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G P Tiley, R T Kimball, E L Braun, J G Burleigh
BACKGROUND: Recent large-scale whole genome sequencing efforts in birds have elucidated broad patterns of avian phylogeny and genome evolution. However, despite the great interest in economically important phasianids like Gallus gallus (Red Junglefowl, the progenitor of the chicken), we know little about the genomes of closely related species. Gallus gallus is highly sexually dichromatic and polygynous, but its sister genus, Bambusicola, is smaller, sexually monomorphic, and monogamous with biparental care...
May 8, 2018: BMC Genomics
Dongyang Liu, Qilin Yi, Yichen Wu, Guangxia Lu, Changhao Gong, Xiaorui Song, Jiejie Sun, Chen Qu, Conghui Liu, Lingling Wang, Linsheng Song
Immunoglobulin superfamily (IgSF), an extensive collection of proteins possessing at least one immunoglobulin-like (Ig-like) domain, performs a wide range of functions in recognition, binding or adhesion process of cells. In the present study, a cysteine-rich motif associated immunoglobulin domain containing protein (designated CgCAICP-1) was identified in Pacific oyster Crassostrea gigas. The deduced protein sequence of CgCAICP-1 contained 534 amino acid residues, with three Ig domains which were designated as IG1, IG2 and IG3, and a cysteine-rich motif between the first and second Ig domain...
May 5, 2018: Developmental and Comparative Immunology
Yuan Zhou, Qinghua Cui
The m6 A modification has been implicated as an important epitranscriptomic marker, which plays extensive roles in the regulation of transcript stability, splicing, translation, and localization. Nevertheless, only some genes are repeatedly modified across various conditions and the principle of m6 A regulation remains elusive. In this study, we performed a systems-level analysis of human genes frequently regulated by m6 A modification (m6 Afreq genes) and those occasionally regulated by m6 A modification (m6 Aocca genes)...
May 3, 2018: Genomics, Proteomics & Bioinformatics
Daniel R Bogema, Melinda L Micallef, Michael Liu, Matthew P Padula, Steven P Djordjevic, Aaron E Darling, Cheryl Jenkins
BACKGROUND: Theileria orientalis (Apicomplexa: Piroplasmida) has caused clinical disease in cattle of Eastern Asia for many years and its recent rapid spread throughout Australian and New Zealand herds has caused substantial economic losses to production through cattle deaths, late term abortion and morbidity. Disease outbreaks have been linked to the detection of a pathogenic genotype of T. orientalis, genotype Ikeda, which is also responsible for disease outbreaks in Asia. Here, we sequenced and compared the draft genomes of one pathogenic (Ikeda) and two apathogenic (Chitose, Buffeli) isolates of T...
April 27, 2018: BMC Genomics
Wanzhen Liu, Hanghui Kong, Juan Zhou, Peter W Fritsch, Gang Hao, Wei Gong
The subfamily Caesalpinioideae of the Fabaceae has long been recognized as non-monophyletic due to its controversial phylogenetic relationships. Cercis chuniana , endemic to China, is a representative species of Cercis L. placed within Caesalpinioideae in the older sense. Here, we report the whole chloroplast (cp) genome of C. chuniana and compare it to six other species from the Caesalpinioideae. Comparative analyses of gene synteny and simple sequence repeats (SSRs), as well as estimation of nucleotide diversity, the relative ratios of synonymous and nonsynonymous substitutions (dn/ds), and Kimura 2-parameter (K2P) interspecific genetic distances, were all conducted...
April 25, 2018: International Journal of Molecular Sciences
Doris G Ransy, Etienne Lord, Martine Caty, Normand Lapointe, Marc Boucher, Abdoulaye Baniré Diallo, Hugo Soudeyns
Pregnancy is associated with modulations of maternal immunity that contribute to foeto-maternal tolerance. To understand whether and how these alterations impact antiviral immunity, a detailed cross-sectional analysis of selective pressures exerted on HIV-1 envelope amino-acid sequences was performed in a group of pregnant (n = 32) and non-pregnant (n = 44) HIV-infected women in absence of treatment with antiretroviral therapy (ART). Independent of HIV-1 subtype, p-distance, dN and dS were all strongly correlated with one another but were not significantly different in pregnant as compared to non-pregnant patients...
