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Genome Biology and Evolution

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https://www.readbyqxmd.com/read/29220487/ancestral-genome-estimation-reveals-the-history-of-ecological-diversification-in-agrobacterium
#1
Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost, Alexandra Calteau, David Vallenet, Damien Mornico, Thomas Bigot, Laurent Guéguen, Ludovic Vial, Daniel Muller, Vincent Daubin, Xavier Nesme
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220486/transcriptome-signatures-of-selection-drift-introgression-and-gene-duplication-in-the-evolution-of-an-extremophile-endemic-plant
#2
Angela K Hawkins, Elyssa R Garza, Valerie A Dietz, Oscar J Hernandez, W Daryl Hawkins, A Millie Burrell, Alan E Pepper
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g. N, P, K, Ca), as well as toxic levels of heavy metals (e.g. Ni, Cr, Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220419/high-resolution-single-cell-sequencing-of-malaria-parasites
#3
Simon G Trevino, Standwell C Nkhoma, Shalini Nair, Benjamin J Daniel, Karla Moncada, Stanley Khoswe, Rachel L Banda, François Nosten, Ian H Cheeseman
Single-cell genomics is a powerful tool for determining the genetic architecture of complex communities of unicellular organisms. In areas of high transmission, malaria patients are often challenged by the activities of multiple Plasmodium falciparum lineages, which can potentiate pathology, spread drug resistance loci and also complicate most genetic analysis. Single-cell sequencing of P. falciparum would be key to understanding infection complexity, though efforts are hampered by the extreme nucleotide composition of its genome (∼80% AT-rich)...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29220418/plant-mediated-female-transcriptomic-changes-post-mating-in-a-tephritid-fruit-fly-bactrocera-tryoni
#4
Kumaran Nagalingam, Chloé A van der Burg, Yujia Qin, Stephen L Cameron, Anthony R Clarke, Peter J Prentis
Female post-mating behaviours are regulated by complex factors involving males, females and the environment. In insects, plant secondary compounds that males actively forage for, may indirectly modify female behaviours by altering male behaviour and physiology. In the tephritid fruit fly, Bactrocera tryoni, females mated with males previously fed on plant-derived phenylpropanoids (= 'lures' based on usage in tephritid literature), have longer mating refractoriness, greater fecundity and reduced longevity than females mated with non-lure fed males...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29216360/comprehensive-genome-wide-classification-reveals-that-many-plant-specific-transcription-factors-evolved-in-streptophyte-algae
#5
Per K I Wilhelmsson, Cornelia Mühlich, K Ullrich Kristian, Stefan A Rensing
Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators...
December 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29211852/migration-selection-balance-drives-genetic-differentiation-in-genes-associated-with-high-altitude-function-in-the-speckled-teal-anas-flavirostris-in-the-andes
#6
Allie M Graham, Philip Lavretsky, Violeta Muñoz-Fuentes, Andy J Green, Robert E Wilson, Kevin G McCracken
Local adaptation frequently occurs across populations as a result of migration-selection balance between divergent selective pressures and gene flow associated with life in heterogeneous landscapes. Studying the effects of selection and gene flow on the adaptation process can be achieved in systems that have recently colonized extreme environments. This study utilizes an endemic South American duck species, the speckled teal (Anas flavirostris), which has both high- and low-altitude populations. High-altitude speckled teal (A...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29211847/changes-in-neuronal-signaling-and-cell-stress-response-pathways-are-associated-with-a-multigenic-response-of-drosophila-melanogaster-to-ddt-selection
#7
Keon Mook Seong, Brad S Coates, Weilin Sun, John M Clark, Barry R Pittendrigh
The adaptation of insect populations to insecticidal control is a continual threat to human health and sustainable agricultural practices, but many complex genomic mechanisms involved in this adaption remain poorly understood. This study applied a systems approach to investigate the interconnections between structural and functional variance in response to dichlorodiphenyltrichloroethane (DDT) within the Drosophila melanogaster strain 91-R. Directional selection in six selective sweeps coincided with constitutive gene expression differences in DDT resistant flies, including the most highly up-regulated transcript, Unc-115b, which plays a central role in axon guidance, and the most highly down-regulated transcript, the angiopoietin-like CG31832, which is involved in directing vascular branching and dendrite outgrowth but likely under trans-regulatory control...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29211839/genomic-loss-and-silencing-on-the-y-chromosomes-of-rumex
#8
Felix Beaudry, Spencer Barrett, Stephen Wright
Across many unrelated lineages of plants and animals, Y chromosomes show a recurrent pattern of gene degeneration and loss, but the relative importance of inefficient selection, adaptive gene silencing, and neutral genetic drift in causing degeneration remain poorly understood. Here, we use next-generation genome and transcriptome sequencing to investigate patterns of ongoing Y chromosome degeneration in two annual plant species of Rumex (Polygonaceae) differing in their degree of degeneration and sex chromosome heteromorphism...
