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Genome Biology and Evolution

Guido A Gnecchi-Ruscone, Paolo Abondio, Sara De Fanti, Stefania Sarno, Mingma G Sherpa, Phurba T Sherpa, Giorgio Marinelli, Luca Natali, Marco Di Marcello, Davide Peluzzi, Donata Luiselli, Davide Pettener, Marco Sazzini
Although Tibetans and Sherpa present several physiological adjustments evolved to cope with selective pressures imposed by the high altitude environment, especially hypobaric hypoxia, few selective sweeps at a limited number of hypoxia related genes were confirmed by multiple genomic studies. Nevertheless, variants at these loci were found to be associated only with downregulation of the erythropoietic cascade, which represents an indirect aspect of the considered adaptive phenotype. Accordingly, the genetic basis of Tibetan/Sherpa adaptive traits remains to be fully elucidated, in part due to limitations of selection scans implemented so far and mostly relying on the hard sweep model...
October 18, 2018: Genome Biology and Evolution
Hugh M Robertson, Robert M Waterhouse, Kimberly K O Walden, Livio Ruzzante, Maarten J M F Reijnders, Brad S Coates, Fabrice Legeai, Joanna C Gress, Sezgi Biyiklioglu, David K Weaver, Kevin W Wanner, Hikmet Budak
The wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents the distinctive Cephoidea superfamily of sawflies (Symphyta) that appeared early during the hymenopteran radiation, but after three early-branching eusymphytan superfamilies that form the base of the order Hymenoptera. We present a high-quality draft genome assembly of 162 Mbp in 1,976 scaffolds with a scaffold N50 of 622 kbp. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 non-coding RNA models...
October 18, 2018: Genome Biology and Evolution
Luke V Blakeway, Aimee Tan, Rachael Lappan, Amir Ariff, Janessa L Pickering, Christopher S Peacock, Christopher C Blyth, Charlene M Kahler, Barbara J Chang, Deborah Lehmann, Lea-Ann S Kirkham, Timothy F Murphy, Michael P Jennings, Lauren O Bakaletz, John M Atack, Ian R A Peak, Kate L Seib
Moraxella catarrhalis is a human-adapted pathogen, and a major cause of otitis media (OM) and exacerbations of chronic obstructive pulmonary disease (COPD). The species is comprised of two main phylogenetic lineages, RB1 and RB2/3. Restriction-modification (R-M) systems are among the few lineage-associated genes identified in other bacterial genera, and have multiple functions including defence against foreign invading DNA, maintenance of speciation, and epigenetic regulation of gene expression. Here we define the repertoire of R-M systems in 51 publicly available M...
October 18, 2018: Genome Biology and Evolution
Cassandra Koh, Scott L Allen, Rosemarie I Herbert, Elizabeth A McGraw, Stephen F Chenoweth
Dengue fever is the most prevalent arboviral disease globally. Dengue virus is transmitted primarily by the Aedes aegypti mosquito. One measure of the mosquito's efficiency as a vector is the extrinsic incubation period (EIP), which is the time between the ingestion of viremic blood and the emergence of virions in the saliva. The longer it takes virus to infect the midgut and traverse to the saliva, the fewer opportunities the mosquito will have to transmit the pathogen over its lifetime. We have shown previously that EIP for dengue virus is highly heritable and that it is negatively correlated with vector lifespan...
October 18, 2018: Genome Biology and Evolution
Christopher M Ward, Simon W Baxter
Cryptic species are genetically distinct taxa without obvious variation in morphology and are occasionally discovered using molecular or sequence datasets of populations previously thought to be a single species. The world-wide Brassica pest, Plutella xylostella (diamondback moth), has been a problematic insect in Australia since 1882, yet a morphologically cryptic species with apparent endemism (P. australiana) was only recognized in 2013. Plutella xylostella and P. australiana are able to hybridize under laboratory conditions, and it was unknown whether introgression of adaptive traits could occur in the field to improve fitness and potentially increase pressure on agriculture...
October 13, 2018: Genome Biology and Evolution
Diego Carriel, Pierre Simon Garcia, Florence Castelli, Patricia Lamourette, François Fenaille, Céline Brochier-Armanet, Sylvie Elsen, Irina Gutsche
Polyamines are small amino-acid derived polycations capable of binding negatively charged macromolecules. Bacterial polyamines are structurally and functionally diverse, and are mainly produced biosynthetically by PLP-dependent amino acid decarboxylases referred to as LAOdcs (Lysine-Arginine-Ornithine decarboxylases). In a phylogenetically limited group of bacteria, LAOdcs are also induced in response to acid stress. Here, we performed an exhaustive phylogenetic analysis of the AAT-fold LAOdcs which showcased the ancient nature of their short forms in Cyanobacteria and Firmicutes, and emergence of distinct subfamilies of long LAOdcs in Proteobacteria...