April 17, 2018: Infection, Genetics and Evolution
Satoko Mori, Masatoshi Matsunami
Acceleration of the amino acid substitution rate is a good indicator of positive selection in adaptive evolutionary changes of functional genes. Genomic information about mammals has become readily available in recent years, as many researchers have attempted to clarify the adaptive evolution of mammals by examining evolutionary rate change based on multiple loci. The order Cetartiodactyla (Artiodactyla and Cetacea) is one of the most diverse orders of mammals. Species in this order are found throughout all continents and seas, except Antarctica, and they exhibit wide variation in morphology and habitat...
April 10, 2018: Genes & Genetic Systems
Tatiana Murillo, Gabriel Ramírez-Vargas, Thomas Riedel, Jörg Overmann, Joakim M Andersen, Caterina Guzmán-Verri, Esteban Chaves-Olarte, César Rodríguez
Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0...
March 1, 2018: Genome Biology and Evolution
Ornpreya Suptawiwat, Alita Kongchanagul, Chompunuch Boonarkart, Prasert Auewarakul
It was previously shown that the seasonal H1N1 influenza virus antigenic drift occurred at a slower rate than the seasonal H3N2 virus during the first decade of the 21 t h century. It was hypothesized that the slower antigenic evolution led to a decrease in average ages of infection, which in turn resulted in lower level of global viral circulation. It is unclear what caused the difference between the two viruses, but a plausible explanation may be related to the fact that the H1N1 virus had been in human population for much longer than the H3N2 virus...
March 30, 2018: Virus Research
Bryan L Payne, David Alvarez-Ponce
The common transition from out-crossing to self-fertilization in plants decreases effective population size. This is expected to result in a reduced efficacy of natural selection and in increased rates of protein evolution in selfing plants compared with their outcrossing congeners. Prior analyses, based on a very limited number of genes, detected no differences between the rates of protein evolution in the selfing Arabidopsis thaliana compared with the out-crosser Arabidopsis lyrata. Here, we reevaluate this trend using the complete genomes of A...
March 1, 2018: Genome Biology and Evolution
Josué Barrera-Redondo, Santiago Ramirez-Barahona, Luis E Eguiarte
Variation in rates of molecular evolution (heterotachy) is a common phenomenon among plants. Although multiple theoretical models have been proposed, fundamental questions remain regarding the combined effects of ecological and morphological traits on rate heterogeneity. Here, we used tree ferns to explore the correlation between rates of molecular evolution in chloroplast DNA sequences and several morphological and environmental factors within a Bayesian framework. We revealed direct and indirect effects of body size, biological productivity, and temperature on substitution rates, where smaller tree ferns living in warmer and less productive environments tend to have faster rates of molecular evolution...
March 31, 2018: Evolution; International Journal of Organic Evolution
Jérémy Gauthier, Philippe Gayral, Bruno Pierre LeRu, Séverine Jancek, Stéphane Dupas, Laure Kaiser, Gabor Gyapay, Elisabeth A Herniou
The African parasitoid wasp Cotesia sesamiae is a generalist species structured in locally adapted populations showing differences in host range. The recent discovery of C. typhae, a specialist, sister species to C. sesamiae, provides a good framework to study the genetic determinants of parasitoid host range. To investigate the genomic bases of divergence between these populations and species, we used a targeted sequencing approach on 24 samples. We targeted the bracovirus genomic region encoding virulence genes involved in the interaction with the lepidopteran hosts of the wasps...
March 30, 2018: Molecular Ecology
Andressa de Oliveira Aragão, Joaquim Pinto Nunes Neto, Ana Cecília Ribeiro Cruz, Samir Mansour Moraes Casseb, Jedson Ferreira Cardoso, Sandro Patroca da Silva, Edna Aoba Yassui Ishikawa
Mosquitoes as Sabethes chloropterus, Sabethes glaucodaemon, Sabethes belisarioi are species of medical and epidemiological importance for arboviruses transmission such as yellow fever and St. Louis encephalitis. Despite this, no information about these three species mitochondrial DNA has been found in literature. Our study presents a mitochondrial genome description, including identity, SNPs, mutation rate, and phylogeny analysis using COX1, COX2, NADH4, NADH5, CYOB genes. The Sa. chloropterus, Sa. glaucodaemon and Sa...