December 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29206915/phylogenetic-distribution-of-cmp-neu5ac-hydroxylase-cmah-the-enzyme-synthetizing-the-pro-inflammatory-human-xeno-antigen-neu5gc
#9
Sateesh Peri, Asmita Kulkarni, Felix Feyertag, Patricia M Berninsone, David Alvarez-Ponce
The enzyme CMP-N-acetylneuraminic acid hydroxylase (CMAH) is responsible for the synthesis of N-glycolylneuraminic acid (Neu5Gc), a sialic acid present on the cell surface proteins of most deuterostomes. The CMAH gene is thought to be present in most deuterostomes, but it has been inactivated in a number of lineages, including humans. The inability of humans to synthesize Neu5Gc has had several evolutionary and biomedical implications. Remarkably, Neu5Gc is a xenoantigen for humans, and consumption of Neu5Gc-containing foods, such as red meats, may promote inflammation, arthritis and cancer...
November 30, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29202180/emergence-and-spread-of-epidemic-multidrug-resistant-pseudomonas-aeruginosa
#10
Tohru Miyoshi-Akiyama, Tatsuya Tada, Norio Ohmagari, Nguyen Viet Hung, Prasit Tharavichitkul, Bharat Mani Pokhrel, Marek Gniadkowski, Masahiro Shimojima, Teruo Kirikae
Pseudomonas aeruginosa (P. aeruginosa) is one of the most common nosocomial pathogens worldwide. Although the emergence of multidrug-resistant (MDR) P. aeruginosa is a critical problem in medical practice, the key features involved in the emergence and spread of MDR P. aeruginosa remain unknown. This study utilized whole genome sequence (WGS) analyses to define the population structure of 185 P. aeruginosa clinical isolates from several countries. Of these 185 isolates, 136 were categorized into sequence type (ST) 235, one of the most common types worldwide...
November 29, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29202176/distribution-and-evolution-of-peroxisomes-in-alveolates-apicomplexa-dinoflagellates-ciliates
#11
Ann-Kathrin Ludewig-Klingner, Victoria Michael, Michael Jarek, Henner Brinkmann, Jörn Petersen
The peroxisome was the last organelle to be discovered and five decades later it is still the Cinderella of eukaryotic compartments. Peroxisomes have a crucial role in the detoxification of reactive oxygen species, the beta-oxidation of fatty acids and the biosynthesis of etherphospholipids, and they are assumed to be present in virtually all aerobic eukaryotes. Apicomplexan parasites including the malaria and toxoplasmosis agents were decribed as the first group of mitochondriate protists devoid of peroxisomes...
November 29, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29202174/autosomal-and-mitochondrial-adaptation-following-admixture-a-case-study-on-the-honeybees-of-reunion-island
#12
David Wragg, Maéva Angélique Techer, Kamila Canale-Tabet, Benjamin Basso, Jean-Pierre Bidanel, Emmanuelle Labarthe, Olivier Bouchez, Yves Le Conte, Johanna Clémencet, Hélène Delatte, Alain Vignal
The honeybee population of the tropical Reunion Island is a genetic admixture of the Apis mellifera unicolor subspecies, originally described in Madagascar, and of European subspecies, mainly A.m. carnica and A. m. ligustica, regularly imported to the island since the late 19th century. We took advantage of this population to study genetic admixing of the tropical-adapted indigenous and temperate-adapted European genetic backgrounds. Whole genome sequencing of 30 workers and 6 males from Reunion, compared to samples from Europe, Madagascar, Mauritius, Rodrigues and the Seychelles, revealed the Reunion honeybee population to be composed on average of 53...
November 29, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29194520/trajectories-and-drivers-of-genome-evolution-in-surface-associated-marine-phaeobacter
#13
Heike M Freese, Johannes Sikorski, Boyke Bunk, Carmen Scheuner, Jan P Meier-Kolthoff, Cathrin Spröer, Lone Gram, Jörg Overmann
The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome...
November 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29194487/comparative-genomics-of-an-unusual-biogeographic-disjunction-in-the-cotton-tribe-gossypieae-yields-insights-into-genome-downsizing
#14
Corrinne E Grover, Mark A Arick, Justin L Conover, Adam Thrash, Guanjing Hu, William S Sanders, Hsu Chuan-Yu, Rubab Zahra Naqvi, Muhammad Farooq, Xiaochong Li, Lei Gong, Joann Mudge, Thiru Ramaraj, Joshua A Udall, Daniel G Peterson, Jonathan F Wendel
Long-distance insular dispersal is associated with divergence and speciation because of founder effects and strong genetic drift. The cotton tribe (Gossypieae) has experienced multiple trans-oceanic dispersals, generating an aggregate geographic range that encompasses much of the tropics and subtropics worldwide. Two genera in the Gossypieae, Kokia and Gossypioides, exhibit a remarkable geographic disjunction, being restricted to the Hawaiian Islands and Madagascar/East Africa, respectively. We assembled and use de novo genome sequences to address questions regarding the divergence of these two genera from each other and from their sister-group, Gossypium...
