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Genome Biology and Evolution

Karin Brigit Holthaus, Bettina Strasser, Julia Lachner, Supawadee Sukseree, Wolfgang Sipos, Anton Weissenbacher, Erwin Tschachler, Lorenzo Alibardi, Leopold Eckhart
The epidermis of amniotes forms a protective barrier against the environment and the differentiation program of keratinocytes, the main cell type in the epidermis, has undergone specific alterations in the course of adaptation of amniotes to a broad variety of environments and lifestyles. The epidermal differentiation complex (EDC) is a cluster of genes expressed at late stages of keratinocyte differentiation in both sauropsids and mammals. In the present study we identified and analyzed the crocodilian equivalent of the EDC...
February 12, 2018: Genome Biology and Evolution
Julien Kincaid-Smith, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, Eve Toulza
Schistosomes are the causative agents of schistosomiasis, a Neglected Tropical Disease affecting over 230 million people worldwide. Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatworms are unique among the common hermaphroditic trematodes as they have separate sexes. This so-called « evolutionary scandal » displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexual dimorphism...
February 12, 2018: Genome Biology and Evolution
Larissa M Dias, Adriana R C Folador, Amanda M Oliveira, Rommel T J Ramos, Artur Silva, Rafael A Baraúna
Exiguobacterium and Psychrobacter are bacterial genera with several cold-adapted species. These extremophiles are commonly isolated from the same habitats in Earth's cryosphere and have great ecological and biotechnological relevance. Thus, through comparative genomic analyses, it was possible to understand the functional diversity of these psychrotrophic and psychrophilic species and present new insights into the microbial adaptation to cold. The nucleotide identity between Exiguobacterium genomes was higher than 90%...
February 8, 2018: Genome Biology and Evolution
Prabh Basra, Ahlam Alsaadi, Gabriel Bernal-Astrain, Michael Liam O'Sullivan, Bryn Hazlett, Leah Marie Clarke, Andrew Schoenrock, Sylvain Pitre, Alex Wong
Evolutionary trade-offs occur when selection on one trait has detrimental effects on other traits. In pathogenic microbes, it has been hypothesized that antibiotic resistance trades off with fitness in the absence of antibiotic. While studies of single resistance mutations support this hypothesis, it is unclear whether trade-offs are maintained over time, due to compensatory evolution and broader effects of genetic background. Here, we leverage natural variation in 39 extra-intestinal clinical isolates of Escherichia coli to assess trade-offs between growth rates and resistance to fluoroquinolone and cephalosporin antibiotics...
February 7, 2018: Genome Biology and Evolution
Nadezhda A Potapova, Maria A Andrianova, Georgii A Bazykin, Alexey S Kondrashov
A gene which carries a bona fide loss-of-function mutation effectively becomes a functionless pseudogene, free from selective constraint. However, there is a number of molecular mechanisms that may lead to at least a partial preservation of the function of genes carrying even drastic alleles. We performed a direct measurement of the strength of negative selection acting on nonsense alleles of protein-coding genes in the Zambian population of Drosophila melanogaster. Within those exons that carry nonsense mutations, negative selection, assayed by the ratio of missense over synonymous nucleotide diversity levels, appears to be absent, consistent with total loss of function...
February 7, 2018: Genome Biology and Evolution
Alejandro Otero-Bravo, Shana Goffredi, Zakee L Sabree
Phytophagous stink bugs are globally-distributed and many harbor vertically-inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont's genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts of distantly-related stink bugs has precluded inferring patterns of extracellular symbiont genome evolution. To address this knowledge gap, we completely sequenced the genomes of the uncultivable bacterial symbionts of four neotropical stink bugs of the Edessa genus...
