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https://www.readbyqxmd.com/read/28531368/molecular-phylogeny-of-loliginidae-inferred-from-mitochondrial-dna-sequence-variation
#1
Lisen Kang, Shuyi Zhang, Changwen Wu, Xiaoxu Liu, Mei Ying Xu, Lihua Jiang
Loliginidae includes many economically important species in trophic systems worldwide. Here, we investigated genetic relationships and diversity in this family. Sequence comparisons and phylogenetic analyses revealed considerable variations between mitochondrial 16 S rRNA gene and cytochrome coxidase subunit I gene among nine Loliginid species. We identified three similar non-coding regions in eight Loliginid species, but not in Sepioteuthislessoniana. We detected a single extended termination-associated sequence and three conserved sequence blocks among these eight species...
May 20, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28531201/evolutionary-forces-affecting-synonymous-variations-in-plant-genomes
#2
Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin
Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28529516/suppression-of-plant-immune-responses-by-the-pseudomonas-savastanoi-pv-savastanoi-ncppb-3335-type-iii-effector-tyrosine-phosphatases-hopao1-and-hopao2
#3
María Pilar Castañeda-Ojeda, Alba Moreno-Pérez, Cayo Ramos, Emilia López-Solanilla
The effector repertoire of the olive pathogen P. savastanoi pv. savastanoi NCPPB 3335 includes two members of the HopAO effector family, one of the most diverse T3E families of the P. syringae complex. The study described here explores the phylogeny of these dissimilar members, HopAO1 and HopAO2, among the complex and reveals their activities as immune defense suppressors. Although HopAO1 is predominantly encoded by phylogroup 3 strains isolated from woody organs of woody hosts, both HopAO1 and HopAO2 are phylogenetically clustered according to the woody/herbaceous nature of their host of isolation, suggesting host specialization of the HopAO family across the P...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28528860/purifying-selection-and-concerted-evolution-of-rna-sensing-toll-like-receptors-in-migratory-waders
#4
Nynke Raven, Simeon Lisovski, Marcel Klaassen, Nathan Lo, Thomas Madsen, Simon Y W Ho, Beata Ujvari
Migratory birds encounter a broad range of pathogens during their journeys, making them ideal models for studying immune gene evolution. Despite the potential value of these species to immunoecology and disease epidemiology, previous studies have typically focused on their adaptive immune gene repertoires. In this study, we examined the evolution of innate immune genes in three long-distance migratory waders (order Charadriiformes). We analysed two parts of the extracellular domains of two Toll-like receptors (TLR3 and TLR7) involved in virus recognition in the Sanderling (Calidris alba), Red-necked Stint (Calidris ruficollis), and Ruddy Turnstone (Arenaria interpres)...
May 18, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28528744/locked-in-the-icehouse-evolution-of-an-endemic-epimeria-amphipoda-crustacea-species-flock-on-the-antarctic-shelf
#5
Marie L Verheye, Thierry Backeljau, Cédric d'Udekem d'Acoz
The Antarctic shelf's marine biodiversity has been greatly influenced by the climatic and glacial history of the region. Extreme temperature changes led to the extinction of some lineages, while others adapted and flourished. The amphipod genus Epimeria is an example of the latter, being particularly diverse in the Antarctic region. By reconstructing a time-calibrated phylogeny based on mitochondrial (COI) and nuclear (28S and H3) markers and including Epimeria species from all oceans, this study provides a temporal and geographical framework for the evolution of Antarctic Epimeria...
May 18, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28526749/the-origin-and-evolution-of-human-glutaminases-and-their-atypical-c-terminal-ankyrin-repeats
#6
Camila Cristina Pascoal, Zeyaul Islam, Douglas Adamoski, Igor Monteze Ferreira, Ricardo Diogo Righetto, Jefferson Bettini, Rodrigo Villares Portugal, Wyatt W Yue, Ana Gonzalez, Sandra Martha Gomes Dias, Andre Luis Berteli Ambrosio
On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. However, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont...