November 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29186370/comparative-genomics-of-pathogenic-and-non-pathogenic-beetle-vectored-fungi-in-the-genus-geosmithia
#15
Taruna A Schuelke, Guangxi Wu, Anthony Westbrook, Keith Woeste, David C Plachetzki, Kirk Broders, Matthew D MacManes
Geosmithia morbida is an emerging fungal pathogen which serves as a model for examining the evolutionary processes behind pathogenicity because it is one of two known pathogens within a genus of mostly saprophytic, beetle-associated, fungi. This pathogen causes thousand cankers disease in black walnut trees and is vectored into the host via the walnut twig beetle. G. morbida was first detected in western US and currently threatens the timber industry concentrated in eastern US. We sequenced the genomes of G...
November 23, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29182740/speciation-generates-mosaic-genomes-in-kangaroos
#16
Maria A Nilsson, Yichen Zheng, Vikas Kumar, Matthew J Phillips, Axel Janke
The iconic Australasian kangaroos and wallabies represent a successful marsupial radiation. However, the evolutionary relationship within the two genera, Macropus and Wallabia, is controversial: mitochondrial and nuclear genes, and morphological data have produced conflicting scenarios regarding the phylogenetic relationships, which in turn impact the classification and taxonomy. We sequenced and analyzed the genomes of eleven kangaroos to investigate the evolutionary cause of the observed phylogenetic conflict...
November 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29177504/pathogenomic-analysis-of-wheat-yellow-rust-lineages-detects-seasonal-variation-and-host-specificity
#17
Vanessa Bueno-Sancho, Antoine Persoons, Amelia Hubbard, Luis Enrique Cabrera-Quio, Clare M Lewis, Pilar Corredor-Moreno, Daniel C E Bunting, Sajid Ali, Soonie Chng, David P Hodson, Ricardo Madariaga Burrows, Rosie Bryson, Jane Thomas, Sarah Holdgate, Diane G O Saunders
Recent disease outbreaks caused by (re-)emerging plant pathogens have been associated with expansions in pathogen geographic distribution and increased virulence. For example, in the past two decades' wheat yellow (stripe) rust, Puccinia striiformis f. sp. tritici, has seen the emergence of new races that are adapted to warmer temperatures, have expanded virulence profiles, and are more aggressive than previous races, leading to wide-scale epidemics. Here, we used field-based genotyping to generate high-resolution data on P...
November 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29177480/comparative-genomic-analysis-of-acanthamoeba-endosymbionts-highlights-the-role-of-amoebae-as-a-melting-pot-shaping-the-rickettsiales-evolution
#18
Zhang Wang, Martin Wu
Amoebae have been considered as a genetic 'melting pot' for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the 'melting pot' hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to family Holosporaceae and two to Candidatus Midichloriaceae. For the first time, we identified plasmids in obligate amoeba endosymbionts, which suggests conjugation as a potential mechanism for lateral gene transfers (LGTs) that underpin the 'melting pot' hypothesis...
November 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29177479/horizontal-acquisition-and-transcriptional-integration-of-novel-genes-in-mosquito-associated-spiroplasma
#19
Wen-Sui Lo, Chih-Horng Kuo
Genetic differentiation among symbiotic bacteria is important in shaping biodiversity. The genus Spiroplasma contains species occupying diverse niches and is a model system for symbiont evolution. Previous studies have established that two mosquito-associated species have diverged extensively in their carbohydrate metabolism genes despite having a close phylogenetic relationship. Notably, while the commensal S. diminutum lacks identifiable pathogenicity factors, the pathogenic S. taiwanense was found to have acquired a virulence factor glpO and its associated genes through horizontal transfer...
November 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29165566/host-genetic-variation-does-not-determine-spatio-temporal-patterns-of-european-bat-1-lyssavirus
#20
Cécile Troupin, Evelyne Picard-Meyer, Simon Dellicour, Isabelle Casademont, Lauriane Kergoat, Anthony Lepelletier, Laurent Dacheux, Guy Baele, Elodie Monchâtre-Leroy, Florence Cliquet, Philippe Lemey, Hervé Bourhy
The majority of bat rabies cases in Europe are attributed to European bat 1 lyssavirus (EBLV-1), circulating mainly in serotine bats (Eptesicus serotinus). Two subtypes have been defined (EBLV-1a and EBLV-1b), each associated with a different geographical distribution. In this study, we undertake a comprehensive sequence analysis based on eighty newly obtained EBLV-1 nearly complete genome sequences from nine European countries over a 45-year period to infer selection pressures, rates of nucleotide substitution and evolutionary time scale of these two subtypes in Europe...
November 20, 2017: Genome Biology and Evolution
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