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Genome Biology and Evolution

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https://www.readbyqxmd.com/read/28549175/selfing-in-haploid-plants-and-efficacy-of-selection-codon-usage-bias-in-the-model-moss-physcomitrella-patens
#1
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
#2
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
#3
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/28541439/the-evolutionary-landscape-of-dbl-like-rhogef-families-adapting-eukaryotic-cells-to-environmental-signals
#4
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...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28541415/transcriptome-wide-identification-and-expression-analysis-of-divaricata-and-radialis-like-genes-of-the-mediterranean-orchid-orchis-italica
#5
Maria Carmen Valoroso, Sofia De Paolo, Giovanni Iazzetti, Serena Aceto
Bilateral symmetry of flowers is a relevant novelty that has occurred many times throughout the evolution of flowering plants. In Antirrhinum majus, establishment of flower dorso-ventral asymmetry is mainly due to interaction of TCP (CYC and DICH) and MYB (DIV, RAD and DRIF) transcription factors. In the present study, we characterized 8 DIV-, 4 RAD- and 2 DRIF-like genes from the transcriptome of Orchis italica, an orchid species with bilaterally symmetric and resupinate flowers. We found a similar number of DIV- and RAD-like genes within the genomes of Phalaenopsis equestris and Dendrobium catenatum orchids...
May 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28525571/one-year-genome-evolution-of-lausannevirus-in-allopatric-versus-sympatric-conditions
#6
Linda Mueller, Claire Bertelli, Trestan Pillonel, Nicolas Salamin, Gilbert Greub
Amoeba-resisting microorganisms (ARMs) raised a great interest during the last decade. Among them, some large DNA viruses present huge genomes up to 2.5 Mb long, exceeding the size of small bacterial genomes. The rate of genome evolution in terms of mutation, deletion and gene acquisition in these genomes is yet unknown. Given the suspected high plasticity of viral genomes, the microevolution of the 346 kb genome of Lausannevirus, a member of Megavirales, was studied. Hence, Lausannevirus was co-cultured within the amoeba Acanthamoeba castellanii over one year...
May 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28505302/the-first-whole-genome-and-transcriptome-of-the-manila-clam-ruditapes-philippinarum-isolated-in-korea
#7
Seyoung Mun, Yun-Ji Kim, Kesavan Markkandan, Wonseok Shin, Sumin Oh, Jiyoung Woo, Jongsu Yoo, Hyesuck An, Kyudong Han
The manila clam, Ruditapes philippinarum, is an important bivalve species in worldwide aquaculture including Korea. The aquaculture production of R. philippinarum is under threat from diverse environmental factors including viruses, microorganisms, parasites, and water conditions with subsequently declining production. In spite of its importance as a marine resource, the reference genome of R. philippinarum for comprehensive genetic studies is largely unexplored. Here, we report the de novo whole-genome and transcriptome assembly of R...
May 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28505260/evolution-of-two-short-interspersed-elements-in-callorhinchus-milii-chondrichthyes-holocephali-and-related-elements-in-sharks-and-the-coelacanth
#8
Andrea Luchetti, Federico Plazzi, Barbara Mantovani
Short interspersed elements (SINEs) are non-autonomous retrotransposons. Although they usually show fast evolutionary rates, in some instances highly conserved domains (HCDs) have been observed in elements with otherwise divergent sequences and from distantly related species. Here we document the life history of two HCD-SINE families in the elephant shark Callorhinchus milii, one specific to the holocephalan lineage (CmiSINEs) and another one (SacSINE1-CM) with homologous elements in sharks and the coelacanth (SacSINE1s, LmeSINE1s)...
May 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28472327/contrasting-sex-and-caste-dependent-pirna-profiles-in-the-transposon-depleted-haplodiploid-honeybee-apis-mellifera
#9
Wei-Wen Wang, Regan Ashby, Hua Ying, Ryszard Maleszka, Sylvain Forêt
Protecting genome integrity against transposable elements is achieved by intricate molecular mechanisms involving PIWI proteins, their associated small RNAs (piRNAs), and epigenetic modifiers such as DNA methylation. Eusocial bees, in particular the Western honeybee, Apis mellifera, have one of the lowest contents of transposable elements in the animal kingdom, and, unlike other animals with a functional DNA methylation system, do not methylate their transposons. This raises the question of whether the PIWI machinery has been retained in this species...
May 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28472322/genetic-architecture-of-natural-variation-underlying-adult-foraging-behavior-that-is-essential-for-survival-of-drosophila-melanogaster
#10
Yuh Chwen, G Lee, Qian Yang, Wanhao Chi, Susie A Turkson, Wei A Du, Claus Kemkemer, Zhao-Bang Zeng, Manyuan Long, Xiaoxi Zhuang
Foraging behavior is critical for the fitness of individuals. However, the genetic basis of variation in foraging behavior and the evolutionary forces underlying such natural variation have rarely been investigated. We developed a systematic approach to assay the variation in survival rate in a foraging environment for adult flies derived from a wild Drosophila melanogaster population. Despite being such an essential trait, there is substantial variation of foraging behavior among D. melanogaster strains. Importantly, we provided the first evaluation of the potential caveats of using inbred Drosophila strains to perform genome-wide association studies on life-history traits, and concluded that inbreeding depression is unlikely a major contributor for the observed large variation in adult foraging behavior...
May 4, 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
#11
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/28449025/reltime-rates-collapses-to-a-strict-clock-when-estimating-the-timeline-of-animal-diversification
#12
Jesus Lozano-Fernandez, Mario Dos Reis, Philip C J Donoghue, Davide Pisani
Establishing an accurate timescale for the history of life is crucial to understand evolutionary processes. To this scope, relaxed molecular clock models implemented in a Bayesian MCMC framework are generally used. However, these methods are time consuming. RelTime, a non-Bayesian method implementing a fast, ad hoc, algorithm for relative dating, was developed to overcome the computational inefficiencies of Bayesian software. RelTime was recently used to investigate the origin of animals, and found results consistent with outdated studies from the 1980es and 1990es that recovered metazoans to have a Mesoproterozoic origin (originating approximately 1...
April 25, 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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
https://www.readbyqxmd.com/read/28383665/a-pan-genomic-approach-to-understand-the-basis-of-host-adaptation-in-achromobacter
#20
J Jeukens, L Freschi, A T Vincent, J G Emond-Rheault, I Kukavica-Ibrulj, S J Charette, R C Levesque
Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis (CF) lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the CF lung, not to mention other host environments...
April 5, 2017: Genome Biology and Evolution
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