May 19, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28524816/phylogenetic-variation-of-chelonid-alphaherpesvirus-5-in-green-turtle-chelonia-mydas-populations-along-the-queensland-coast-australia
#7
E Ariel, F Nainu, K Jones, K Juntunen, I Bell, J Gaston, J Scott, S Trocini, G W Burgess
Sea turtle fibropapillomatosis (FP) is a disease marked by proliferation of benign but debilitating cutaneous and occasional visceral tumours, likely to be caused by chelonid alphaherpesvirus 5 (ChHV5). This study presents a phylogeny of ChHV5 strains on the east coast of Queensland, Australia and a validation for previously unused primers. Two different primer sets (gB-1534 and gB-813) were designed to target a region including part of the UL27 glycoprotein B (gB) gene and part of UL28 of ChHV5. Sequences obtained from FP tumours on juvenile green turtles (<65 cm CCL) had substantial homology with published ChHV5 sequences while a skin biopsy from a turtle without FP failed to react in the PCRs used in this study...
May 19, 2017: Journal of Aquatic Animal Health
https://www.readbyqxmd.com/read/28522869/ancient-river-inference-explains-exceptional-oriental-freshwater-mussel-radiations
#8
Ivan N Bolotov, Alexander V Kondakov, Ilya V Vikhrev, Olga V Aksenova, Yulia V Bespalaya, Mikhail Yu Gofarov, Yulia S Kolosova, Ekaterina S Konopleva, Vitaly M Spitsyn, Kitti Tanmuangpak, Sakboworn Tumpeesuwan
The concept of long-lived (ancient) lakes has had a great influence on the development of evolutionary biogeography. According to this insight, a number of lakes on Earth have existed for several million years (e.g., Baikal and Tanganyika) and represent unique evolutionary hotspots with multiple intra-basin radiations. In contrast, rivers are usually considered to be variable systems, and the possibility of their long-term existence during geological epochs has never been tested. In this study, we reconstruct the history of freshwater basin interactions across continents based on the multi-locus fossil-calibrated phylogeny of freshwater mussels (Unionidae)...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28516735/assessment-of-trophic-ecomorphology-in-non-alligatoroid-crocodylians-and-its-adaptive-and-taxonomic-implications
#9
Masaya Iijima
Although the establishment of trophic ecomorphology in living crocodylians can contribute to estimating feeding habits of extinct large aquatic reptiles, assessment of ecomorphological traits other than the snout shape has scarcely been conducted in crocodylians. Here, I tested the validity of the proposed trophic ecomorphological traits in crocodylians by examining the correlation between those traits and the snout shape (an established trophic ecomorphology), using 10 non-alligatoroid crocodylian species with a wide range of snout shape...
May 18, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28515739/patterns-of-inter-chromosomal-gene-conversion-on-the-male-specific-region-of-the-human-y-chromosome
#10
REVIEW
Beniamino Trombetta, Eugenia D'Atanasio, Fulvio Cruciani
The male-specific region of the human Y chromosome (MSY) is characterized by the lack of meiotic recombination and it has long been considered an evolutionary independent region of the human genome. In recent years, however, the idea that human MSY did not have an independent evolutionary history begun to emerge with the discovery that inter-chromosomal gene conversion (ICGC) can modulate the genetic diversity of some portions of this genomic region. Despite the study of the dynamics of this molecular mechanism in humans is still in its infancy, some peculiar features and consequences of it can be summarized...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28515730/analysis-of-mads-box-gene-family-reveals-conservation-in-floral-organ-abcde-model-of-moso-bamboo-phyllostachys-edulis
#11
Zhanchao Cheng, Wei Ge, Long Li, Dan Hou, Yanjun Ma, Jun Liu, Qingsong Bai, Xueping Li, Shaohua Mu, Jian Gao