March 23, 2018: Genomics
Debi Prasad Mohapatra, Santosh Kumar Singh, Minu Sahoo, Shashank Patole, Mitali Mishra, Nagen Kumar Debata, Harapriya Mohapatra
PURPOSE: Antibiotic resistance patterns often exhibit geographical variations. Periodic analyses of resistance spectra and phylogenetic trends are important guides for facilitating judicious use of therapeutic interventions. The present study retrospectively analysed the infection trends, resistance patterns, and clonal relationships between isolates of Klebsiella spp. from a tertiary care hospital. METHODOLOGY: Bacterial isolates were collected from January 2013 to June 2014 and their resistance profiles were identified using an automated bacterial identification system...
March 9, 2018: Journal of Medical Microbiology
Rolando Robert, Kenneth Francis Rodrigues, Zarinah Waheed, Subbiah Vijay Kumar
This study is aimed at establishing a baseline on the genetic diversity of the Acropora corals of Sabah, North Borneo based on variations in the partial COI and CYB nucleotide sequences. Comparison across 50 shallow-water Acropora morphospecies indicated that the low substitution rates in the two genes were due to negative selection and that rate heterogeneity between them was asymmetric. CYB appeared to have evolved faster than COI in the Acropora as indicated by differences in the rate of pairwise genetic distance, degrees of transition bias (Ts /Tv ), synonymous-to-nonsynonymous rate ratio (dN /dS ), and substitution patterns at the three codon positions...
March 9, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Drozdstoy Stoyanov, Sevdalina Kandilarova, Stefan Borgwardt, Rolf-Dieter Stieglitz, Kenneth Hugdahl, Stefan Kostianev
We present in this article a study design that combines clinical self-assessment scale, simultaneously administered with fMRI data acquisition. We have used a standard block-design with two different conditions. Each active block consisted of four text statements (items), alternating diagnostically specific (DS) blocks comprising items from von Zerssen depression scale and diagnostically neutral (DN) blocks with items from a questionnaire about general interests. All items were rated on four degree Likert scale, and patients provided responses with corresponding four buttons during the fMRI session...
2018: Frontiers in Psychiatry
Sahar Parto, Nicolas Lartillot
Rubisco (Ribulose-1, 5-biphosphate carboxylase/oxygenase) is the most important enzyme on earth, catalyzing the first step of photosynthetic CO2 fixation. So, without it, there would be no storing of the sun's energy in plants. Molecular adaptation of Rubisco to C4 photosynthetic pathway has attracted a lot of attention. C4 plants, which comprise less than 5% of land plants, have evolved more efficient photosynthesis compared to C3 plants. Interestingly, a large number of independent transitions from C3 to C4 phenotype have occurred...
2018: PloS One
Sara Domínguez-Rodríguez, Patricia Rojas, Carolina Fernández McPhee, Israel Pagán, María Luisa Navarro, José Tomás Ramos, África Holguín
This pilot study evaluates in pediatric patients the impact of HIV/HCV coinfection in the molecular evolution of the HIV-1 subtype B protease (HIV-1BPR). For this study, HIV-1B/HCV coinfected (15) and HIV-1B monoinfected (56) patients with available HIV-1B pol sequences were enrolled. Both groups of patients had comparable gender frequencies and average age, time of infection, antiretroviral treatment (ART) exposure and time under ART. Prevalence of drug resistance mutations (DRM), genetic diversity, number of synonymous (dS ) and non-synonymous (dN ) mutations per site and selection pressures (dN  - dS ) in the HIV-1BPR were estimated and compared between mono- and coinfected patients...
February 5, 2018: Scientific Reports
M Cortázar-Chinarro, Y Meyer-Lucht, A Laurila, J Höglund
MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient...
February 1, 2018: Immunogenetics
Mario A Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A Katz
The genome of Plasmodium falciparum, the causative agent of malaria in Africa, has been extensively studied since it was first fully sequenced in 2002. However, many open questions remain, including understanding the chromosomal context of molecular evolutionary changes (e.g., relationship between chromosome map and phylogenetic conservation, patterns of gene duplication, and patterns of selection). Here, we present PhyloChromoMap, a method that generates a phylogenomic map of chromosomes from a custom-built bioinformatics pipeline...
February 1, 2018: Genome Biology and Evolution
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