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Genome Biology and Evolution

Kåre Olav Holm, Cecilie Bækkedal, Jenny Johansson Söderberg, Peik Haugen
We report here the complete genome sequences of seven Vibrio anguillarum strains isolated from multiple geographic locations, thus increasing the total number of genomes of finished quality to eleven. The genomes were de novo assembled from long sequence PacBio reads. Including draft genomes, a total of 44 V. anguillarum genomes are currently available in the genome databases. They represent an important resource in the study of e.g. genetic variations and for identifying virulence determinants. In this paper, we present the genomes and basic genome comparisons of the eleven complete genomes, including a BRIG analysis, and pan genome calculation...
April 7, 2018: Genome Biology and Evolution
Mari Tohya, Tsutomu Sekizaki, Tohru Miyoshi-Akiyama
Streptococcus ruminantium sp. nov. of type strain GUT-187T, previously classified as S. suis serotype 33, is a recently described novel streptococcal species. This study was designed to determine the complete genome sequence of S. ruminantium GUT-187T using a combination of Oxford Nanopore and the Illumina platform, and to compare this sequence with the genomes of 27 S. suis representative strains. The genome of GUT-187T was 2,090,539 bp in size, with a GC content of 40.01%. This genome contained 1,961 predicted protein coding DNA sequences (CDSs); of these, 1,685 (85...
April 6, 2018: Genome Biology and Evolution
Jordi Morata, Fatima Marín, Jordi Payet, Josep M Casacuberta
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. MITEs are a type of non-coding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution...
April 5, 2018: Genome Biology and Evolution
Anna M Floriano, Michele Castelli, Sascha Krenek, Thomas U Berendonk, Chiara Bazzocchi, Giulio Petroni, Davide Sassera
"Candidatus Fokinia solitaria" is an obligate intracellular endosymbiont of a unicellular eukaryote, a ciliate of the genus Paramecium. Here we present the genome sequence of this bacterium and subsequent analysis. Phylogenomic analysis confirmed the previously reported positioning of the symbiont within the "Candidatus Midichloriaceae" family (order Rickettsiales), as well as its high sequence divergence from other members of the family, indicative of fast sequence evolution. Consistently with this high evolutionary rate, a comparative genomic analysis revealed that the genome of this symbiont is the smallest of the Rickettsiales to date...
April 5, 2018: Genome Biology and Evolution
Jessica Nye, Hafid Laayouni, Martin Kuhlwilm, Mayukh Mondal, Tomas Marques-Bonet, Jaume Bertranpetit
During the demographic history of the Pan clade there has been gene-flow between species, likely more than 200,000 years ago. Bonobo haplotypes in three subspecies of chimpanzee have been identified to be segregating in modern-day chimpanzee populations, suggesting that these haplotypes, with increased differentiation, may be a target of natural selection. Here, we investigate signatures of adaptive introgression within the bonobo-like haplotypes in chimpanzees using site frequency spectrum-based tests. We find evidence for subspecies-specific adaptations in introgressed regions involved with male reproduction in central chimpanzees, the immune system in eastern chimpanzees, female reproduction and the nervous system in Nigeria-Cameroon chimpanzees...
April 4, 2018: Genome Biology and Evolution
Waldan K Kwong, Margaret I Steele, Nancy A Moran
Honey bees have distinct gut microbiomes consisting almost entirely of several host-specific bacterial species. We present the genomes of three strains of Apibacter spp., bacteria of the Bacteroidetes phylum that are endemic to Asian honey bee species (Apis dorsata and Apis cerana). The Apibacter strains have similar metabolic abilities to each other and to Apibacter mensalis, a species isolated from a bumble bee. They use microaerobic respiration and fermentation to catabolize a limited set of monosaccharides and di-carboxylic acids...
April 4, 2018: Genome Biology and Evolution
Cristina Valente, Luis Alvarez, Patrícia Isabel Marques, Leonor Gusmão, António Amorim, Susana Seixas, Maria João Prata
Taste perception is crucial in monitoring food intake and, hence, is thought to play a significant role in human evolution. To gain insights into possible adaptive signatures in genes encoding bitter, sweet, and umami taste receptors, we surveyed the available sequence variation data from the 1000 Genomes Project Phase 3 for TAS1R (TAS1R1-3) and TAS2R (TAS2R16 and TAS2R38) families. Our study demonstrated that genes from these two families have experienced contrasting evolutionary histories: While TAS1R1 and TAS1R3 showed worldwide evidence of positive selection, probably correlated with improved umami and sweet perception, the patterns of variation displayed by TAS2R16 and TAS2R38 were more consistent with scenarios of balancing selection that possibly conferred a heterozygous advantage associated with better capacity to perceive a wide range of bitter compounds...
April 4, 2018: Genome Biology and Evolution
Liam Abrahams, Laurence D Hurst
Stop codons are frequently selected for beyond their regular termination function for error control. The 'ambush hypothesis' proposes out of frame stop codons (OSCs) terminating frameshifted translations are selected for. Although early indirect evidence was partially supportive, recent evidence suggests OSC frequencies are not exceptional when considering underlying nucleotide content. However, prior null tests fail to control amino acid/codon usages or possible local mutational biases. We therefore return to the issue using bacterial genomes, considering several tests defining and testing against a null...
April 2, 2018: Genome Biology and Evolution
Guillaume Méric, Alan McNally, Alberto Pessia, Evangelos Mourkas, Ben Pascoe, Leonardos Mageiros, Minna Vehkala, Jukka Corander, Samuel K Sheppard
Human infection with the gastrointestinal pathogen C. jejuni is dependent upon the opportunity for zoonotic transmission and the ability of strains to colonize the human host. Certain lineages of this diverse organism are more common in human infection but the factors underlying this overrepresentation are not fully understood. We analysed 601 isolate genomes from agricultural animals and human clinical cases, including isolates from the multi-host (ecological generalist) ST-21 and ST-45 clonal complexes (CCs)...
February 14, 2018: Genome Biology and Evolution
Germain Chevignon, Bret M Boyd, Jayce W Brandt, Kerry M Oliver, Michael R Strand
Many insects host facultative, bacterial symbionts that confer conditional fitness benefits to their hosts. Hamiltonella defensa is a common facultative symbiont of aphids that provides protection against parasitoid wasps. Protection levels vary among strains of H. defensa that are also differentially infected by bacteriophages named APSEs. However, little is known about trait variation among strains because only one isolate has been fully sequenced. Generating complete genomes for facultative symbionts is hindered by relatively large genome sizes but low abundances in hosts like aphids that are very small...
February 14, 2018: 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
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