Mini chromosome maintenance 1, agamous, deficiens, and serum response factor (MADS)-box genes are transcription factors which play fundamental roles in flower development and regulation of floral organ identity. However, till date, identification and functions of MADS-box genes remain largely unclear in Phyllostachys edulis. In view of this, we performed a whole-genome survey and identified 34 MADS-box genes in P. edulis, and based on phylogeny, they were classified as MIKC(C), MIKC(∗), Mα, and Mβ. The detailed analysis about gene structure and motifs, phylogenetic classification, comparison of gene divergence and duplication are provided...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515478/molecular-phylogenetics-and-biogeography-of-the-mint-tribe-elsholtzieae-nepetoideae-lamiaceae-with-an-emphasis-on-its-diversification-in-east-asia
#12
Pan Li, Zhe-Chen Qi, Lu-Xian Liu, Tetsuo Ohi-Toma, Joongku Lee, Tsung-Hsin Hsieh, Cheng-Xin Fu, Kenneth M Cameron, Ying-Xiong Qiu
Elsholtzia and its allied genera such as Collinsonia and Perilla (tribe Elsholtzieae, Lamiaceae) are an ecologically and economically important plant group consisting of ~71 species, with most species distributed in East and Southeast Asia, and several species in North America. Their phylogeny and historical biogeography resulting in a distant intercontinental disjunction are poorly understood. Here we use two nuclear (ETS, ITS) and five chloroplast (rbcL, matK, trnL-F, ycf1, ycf1-rps15) fragments to reconstruct the phylogeny, biogeographic history, and patterns of diversification of Elsholtzieae...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515295/natural-variation-of-epstein-barr-virus-genes-proteins-and-pri-mirna-revised
#13
Samantha Correia, Anne Palser, Claudio Elgueta Karstegl, Jaap M Middeldorp, Octavia Ramayanti, Jeffrey I Cohen, Allan Hildesheim, Maria Dolores Fellner, Joelle Wiels, Robert E White, Paul Kellam, Paul J Farrell
Viral gene sequences from an enlarged set of about 200 Epstein-Barr virus (EBV) strains including many primary isolates have been used to investigate variation in key viral genetic regions, particularly LMP1, Zp, gp350, EBNA1 and the BART miRNA cluster 2. Determination of type 1 and type 2 EBV in saliva samples from people from a wide range of geographic and ethnic backgrounds demonstrates a small percentage of healthy white Caucasian British people carrying predominantly type 2 EBV. Linkage of Zp and gp350 variants to type 2 EBV is likely to be due to their genes being adjacent to the EBNA3 locus, which is one of the major determinants of the type 1/type 2 distinction...
May 17, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28515206/widespread-ecomorphological-convergence-in-multiple-fish-families-spanning-the-marine-freshwater-interface
#14
Aaron M Davis, Ricardo Betancur-R
The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments...
May 17, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28515204/a-genetic-legacy-of-introgression-confounds-phylogeny-and-biogeography-in-oaks
#15
John D McVay, Andrew L Hipp, Paul S Manos
Oaks (Quercus L.) have long been suspected to hybridize in nature, and widespread genetic exchange between morphologically defined species is well documented in two- to six-species systems, but the phylogenetic consequences of hybridization in oaks have never been demonstrated in a phylogenetically diverse sample. Here, we present phylogenomic analyses of a ca 30 Myr clade that strongly support morphologically defined species and the resolution of novel clades of white oaks; however, historical hybridization across clade boundaries is detectable and, undiagnosed, would obscure the imprint of biogeographic history in the phylogeny...
May 17, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28510723/decreased-azithromycin-susceptibility-of-neisseria-gonorrhoeae-isolates-in-patients-recently-treated-with-azithromycin
#16
Carolien M Wind, Esther de Vries, Maarten F Schim van der Loeff, Martijn S van Rooijen, Alje P van Dam, Walter H B Demczuk, Irene Martin, Henry J C de Vries
Background.: Increasing azithromycin usage and resistance in Neisseria gonorrhoeae threatens current dual treatment. Because antimicrobial exposure influences resistance, we analyzed the association between azithromycin exposure and decreased susceptibility of N. gonorrhoeae. Methods.: We included N. gonorrhoeae isolates of patients who visited the Amsterdam STI Clinic between 1999 and 2013 (t0), with another clinic visit in the previous 60 days (t-1). Exposure was defined as the prescription of azithromycin at t-1...