February 6, 2018: Genome Biology and Evolution
David C H Metzger, Patricia M Schulte
Epigenetic mechanisms such as DNA methylation are a key component of dosage compensation on sex chromosomes and have been proposed as an important source of phenotypic variation influencing plasticity and adaptive evolutionary processes, yet little is known about the role of DNA methylation in an ecological or evolutionary context in vertebrates. The threespine stickleback (Gasterosteus aculeatus) is an ecological an evolutionary model system that has been used to study mechanisms involved in the evolution of adaptive phenotypes in novel environments as well as the evolution heteromorphic sex chromosomes and dosage compensation in vertebrates...
February 6, 2018: Genome Biology and Evolution
Guillaume Bernard, Jananan S Pathmanathan, Romain Lannes, Philippe Lopez, Eric Bapteste
Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics datasets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists...
February 5, 2018: Genome Biology and Evolution
Marcus V X Senra, Way Sung, Matthew Ackerman, Samuel F Miller, Michael Lynch, Carlos Augusto G Soares
Mutations contribute to genetic variation in all living systems. Thus, precise estimates of mutation rates and spectra across a diversity of organisms are required for a full comprehension of evolution. Here, a mutation-accumulation (MA) assay was carried out on the endosymbiotic bacterium Teredinibacter turnerae. After ∼3025 generations, base-pair substitutions (BPSs) and insertion-deletion (indel) events were characterized by whole-genome sequencing analysis of 47 independent MA lines, yielding a BPSs rate of 1...
February 3, 2018: Genome Biology and Evolution
Dongfei Han, Svetlana N Dedysh, Werner Liesack
The genus Methylocystis belongs to the class Alphaproteobacteria, the family Methylocystaceae, and encompasses aerobic methanotrophic bacteria with the serine pathway of carbon assimilation. All Methylocystis species are able to fix dinitrogen and several members of this genus are also capable of using acetate or ethanol in the absence of methane, which explains their wide distribution in various habitats. One additional trait that enables their survival in the environment is possession of two methane-oxidizing isozymes, the conventional particulate methane monooxygenase with low-affinity to substrate (pMMO1) and the high-affinity enzyme (pMMO2)...
January 30, 2018: Genome Biology and Evolution
Gabriel Schweizer, Karin Münch, Gertrud Mannhaupt, Jan Schirawski, Regine Kahmann, Julien Y Dutheil
Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example are secreted fungal effector proteins and their host targets, which play an important role in pathogenic interactions. Biotrophic smut fungi (Basidiomycota) are well-suited to investigate the evolution of plant pathogens, because several reference genomes and genetic tools are available for these species...
January 30, 2018: Genome Biology and Evolution
Katrin Grosser, Pathmanaban Ramasamy, Azim Dehghani Amirabad, Marcel H Schulz, Gilles Gasparoni, Martin Simon, Martina Schrallhammer
Endosymbiosis is a widespread phenomenon and hosts of bacterial endosymbionts can be found all-over the eukaryotic tree of life. Likely, this evolutionary success is connected to the altered phenotype arising from a symbiotic association. The potential variety of symbiont's contributions to new characteristics or abilities of host organisms are largely unstudied. Addressing this aspect, we focused on an obligate bacterial endosymbiont that confers an intraspecific killer phenotype to its host. The symbiosis between Paramecium tetraurelia and Caedibacter taeniospiralis, living in the host's cytoplasm, enables the infected paramecia to release Caedibacter symbionts, which can simultaneously produce a peculiar protein structure and a toxin...
January 30, 2018: Genome Biology and Evolution
Saurabh Mahajan, Deepa Agashe
Increasing growth rate across bacteria strengthens selection for faster translation, concomitantly increasing the total number of tRNA genes and codon usage bias (CUB: enrichment of specific synonymous codons in highly expressed genes). Typically, enriched codons are translated by tRNAs with higher gene copy numbers (GCN). A model of tRNA-CUB coevolution based on fast growth associated selection on translational speed recapitulates these patterns. A key untested implication of the coevolution model is that translational selection should favor higher tRNA GCN for more frequently used amino acids, potentially weakening the effect of growth associated selection on CUB...
