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Genome Biology and Evolution

Liandong Yang, Zhaolei Zhang, Shunping He
Males and females often display extensive phenotypic differences, and many of these sexual dimorphisms are thought to result from differences between males and females in expression of genes present in both sexes. Sex-biased genes have been shown to exhibit accelerated rates of evolution in a wide array of species, however the cause of this remains enigmatic. In this study, we investigate the extent and evolutionary dynamics of sex-biased gene expression in zebrafish. Our results indicate that both male-biased genes and female-biased genes exhibit accelerated evolution at the protein level...
October 13, 2016: Genome Biology and Evolution
Pooja Narang, Melissa A Wilson Sayres
Male mutation bias, when more mutations are passed on via the male germline than via the female germline, is observed across mammals. One common way to infer the magnitude of male mutation bias, α, is to compare levels of neutral sequence divergence between genomic regions that spend different amounts of time in the male and female germline. For great apes, including human, we show that estimates of divergence are reduced in putatively unconstrained regions near genes relative to unconstrained regions far from genes...
October 4, 2016: Genome Biology and Evolution
A Fijarczyk, K Dudek, W Babik
Host-pathogen interactions may result in either directional selection or in pressure for the maintenance of polymorphism at the molecular level. Hence signatures of both positive and balancing selection are expected in immune genes. Because both overall selective pressure and specific targets may differ between species, large-scale population genomic studies are useful in detecting functionally important immune genes and comparing selective landscapes between taxa. Such studies are of particular interest in amphibians, a group threatened worldwide by emerging infectious diseases...
October 4, 2016: Genome Biology and Evolution
Atma M Ivancevic, R Daniel Kortschak, Terry Bertozzi, David L Adelson
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to 'jump' around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterised domain organisation. For the past 30 years, model organisms have been used to define L1s as 6-8kb sequences containing a 5'-UTR, two open reading frames working harmoniously in cis, and a 3'-UTR with a polyA tail...
October 3, 2016: Genome Biology and Evolution
Mihai Miclaus, Ovidiu Balacescu, Ioan Has, Loredana Balacescu, Voichita Has, Dana Suteu, Samuel Neuenschwander, Irene Keller, Rémy Bruggmann
The genomes of the two plant organelles encode for a relatively small number of proteins. Thus, nuclear genes encode the vast majority of their proteome. Organelleto-nucleus communication takes place through retrograde signaling (RS) pathways. Signals relayed through RS pathways have an impact on nuclear gene expression (NGE) but their target-genes remain elusive in a normal state of the cell (considering that only mutants and stress have been used so far). Here we use maize cytolines as an alternative. The nucleus of a donor line was transferred into two other cytoplasmic environments through at least nine back-crosses, in a time-span of more than 10 years...
October 3, 2016: Genome Biology and Evolution
Kirill V Mikhailov, Timur G Simdyanov, Vladimir V Aleoshin
Metchnikovellidae are a group of unusual microsporidians that lack some of the defining ultrastructural features characteristic of derived Microsporidia and are thought to be one of their earliest-branching lineages. The basal position of metchnikovellids was never confirmed by molecular phylogeny in published research, and thus far no genomic data for this group were available. In this work we obtain a partial genome of metchnikovellid Amphiamblys sp. using multiple displacement amplification, next-generation sequencing, and metagenomic binning approaches...
September 30, 2016: Genome Biology and Evolution
Maliha Rahman, Scott V Nguyen, Kimberly A McCullor, Catherine J King, James H Jorgensen, W Michael McShan
Streptococcus anginosus is a member of the normal oral flora that can become a pathogen causing pyogenic infections in humans. The genome of daptomycin-resistant strain J4206, originally isolated from a patient suffering from breakthrough bacteremia and septic shock at the University of Texas Health Science Center at San Antonio, was determined. The circular genome is 2,001,352 bp long with a GC content of 38.62% and contains multiple mobile genetic elements, including the phage-like chromosomal island SanCI that mediates a mutator phenotype, transposons, and integrative conjugative elements...
September 27, 2016: Genome Biology and Evolution
Susanne P Pfeifer, Jeffrey D Jensen
Levels of nucleotide diversity vary greatly across the genomes of most species owing to multiple factors. These include variation in the underlying mutation rates, as well as the effects of both direct and linked selection. Fundamental to interpreting the relative importance of these forces is the common observation of a strong positive correlation between nucleotide diversity and recombination rate. While indeed observed in humans, the interpretation of this pattern has been difficult in the absence of high quality polymorphism data and recombination maps in closely related species...