March 24, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28509910/convergence-of-gut-microbiotas-in-the-adaptive-radiations-of-african-cichlid-fishes
#17
Laura Baldo, Joan Lluís Pretus, Joan Lluís Riera, Zuzana Musilova, Arnold Roger Bitja Nyom, Walter Salzburger
Ecoevolutionary dynamics of the gut microbiota at the macroscale level, that is, in across-species comparisons, are largely driven by ecological variables and host genotype. The repeated explosive radiations of African cichlid fishes in distinct lakes, following a dietary diversification in a context of reduced genetic diversity, provide a natural setup to explore convergence, divergence and repeatability in patterns of microbiota dynamics as a function of the host diet, phylogeny and environment. Here we characterized by 16S rRNA amplicon sequencing the gut microbiota of 29 cichlid species from two distinct lakes/radiations (Tanganyika and Barombi Mbo) and across a broad dietary and phylogenetic range...
May 16, 2017: ISME Journal
https://www.readbyqxmd.com/read/28509612/defining-the-phylogenetic-position-of-amanita-species-from-andean-colombia
#18
Natalia Vargas, Carlos José Pardo-de La Hoz, Giovanna Danies, Ana Esperanza Franco-Molano, Pedro Jiménez, Silvia Restrepo, Alejandro Grajales
Amanita is a worldwide-distributed fungal genus, with approximately 600 known species. Most species within the genus are ectomycorrhizal (ECM), with some saprotrophic representatives. In this study, we constructed the first comprehensive phylogeny including ECM species from Colombia collected in native Quercus humboldtii forests and in introduced Pinus patula plantations. We included 8 species (A. brunneolocularis, A. colombiana, A. flavoconia, A. fuligineodisca, A. muscaria, A. rubescens, A. sororcula, and A...
April 12, 2017: Mycologia
https://www.readbyqxmd.com/read/28509342/morphological-and-molecular-characterization-of-bysmatrum-subsalsum-dinophyceae-from-the-western-mediterranean-sea-reveals-the-existence-of-cryptic-species
#19
Sílvia Anglès, Albert Reñé, Esther Garcés, Antonella Lugliè, Nicola Sechi, Jordi Camp, Cecilia Teodora Satta
Bysmatrum subsalsum is a cosmopolitan dinoflagellate species that inhabits marine and transitional habitats. Despite its wide distribution, information on the morphological variability, phylogeny and ecology of B. subsalsum is scarce. In this study, we provide morphological and molecular data on B. subsalsum strains and wild cells from different locations in the Mediterranean Basin. The dynamics of cell abundances and the associated environmental conditions during a field bloom are also described. Genetic sequences of B...
May 16, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28507536/temporal-genomic-phylogeny-reconstruction-indicates-a-geospatial-transmission-path-of-salmonella-cerro-in-the-united-states-and-a-clade-specific-loss-of-hydrogen-sulfide-production
#20
Jasna Kovac, Kevin J Cummings, Lorraine D Rodriguez-Rivera, Laura M Carroll, Anil Thachil, Martin Wiedmann
Salmonella Cerro has become one of the most prevalent Salmonella serotypes isolated from dairy cattle in several U.S. states, including New York where it represented 36% of all Salmonella isolates of bovine origin in 2015. This serotype is commonly isolated from dairy cattle with clinical signs of salmonellosis, including diarrhea and fever, although it has also been identified in herds without evidence of clinical disease or decreased production. To better understand the transmission patterns and drivers of its geographic spread, we have studied the genomic similarity and microevolution of S...
2017: Frontiers in Microbiology
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