January 29, 2018: Genome Biology and Evolution
Jonathan G Gerhart, H Auguste Dutcher, Amanda E Brenner, Abraham S Moses, Libor Grubhoffer, Rahul Raghavan
Bacterial endosymbionts of ticks are of interest due to their close evolutionary relationships with tick-vectored pathogens. For instance, while many ticks contain Francisella-like endosymbionts (FLEs), others transmit the mammalian pathogen Francisella tularensis. We recently sequenced the genome of an FLE present in the hard tick Amblyomma maculatum (FLE-Am) and showed that it likely evolved from a pathogenic ancestor. In order to expand our understanding of FLEs, in the current study we sequenced the genome of an FLE in the soft tick Ornithodoros moubata (FLE-Om) and compared it to the genomes of FLE-Am, F...
January 29, 2018: Genome Biology and Evolution
Marie-Ka Tilak, Fidel Botero-Castro, Nicolas Galtier, Benoit Nabholz
Standard Illumina libraries are biased towards sequences of intermediate GC-content. This results in an underrepresentation of GC-rich regions in sequencing projects of genomes with heterogeneous base composition, such as mammals and birds. We developed a simple, cost-effective protocol to enrich sheared genomic DNA in its GC-rich fraction by subtracting AT-rich DNA. This was achieved by heating DNA up to 90 °C before applying Illumina library preparation. We tested the new approach on chicken DNA and found that heated DNA increased average coverage in the GC-richest chromosomes by a factor up to six...
January 27, 2018: Genome Biology and Evolution
Ilona Urbarova, Hardip Patel, Sylvain Forêt, Bård Ove Karlsen, Tor Erik Jørgensen, Jason M Hall-Spencer, Steinar D Johansen
Cnidarians harbour a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons...
January 27, 2018: Genome Biology and Evolution
Pingping Liang, Hafiz Sohaib Ahmed Saqib, Xingtan Zhang, Liangsheng Zhang, Haibao Tang
Conserved noncoding sequences (CNS) are evolutionarily conserved DNA sequences that do not encode proteins but may have potential regulatory roles in gene expression. CNS in crop genomes could be linked to many important agronomic traits and ecological adaptations. Compared to the relatively mature exon annotation protocols, efficient methods are lacking to predict the location of noncoding sequences in the plant genomes. We implemented a computational pipeline that is tailored to the comparisons of plant genomes, yielding a large number of conserved sequences using rice genome as the reference...
January 25, 2018: Genome Biology and Evolution
Falk Hillmann, Gillian Forbes, Silvia Novohradská, Iuliia Ferling, Konstantin Riege, Marco Groth, Martin Westermann, Manja Marz, Thomas Spaller, Thomas Winckler, Pauline Schaap, Gernot Glöckner
Establishment of multicellularity represents a major transition in eukaryote evolution. A subgroup of Amoebozoa, the dictyosteliids, has evolved a relatively simple aggregative multicellular stage resulting in a fruiting body supported by a stalk. Protosteloid amoeba, which are scattered throughout the amoebozoan tree, differ by producing only one or few single stalked spores. Thus, one obvious difference in the developmental cycle of protosteliids and dictyosteliids seems to be the establishment of multicellularity...
January 25, 2018: Genome Biology and Evolution
Cong Liang, Jacob M Musser, Alison Cloutier, Richard O Prum, Günter P Wagner
The evolution and diversification of cell types is a key means by which animal complexity evolves. Recently, hierarchical clustering and phylogenetic methods have been applied to RNA-seq data to infer cell type evolutionary history and homology. A major challenge for interpreting this data is that cell type transcriptomes may not evolve independently due to correlated changes in gene expression. This non-independence can arise for several reasons, such as common regulatory sequences for genes expressed in multiple tissues, i...
January 23, 2018: Genome Biology and Evolution
Mario A Cerón-Romero, Esther Nwaka, Zuliat Owoade, Laura A Katz
The genome of P. 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...
January 22, 2018: Genome Biology and Evolution
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