xia, Yury Khudyakov
Motivation: Genomic analysis has become one of the major tools for disease outbreak investigations. However, existing computational frameworks for inference of transmission history from viral genomic data often do not consider intra-host diversity of pathogens and heavily rely on additional epidemiological data, such as sampling times and exposure intervals. This impedes genomic analysis of outbreaks of highly mutable viruses associated with chronic infections, such as human immunodeficiency virus and hepatitis C virus, whose transmissions are often carried out through minor intra-host variants, while the additional epidemiological information often is either unavailable or has a limited use...
January 1, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29299290/the-virulence-transmission-relationship-in-an-obligate-killer-holds-under-diverse-epidemiological-and-ecological-conditions-but-where-is-the-tradeoff
#11
Frida Ben-Ami
Parasite virulence is a leading theme in evolutionary biology. Modeling the course of virulence evolution holds the promise of providing practical insights into the management of infectious diseases and the implementation of vaccination strategies. A key element of virulence modeling is a tradeoff between parasite transmission rate and host lifespan. This assumption is crucial for predicting the level of optimal virulence. Here, I test this assumption using the water flea Daphnia magna and its castrating and obligate-killing bacterium Pasteuria ramosa...
December 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29297281/suggested-mechanisms-for-zika-virus-causing-microcephaly-what-do-the-genomes-tell-us
#12
Se-Ran Jun, Trudy M Wassenaar, Visanu Wanchai, Preecha Patumcharoenpol, Intawat Nookaew, David W Ussery
BACKGROUND: Zika virus (ZIKV) is an emerging human pathogen. Since its arrival in the Western hemisphere, from Africa via Asia, it has become a serious threat to pregnant women, causing microcephaly and other neuropathies in developing fetuses. The mechanisms behind these teratogenic effects are unknown, although epidemiological evidence suggests that microcephaly is not associated with the original, African lineage of ZIKV. The sequences of 196 published ZIKV genomes were used to assess whether recently proposed mechanistic explanations for microcephaly are supported by molecular level changes that may have increased its virulence since the virus left Africa...
December 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29290090/rates-of-gut-microbiome-divergence-in-mammals
#13
Alex H Nishida, Howard Ochman
The variation and taxonomic diversity among mammalian gut microbiomes raises several questions about the factors that contribute to the rates and patterns of change in these microbial communities. By comparing the microbiome compositions of 112 species representing 14 mammalian orders, we assessed how host and ecological factors contribute to microbiome diversification. Except in rare cases, the same bacterial phyla predominate in mammalian gut microbiomes, and there has been some convergence of microbiome compositions according to dietary category across all mammalians lineages except Chiropterans (bats), which possess high proportions of Proteobacteria and tend to be most similar to one another regardless of diet...
December 31, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29282842/evolution-within-the-fungal-genus-verticillium-is-characterized-by-chromosomal-rearrangement-and-gene-loss
#14
Xiaoqian Shi-Kunne, Luigi Faino, Grardy C M van den Berg, Bart P H J Thomma, Michael F Seidl
The fungal genus Verticillium contains ten species, some of which are notorious plant pathogens causing vascular wilt diseases in host plants, while others are known as saprophytes and opportunistic plant pathogens. Whereas the genome of V. dahliae, the most notorious plant pathogen of the genus, has been well characterized, evolution and speciation of other members of the genus received little attention thus far. Here, we sequenced the genomes of the nine haploid Verticillium spp. to study evolutionary trajectories of their divergence from a last common ancestor...
December 28, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29282103/within-host-evolution-of-enterococcus-faecium-during-longitudinal-carriage-and-transition-to-bloodstream-infection-in-immunocompromised-patients
#15
Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. METHODS: We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment...
December 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29282064/q-a-friends-but-sometimes-foes-within-the-complex-evolutionary-ecology-of-symbioses-between-host-and-microbes
#16
Nicole Gerardo, Gregory Hurst
Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes)...
December 27, 2017: BMC Biology
https://www.readbyqxmd.com/read/29281664/diversification-rates-host-plant-shifts-and-an-updated-molecular-phylogeny-of-andean-eois-moths-lepidoptera-geometridae
#17
Patrick Strutzenberger, Gunnar Brehm, Brigitte Gottsberger, Florian Bodner, Carlo Lutz Seifert, Konrad Fiedler
Eois is one of the best-investigated genera of tropical moths. Its close association with Piper plants has inspired numerous studies on life histories, phylogeny and evolutionary biology. This study provides an updated view on phylogeny, host plant use and temporal patterns of speciation in Eois. Using sequence data (2776 bp) from one mitochondrial (COI) and one nuclear gene (Ef1-alpha) for 221 Eois species, we confirm and reinforce previous findings regarding temporal patterns of diversification. Deep diversification within Andean Eois took place in the Miocene followed by a sustained high rate of diversification until the Pleistocene when a pronounced slowdown of speciation is evident...
2017: PloS One
https://www.readbyqxmd.com/read/29277154/comparing-behavior-and-clock-gene-expression-between-caterpillars-butterflies-and-moths
#18
Natalie Niepoth, Gao Ke, Jacobus C de Roode, Astrid T Groot
Circadian behavior is widely observed in insects; however, the mechanisms that drive its evolution remain a black box. While circadian activity rhythms are well characterized in adults within the order Lepidoptera (i.e., most butterfly species are day active, while most moths are night active), much less is known about daily activity and clock gene expression in the larval stage. Additionally, direct comparison of clock gene expression between day-active and night-active species reared together has not been quantified...
December 1, 2017: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/29275182/the-impact-of-hiv-1-within-host-evolution-on-transmission-dynamics
#19
REVIEW
Kristof Theys, Pieter Libin, Andrea-Clemencia Pineda-Peña, Ann Nowé, Anne-Mieke Vandamme, Ana B Abecasis
The adaptive potential of HIV-1 is a vital mechanism to evade host immune responses and antiviral treatment. However, high evolutionary rates during persistent infection can impair transmission efficiency and alter disease progression in the new host, resulting in a delicate trade-off between within-host virulence and between-host infectiousness. This trade-off is visible in the disparity in evolutionary rates at within-host and between-host levels, and preferential transmission of ancestral donor viruses. Understanding the impact of within-host evolution for epidemiological studies is essential for the design of preventive and therapeutic measures...
December 21, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/29274498/species-delimitation-within-the-bothryorrhynchapion-weevils-multiple-evidence-from-genetics-morphology-and-ecological-associations
#20
Łukasz Kajtoch, Matteo Montagna, Marek Wanat
Curculionidae is a hyperdiverse group of beetles, whose taxonomy and phylogenetics is still poorly understood, especially at the genus level. The latest work on the evolution of Apionini showed a noticeable "mess" in the subtribe Oxystomatina, where most of the morphology-based genera were found to be polyphyletic or paraphyletic. These discrepancies between classical taxonomy and molecular phylogenetics implied the need for further taxonomic revision of these groups. Here, we used sets of morphological, molecular and ecological characters to verify the taxonomic statuses and disentangle the phylogenetic relations among the Bothryorrhynchapion apionids, which are classified as a subgenus of Cyanapion...
December 20, 2017: Molecular Phylogenetics and Evolution
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