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Genome Biology and Evolution

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https://www.readbyqxmd.com/read/28633494/silencing-effect-of-hominoid-highly-conserved-non-coding-sequences-on-embryonic-brain-development
#1
Morteza Mahmoudi Saber, Naruya Saitou
Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633450/comparative-genomics-of-all-three-campylobacter-sputorum-biovars-and-a-novel-cattle-associated-c-sputorum-clade
#2
William G Miller, Emma Yee, Mary H Chapman, James L Bono
Campylobacter sputorum is a non-thermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase negative, urease negative), bv. fecalis (catalase positive, urease negative), and bv. paraureolyticus (catalase negative, urease positive). A multi-locus sequence typing (MLST) method was recently constructed for C...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633446/genetic-indicators-of-drug-resistance-in-the-highly-repetitive-genome-of-trichomonas-vaginalis
#3
Martina Bradic, Sally D Warring, Grace E Tooley, Paul Scheid, William E Secor, Kirkwood M Land, Po-Jung Huang, Ting-Wen Chen, Chi-Ching Lee, Petrus Tang, Steven A Sullivan, Jane M Carlton
Trichomonas vaginalis, the most common non-viral sexually transmitted parasite, causes ∼283 million trichomoniasis infections annually and is associated with pregnancy complications and increased risk of HIV-1 acquisition. The antimicrobial drug metronidazole is used for treatment, but in a fraction of clinical cases, the parasites can become resistant to this drug. We undertook sequencing of multiple clinical isolates and lab derived lines to identify genetic markers and mechanisms of metronidazole resistance...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#4
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28637261/further-simulations-and-analyses-demonstrate-open-problems-of-phylostratigraphy
#5
Bryan A Moyers, Jianzhi Zhang
Phylostratigraphy, originally designed for gene age estimation by BLAST-based protein homology searches of sequenced genomes, has been widely used for studying patterns and inferring mechanisms of gene origination and evolution. We previously showed by computer simulation that phylostratigraphy underestimates gene age for a non-negligible fraction of genes and that the underestimation is severer for genes with certain properties such as fast evolution and short protein sequences. Consequently, many previously reported age distributions of gene properties may have been methodological artifacts rather than biological realities...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#6
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633361/evolution-of-mirna-tailing-by-3-terminal-uridylyl-transferases-in-metazoa
#7
Vengamanaidu Modepalli, Yehu Moran
In bilaterian animals the 3' ends of microRNAs (miRNAs) are frequently modified by tailing and trimming. These modifications affect miRNA-mediated gene regulation by modulating miRNA stability. Here we analyzed data from three non-bilaterian animals: two cnidarians (Nematostella vectensis and Hydra magnipapillata) and one poriferan (Amphimedon queenslandica). Our analysis revealed that non-bilaterian miRNAs frequently undergo modifications like the bilaterian counterparts: the majority are expressed as different length isoforms and frequent modifications of the 3' end by mono U or mono A tailing are observed...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633296/similar-ratios-of-introns-to-intergenic-sequence-across-animal-genomes
#8
Warren R Francis, Gert Wörheide
One central goal of genome biology is to understand how the usage of the genome differs between organisms. Our knowledge of genome composition, needed for downstream inferences, is critically dependent on gene annotations, yet problems associated with gene annotation and assembly errors are usually ignored in comparative genomics. Here we analyze the genomes of 68 species across 12 animal phyla and some single-cell eukaryotes for general trends in genome composition and transcription, taking into account problems of gene annotation...
June 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28575204/analysis-of-copy-number-variation-in-the-abp-gene-regions-of-two-house-mouse-subspecies-suggests-divergence-during-the-gene-family-expansions
#9
Željka Pezer, Amanda G Chung, Robert C Karn, Christina M Laukaitis
The Androgen-binding protein (Abp) gene region of the mouse genome contains 64 genes, some encoding pheromones that influence assortative mating between mice from different subspecies. Using CNVnator and quantitative PCR, we explored copy number variation in this gene family in natural populations of Mus musculus domesticus (Mmd) and M. m. musculus (Mmm), two subspecies of house mice that form a narrow hybrid zone in Central Europe. We found that copy number variation in the center of the Abp gene region is very common in wild Mmd, primarily representing the presence/absence of the final duplications described for the mouse genome...
May 29, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28549175/selfing-in-haploid-plants-and-efficacy-of-selection-codon-usage-bias-in-the-model-moss-physcomitrella-patens
#10
Péter Szövényi, Kristian K Ullrich, Stefan A Rensing, Daniel Lang, Nico van Gessel, Hans K Stenøien, Elena Conti, Ralf Reski
Long term reduction in effective population size will lead to major shift in genome evolution. In particular, when effective population size is small, genetic drift becomes dominant over natural selection. The onset of self-fertilization is one evolutionary event considerably reducing effective size of populations. Theory predicts that this reduction should be more dramatic in organisms capable for haploid than for diploid selfing. Although theoretically well-grounded, this assertion received mixed experimental support...