October 13, 2018: Genome Biology and Evolution
Mark J Margres, Manuel Ruiz-Aravena, Rodrigo Hamede, Menna E Jones, Matthew F Lawrance, Sarah A Hendricks, Austin Patton, Brian W Davis, Elaine A Ostrander, Hamish McCallum, Paul A Hohenlohe, Andrew Storfer
Understanding the genetic basis of disease-related phenotypes, such as cancer susceptibility, is crucial for the advancement of personalized medicine. Although most cancers are somatic in origin, a small number of transmissible cancers have been documented. Two such cancers have emerged in the Tasmanian devil (Sarcophilus harrisii ) and now threaten the species with extinction. Recently, cases of natural tumor regression in Tasmanian devils infected with the clonally contagious cancer have been detected. We used whole-genome sequencing and FST -based approaches to identify the genetic basis of tumor regression by comparing the genomes of seven individuals that underwent tumor regression with those of three infected individuals that did not...
October 13, 2018: Genome Biology and Evolution
Agnieszka Marek, Katarzyna Tomala
The negative correlation between the rate of protein evolution and expression level of a gene has been recognized as a universal law of the evolutionary biology (Koonin 2011). In our study we apply a population-based approach to systematically investigate the relative importance of unequal mutation rate, linkage and selection in the origin of the expression-polymorphism anticorrelation. We analyzed the DNA sequence of protein coding genes of 24 Saccharomyces cerevisiae and 58 Schizosaccharomyces pombe strains...
October 13, 2018: Genome Biology and Evolution
M Rouard, G Droc, G Martin, J Sardos, Y Hueber, V Guignon, A Cenci, B Geigle, M S Hibbins, N Yahiaoui, F-C Baurens, V Berry, M W Hahn, A D'Hont, N Roux
Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M...
October 13, 2018: Genome Biology and Evolution
Chih-Chi Lee, John Wang
Transposable elements (TEs) are present in almost all organisms and affect the host in various ways. TE activity can increase genomic variation and thereby affect host evolution. Currently active TEs are particularly interesting because they are likely generating new genomic diversity. These active TEs have been poorly studied outside of model organisms. In this study, we aimed to identify currently active TEs of a notorious invasive species, the red imported fire ant Solenopsis invicta. Using RNA profiling of male and female germline tissues, we found that the majority of TE-containing transcripts in the fire ant germline belong to the IS630-Tc1-Mariner superfamily...
October 9, 2018: Genome Biology and Evolution
J Nicolás Lazarte, Rocio P Lopez, P Daniel Ghiringhelli, Corina M Berón
Bacillus cereus sensu lato also known as Bacillus cereus group is composed of an ecologically diverse bacterial group with an increasing number of related species, some of which are medically or agriculturally important. Numerous efforts have been undertaken to allow presumptive differentiation of B. cereus group species from one another. FCC41 is a Bacillus sp. strain toxic against mosquito species like Aedes aegypti, Aedes (Ochlerotatus) albifasciatus, Culex pipiens, Culex quinquefasciatus and Culex apicinus, some of them responsible for the transmission of vector-borne diseases...
October 4, 2018: Genome Biology and Evolution
Joana Pereira, Andrei N Lupas
Outer membrane β-barrels (OMBBs) are toroidal arrays of anti-parallel β-strands that span the outer membrane of Gram-negative bacteria and eukaryotic organelles. Although homologous, most families of bacterial OMBBs evolved through the independent amplification of an ancestral ββ-hairpin. In mitochondria, one family (SAM50) has a clear bacterial ancestry; the origin of the other family, consisting of 19-stranded OMBBs found only in mitochondria (MOMBBs), is substantially unclear. In a large-scale comparison of mitochondrial and bacterial OMBBs, we find evidence that the common ancestor of all MOMBBs emerged by the amplification of a double ββ-hairpin of bacterial origin, probably at the time of the Last Eukaryotic Common Ancestor (LECA)...
September 28, 2018: Genome Biology and Evolution
Eva Pyrihová, Alžbeta Motycková, Luboš Voleman, Natalia Wandyszewska, Radovan Fišer, Gabriela Seydlová, Andrew Roger, Martin Kolísko, Pavel Doležal
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology...