September 27, 2016: Genome Biology and Evolution
Muthukrishnan Eaaswarkhanth, Duo Xu, Colin Flanagan, Margarita Rzhetskaya, M Geoffrey Hayes, Ran Blekhman, Nina Jablonski, Omer Gokcumen
Human skin has evolved rapidly, leaving evolutionary signatures in the genome. The filaggrin (FLG) gene is widely studied for its skin-barrier function in humans. The extensive genetic variation in this gene, especially common loss-of-function (LoF) mutations, has been established as primary risk factors for atopic dermatitis. To investigate the evolution of this gene, we analyzed 2,504 human genomes and genotyped the copy number variation of filaggrin repeats within FLG in 126 individuals from diverse ancestral backgrounds...
September 27, 2016: Genome Biology and Evolution
Raquel Assis
Nested genes are the most common form of protein-coding overlap in eukaryotic genomes. Previous studies have shown that nested genes accumulate rapidly over evolutionary time, typically via the insertion of short young duplicate genes into long introns. However, the evolutionary relationship between nested genes remains unclear. Here, I compare RNA-seq expression profiles of nested, proximal intra-chromosomal, intermediate intra-chromosomal, distant intra-chromosomal, and inter-chromosomal gene pairs in two Drosophila species...
September 23, 2016: Genome Biology and Evolution
Geromy G Moore, Brian M Mack, Shannon B Beltz, Matthew K Gilbert
Aspergillus bombycis was first isolated from silkworm frass in Japan. It has been reportedly misidentified as A. nomius due to their macro-morphological and chemotype similarities. We sequenced the genome of the A. bombycis Type strain and found it to be comparable in size (37 Mb), as well as in numbers of predicted genes (12,266), to other sequenced Aspergilli. The aflatoxin gene cluster in this strain is similar in size and the genes are oriented the same as other B- + G-aflatoxin producing species, and this strain contains a complete but non-functional gene cluster for the production of cyclopiazonic acid...
September 23, 2016: Genome Biology and Evolution
Felix Grewe, Andan Zhu, Jeffrey P Mower
The mitochondrial nad1 gene of seed plants has a complex structure, including four introns in cis or trans configurations and a maturase gene (matR) hosted within the final intron. In the geranium family (Geraniaceae), however, sequencing of representative species revealed that three of the four introns, including one in a trans configuration and another that hosts matR, were lost from the nad1 gene in their common ancestor. Despite the loss of the host intron, matR has been retained as a freestanding gene in most genera of the family, indicating that this maturase has additional functions beyond the splicing of its host intron...
September 23, 2016: Genome Biology and Evolution
Elisa Anastasi, Iain MacArthur, Mariela Scortti, Sonsiray Alvarez, Steeve Giguère, Jose A Vazquez-Boland
We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates' gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core-genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome...
September 16, 2016: Genome Biology and Evolution
Ana M N Botelho, Maiana O C Costa, Cristiana O Beltrame, Fabienne A Ferreira, Nicholas C B Lima, Bruno S S Costa, Guilherme L de Morais, Rangel C Souza, Luiz G P Almeida, Ana T R Vasconcelos, Marisa F Nicolás, Agnes M S Figueiredo
Methicillin-resistant Staphylococcus aureus (MRSA) is still one of the most important hospital pathogen globally. The multiresistant isolates of the ST239-SCCmecIII lineage are spread over large geographic regions, colonizing and infecting hospital patients in virtually all continents. The balance between fitness (adaptability) and virulence potential is likely to represent an important issue in the clonal shift dynamics leading the success of some specific MRSA clones over another. The accessory gene regulator (agr) is the master quorum sensing system of staphylococci playing a role in the global regulation of key virulence factors...
September 15, 2016: Genome Biology and Evolution
Hongan Long, David J Winter, Allan Y-C Chang, Way Sung, Steven H Wu, Mariel Balboa, Ricardo B R Azevedo, Reed A Cartwright, Michael Lynch, Rebecca A Zufall
Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on Paramecium tetraurelia found an unusually low germline base-substitution mutation rate in this ciliate. Here, we tested the generality of this result among ciliates using Tetrahymena thermophila We sequenced the genomes of 10 lines of T. thermophila that had each undergone approximately 1,000 generations of mutation accumulation (MA). We applied an existing mutation-calling pipeline and developed a new probabilistic mutation detection approach that directly models the design of an MA experiment and accommodates the noise introduced by mismapped reads...