May 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541535/genome-wide-snp-analysis-reveals-distinct-origins-of-trypanosoma-evansi-and-trypanosoma-equiperdum
#11
Bart Cuypers, Frederik Van den Broeck, Nick Van Reet, Conor J Meehan, Julien Cauchard, Jonathan M Wilkes, Filip Claes, Bruno Goddeeris, Hadush Birhanu, Jean-Claude Dujardin, Kris Laukens, Philippe Büscher, Stijn Deborggraeve
Trypanosomes cause a variety of diseases in man and domestic animals in Africa, Latin America, and Asia. In the Trypanozoon subgenus, Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense cause human African trypanosomiasis, whereas Trypanosoma brucei brucei, Trypanosoma evansi, and Trypanosoma equiperdum are responsible for nagana, surra, and dourine in domestic animals, respectively. The genetic relationships between T. evansi and T. equiperdum and other Trypanozoon species remain unclear because the majority of phylogenetic analyses has been based on only a few genes...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810713/co-opted-megasatellite-dna-drives-evolution-of-secondary-night-vision-in-azara-s-owl-monkey
#12
Akihiko Koga, Hideyuki Tanabe, Yuriko Hirai, Hiroo Imai, Masanori Imamura, Takao Oishi, Roscoe Stanyon, Hirohisa Hirai
Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810712/genomic-analysis-of-the-evolution-of-phototrophy-among-haloalkaliphilic-rhodobacterales
#13
Karel Kopejtka, Jürgen Tomasch, Yonghui Zeng, Martin Tichý, Dimitry Y Sorokin, Michal Koblížek
A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810711/whole-rna-sequencing-and-transcriptome-assembly-of-candida-albicans-and-candida-africana-under-chlamydospore-inducing-conditions
#14
Domenico Giosa, Maria Rosa Felice, Travis J Lawrence, Megha Gulati, Fabio Scordino, Letterio Giuffrè, Carla Lo Passo, Enrico D'Alessandro, Giuseppe Criseo, David H Ardell, Aaron D Hernday, Clarissa J Nobile, Orazio Romeo
Candida albicans is the most common cause of life-threatening fungal infections in humans, especially in immunocompromised individuals. Crucial to its success as an opportunistic pathogen is the considerable dynamism of its genome, which readily undergoes genetic changes generating new phenotypes and shaping the evolution of new strains. Candida africana is an intriguing C. albicans biovariant strain that exhibits remarkable genetic and phenotypic differences when compared with standard C. albicans isolates...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810710/testing-convergent-evolution-in-auditory-processing-genes-between-echolocating-mammals-and-the-aye-aye-a-percussive-foraging-primate
#15
Richard J Bankoff, Michael Jerjos, Baily Hohman, M Elise Lauterbur, Logan Kistler, George H Perry
Several taxonomically distinct mammalian groups-certain microbats and cetaceans (e.g., dolphins)-share both morphological adaptations related to echolocation behavior and strong signatures of convergent evolution at the amino acid level across seven genes related to auditory processing. Aye-ayes (Daubentonia madagascariensis) are nocturnal lemurs with a specialized auditory processing system. Aye-ayes tap rapidly along the surfaces of trees, listening to reverberations to identify the mines of wood-boring insect larvae; this behavior has been hypothesized to functionally mimic echolocation...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28810709/parallel-evolution-of-sperm-hyper-activation-ca2-channels
#16
Jacob C Cooper, Nitin Phadnis
Sperm hyper-activation is a dramatic change in sperm behavior where mature sperm burst into a final sprint in the race to the egg. The mechanism of sperm hyper-activation in many metazoans, including humans, consists of a jolt of Ca2+ into the sperm flagellum via CatSper ion channels. Surprisingly, all nine CatSper genes have been independently lost in several animal lineages. In Drosophila, sperm hyper-activation is performed through the cooption of the polycystic kidney disease 2 (pkd2) Ca2+ channel. The parallels between CatSpers in primates and pkd2 in Drosophila provide a unique opportunity to examine the molecular evolution of the sperm hyper-activation machinery in two independent, nonhomologous calcium channels separated by > 500 million years of divergence...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28605529/the-genomic-impact-of-gene-retrocopies-what-have-we-learned-from-comparative-genomics-population-genomics-and-transcriptomic-analyses
#17
Claudio Casola, Esther Betrán
Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene's transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28595281/unraveling-the-population-history-of-indian-siddis
#18
Ranajit Das, Priyanka Upadhyai
The Siddis are a unique Indian tribe of African, South Asian, and European ancestry. While previous investigations have traced their ancestral origins to the Bantu populations from subSaharan Africa, the geographic localization of their ancestry has remained elusive. Here, we performed biogeographical analysis to delineate the ancestral origin of the Siddis employing an admixture based algorithm, Geographical Population Structure (GPS). We evaluated the Siddi genomes in reference to five African populations from the 1000 Genomes project, two Bantu groups from the Human Genome Diversity Panel (HGDP) and five South Indian populations...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541478/genome-size-in-north-american-fireflies-substantial-variation-likely-driven-by-neutral-processes
#19
Sarah Sander Lower, J Spencer Johnston, Kathrin F Stanger-Hall, Carl E Hjelmen, Shawn J Hanrahan, Katharine Korunes, David Hall
Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies)...
June 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541439/the-evolutionary-landscape-of-dbl-like-rhogef-families-adapting-eukaryotic-cells-to-environmental-signals
#20
Philippe Fort, Anne Blangy
The dynamics of cell morphology in eukaryotes is largely controlled by small GTPases of the Rho family. Rho GTPases are activated by guanine nucleotide exchange factors (RhoGEFs), of which diffuse B-cell lymphoma (Dbl)-like members form the largest family. Here, we surveyed Dbl-like sequences from 175 eukaryotic genomes and illuminate how the Dbl family evolved in all eukaryotic supergroups. By combining probabilistic phylogenetic approaches and functional domain analysis, we show that the human Dbl-like family is made of 71 members, structured into 20 subfamilies...
June 1, 2017: Genome Biology and Evolution
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