September 28, 2018: Genome Biology and Evolution
Vanessa Romero, Hirofumi Nakaoka, Kazuyoshi Hosomichi, Ituro Inoue
Genomic duplication or loss can accelerate evolution because the number of repeats could affect molecular pathways and phenotypes. We have previously reported that the repeated region of filaggrin (FLG), a crucial component of the outer layers of mammalian skin, had high levels of nucleotide diversity with species-specific divergence and expansion and that it evolved under the birth-and-death model. We focused on hornerin (HRNR), a member of the same gene family that harbor similar tandem repeats as FLG, and examined the formation process of repeated regions and the evolutional model that best fit the HRNR repeated region in the crab-eating macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes) and compared them with the human (Homo sapiens) sequence...
September 26, 2018: Genome Biology and Evolution
Susan F Bailey, Qianyun Guo, Thomas Bataillon
Parallel evolution, defined as identical changes arising in independent populations, is often attributed to similar selective pressures favoring the fixation of identical genetic changes. However, some level of parallel evolution is also expected if mutation rates are heterogeneous across regions of the genome. Theory suggests that mutation and selection can have equal impacts on patterns of parallel evolution; however empirical studies have yet to jointly quantify the importance of these two processes. Here, we introduce several statistical models to examine the contributions of mutation and selection heterogeneity to shaping parallel evolutionary changes at the gene-level...
September 25, 2018: Genome Biology and Evolution
Erin S Kelleher, Ricardo B R Azevedo, Yichen Zheng
Transposable elements (TEs) are genomic parasites that impose fitness costs on their hosts by producing deleterious mutations and disrupting gametogenesis. Host genomes avoid these costs by regulating TE activity, particularly in germline cells where new insertions are heritable and TEs are exceptionally active. However, the capacity of different TE-associated fitness costs to select for repression in the host, and the role of selection in the evolution of TE regulation more generally, remain controversial...
September 25, 2018: Genome Biology and Evolution
Samar Kabbara, Anaïs Hérivaux, Thomas Dugé de Bernonville, Vincent Courdavault, Marc Clastre, Amandine Gastebois, Marwan Osman, Monzer Hamze, J Mark Cock, Pauline Schaap, Nicolas Papon
Histidine kinases (HKs) are primary sensor proteins that act in cell signaling pathways generically referred to as "two component systems" (TCSs). TCSs are among the most widely distributed transduction systems used by both prokaryotic and eukaryotic organisms to detect and respond to a broad range of environmental cues. The structure and distribution of HK proteins are now well documented in prokaryotes but information is still fragmentary for eukaryotes. Here, we have taken advantage of recent genomic resources to explore the structural diversity and the phylogenetic distribution of HKs in the prominent eukaryotic supergroups...
September 25, 2018: Genome Biology and Evolution
Eduardo Corel, Jananan S Pathmanathan, Andrew K Watson, Slim Karkar, Philippe Lopez, Eric Bapteste
The inclusion of introgressive processes in evolutionary studies induces a less constrained view of evolution. Network-based methods (like large-scale similarity networks) allow to include in comparative genomics all extra-chromosomic carriers (like viruses, the most abundant biological entities on the planet) with their cellular hosts. The integration of several levels of biological organization (genes, genomes, communities, environments) enables more comprehensive analyses of gene sharing and improved sequence-based classifications...
September 22, 2018: Genome Biology and Evolution
Ann-Kathrin Mix, Ugo Cenci, Thomas Heimerl, Pia Marter, Marie-Louise Wirkner, Daniel Moog
Peroxisomes are single-membrane-bound organelles with a huge metabolic versatility, including the degradation of fatty acids (β-oxidation) and the detoxification of reactive oxygen species as most conserved functions. Although peroxisomes seem to be present in the majority of investigated eukaryotes, where they are responsible for many eclectic and important spatially separated metabolic reactions, knowledge about their existence in the plethora of protists (eukaryotic microorganisms) is scarce.Here we investigated genomic data of organisms containing complex plastids with red algal ancestry (so-called 'chromalveolates') for the presence of genes encoding peroxins - factors specific for the biogenesis, maintenance and division of peroxisomes in eukaryotic cells...
September 22, 2018: Genome Biology and Evolution
George P Tiley, Michael S Barker, J Gordon Burleigh
Genomic data have provided evidence of previously unknown ancient whole genome duplications (WGDs) and highlighted the role of WGDs in the evolution of many eukaryotic lineages. Ancient WGDs often are detected by examining distributions of synonymous substitutions per site (Ks) within a genome, or "Ks plots". For example, WGDs can be detected from Ks plots by using univariate mixture models to identify peaks in Ks distributions. We performed gene family simulation experiments to evaluate the effects of different Ks estimation methods and mixture models on our ability to detect ancient WGDs from Ks plots...
September 18, 2018: Genome Biology and Evolution
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