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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 T. b. rhodesiense cause human African trypanosomiasis, while T. b. brucei, T. evansi and T. 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 have been based on only a few genes...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541478/genome-size-in-north-american-fireflies-substantial-variation-likely-driven-by-neutral-processes
#12
Sarah Sander Lower, J Spencer Johnston, Kathrin 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)...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28453630/the-effects-of-cpg-densities-around-transcription-start-sites-on-sex-biased-gene-expression-in-poecilia-reticulata
#13
Katsunori Tamagawa, Takashi Makino, Masakado Kawata
Since most genes are shared between females and males, DNA methylation is assumed to play a crucial role in sex-biased gene expression. DNA methylation exclusively occurs at CpG dinucleotides, and therefore, we would expect that CpG density around transcription start sites (TSSs) relate to sex-biased gene expression. Here we investigated the relationship between CpG densities around TSSs and the ratio of gene expression levels between sexes in the guppy (Poecilia reticulata), which displays remarkable sexual dimorphisms...
April 26, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28444372/quantifying-the-number-of-independent-organelle-dna-insertions-in-genome-evolution-and-human-health
#14
Einat Hazkani-Covo, William F Martin
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28444194/evolution-of-the-3r-myb-gene-family-in-plants
#15
Guanqiao Feng, J Gordon Burleigh, Edward L Braun, Wenbin Mei, W Brad Barbazuk
Plant 3R-MYB transcription factors are an important subgroup of the MYB super family in plants; however, their evolutionary history and functions remain poorly understood. We identified 225 3R-MYB proteins from 65 plant species, including algae and all major lineages of land plants. Two segmental duplication events preceding the common ancestor of angiosperms have given rise to three subgroups of the 3R-MYB proteins. Five conserved introns in the domain region of the 3R-MYB genes were identified, which arose through a step-wise pattern of intron gain during plant evolution...
April 20, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#16
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28431042/cis-regulatory-divergence-in-gene-expression-between-two-thermally-divergent-yeast-species
#17
Xueying C Li, Justin C Fay
Gene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomyces species, S. cerevisiae and S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species' hybrid at three temperatures, the highest of which is lethal to S...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28419285/genomic-differentiation-and-demographic-histories-of-atlantic-and-indo-pacific-yellowfin-tuna-thunnus-albacares-populations
#18
J M I Barth, M Damerau, M Matschiner, S Jentoft, R Hanel
Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations...
April 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28419219/dna-remodelling-by-strict-partial-endoreplication-in-orchids-an-original-process-in-the-plant-kingdom
#19
Spencer C Brown, Mickaël Bourge, Nicolas Maunoury, Maurice Wong, Michele Wolfe Bianchi, Sandra Lepers-Andrzejewski, Pascale Besse, Sonja Siljak-Yakovlev, Michel Dron, Béatrice Satiat-Jeunemaître
DNA remodelling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analysed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodelling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc...
April 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28402527/the-relationship-between-selection-network-connectivity-and-regulatory-variation-within-a-population-of-capsella-grandiora
#20
Emily B Josephs, Stephen I Wright, John R Stinchcombe, Daniel J Schoen
Interactions between genes can have important consequences for how selection shapes sequence variation at these genes. Specifically, genes that have pleiotropic effects by affecting the expression level of many other genes may be under stronger selective constraint. We used coexpression networks to measure connectivity between genes and investigated the relationship between gene connectivity and selection in a natural population of the plant Capsella grandiora. We observed that network connectivity was negatively correlated with genetic divergence due to stronger negative selection on highly-connected genes even when controlling for variation in gene expression level...
April 8, 2017: Genome Biology and Evolution
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