September 15, 2016: Genome Biology and Evolution
Oliver W Griffith, Matthew C Brandley, Katherine Belov, Michael B Thompson
The evolution of new organs is difficult to study because most vertebrate organs evolved only once, more than 500 million years ago. An ideal model for understanding complex organ evolution is the placenta, a structure that is present in live bearing reptiles and mammals (amniotes), which has evolved independently more than 115 times. Using transcriptomics, we characterised the uterine gene expression patterns through the reproductive cycle of a viviparous skink lizard, Pseudemoia entrecasteauxii Then we compare these patterns with the patterns of gene expression from two oviparous skinks Lampropholis guichenoti and Lerista bougainvillii While thousands of genes are differentially expressed between pregnant and non-pregnant uterine tissue in the viviparous skink, few differentially expressed genes were identified between gravid and non-gravid oviparous skinks...
September 15, 2016: Genome Biology and Evolution
Kevin N Chesmore, Jacquelaine Bartlett, Chao Cheng, Scott M Williams
Pleiotropy has been claimed to constrain gene evolution but specific mechanism and extent of these constraints have been difficult to demonstrate. The expansion of molecular data makes it possible to investigate these pleiotropic effects. Few classes of genes have been characterized as intensely as human transcription factors (TF). We therefore analyzed the evolutionary rates of full TF proteins, along with their DNA binding domains and protein-protein interacting domains in light of the degree of pleiotropy, measured by the number of TF-TF interaction, or the number of DNA binding targets...
September 15, 2016: Genome Biology and Evolution
Matteo Chiara, Caterina Manzari, Claudia Lionetti, Rosella Mechelli, Eleni Anastasiadou, Maria Chiara Buscarinu, Giovanni Ristori, Marco Salvetti, Ernesto Picardi, Anna Maria D'Erchia, Graziano Pesole, David S Horner
Epstein-Barr virus (EBV) latently infects the majority of the human population and is implicated as a causal or contributory factor in numerous diseases. We sequenced 27 complete EBV genomes from a cohort of Multiple Sclerosis (MS) patients and healthy controls from Italy, although no variants showed a statistically significant association with MS. Taking advantage of the availability of ~130 EBV genomes with known geographical origins, we reveal a striking geographic distribution of EBV sub-populations with distinct allele frequency distributions...
September 15, 2016: Genome Biology and Evolution
Thomas J Meyer, Ulrike Held, Kimberly A Nevonen, Sabine Klawitter, Thomas Pirzer, Lucia Carbone, Gerald G Schumann
LAVA ( L: INE- A: lu- V: NTR- A: lu-like) elements comprise a family of non-autonomous, composite, non-LTR retrotransposons specific to gibbons and may have played a role in the evolution of this lineage. A full-length LAVA element consists of portions of repeats found in most primate genomes: CT-rich, Alu-like, and VNTR regions from the SVA retrotransposon, and portions of the AluSz and L1ME5 elements. To evaluate whether the gibbon genome currently harbors functional LAVA elements capable of mobilization by the endogenous LINE-1 (L1) protein machinery and which LAVA components are important for retrotransposition, we established a trans-mobilization assay in HeLa cells...
September 15, 2016: Genome Biology and Evolution
Lilin Huang, Wenchao Gao, Domenico Giosa, Giuseppe Criseo, Jing Zhang, Tailong He, Xiaowen Huang, Jiufeng Sun, Yao Sun, Jiamin Huang, Yunqing Zhang, Balazs Brankovics, Fabio Scordino, Enrico D'Alessandro, Anne van Diepeningen, Sybren de Hoog, Huaiqiu Huang, Orazio Romeo
Sporothrix globosa is a thermo-dimorphic fungus belonging to a pathogenic clade that also includes Sporothrix schenckii, which causes human and animal sporotrichosis. Here, we present the first genome assemblies of two S. globosa strains providing data for future comparative genomic studies in pathogenic Sporothrix species.
September 15, 2016: Genome Biology and Evolution
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