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Genome Biology and Evolution

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https://www.readbyqxmd.com/read/28104679/genome-sequencing-of-the-behaviour-manipulating-virus-lbfv-reveals-a-possible-new-virus-family
#1
D Lepetit, B Gillet, S Hughes, K Kraaijeveld, J Varaldi
Parasites are sometimes able to manipulate the behaviour of their hosts. However, the molecular cues underlying this phenomenon are poorly documented. We previously reported that the parasitoid wasp Leptopilina boulardi which develops from Drosophila larvae is often infected by an inherited DNA virus. In addition to being maternally transmitted, the virus benefits from horizontal transmission in superparasitized larvae (Drosophila that have been parasitized several times). Interestingly, the virus forces infected females to lay eggs in already parasitized larvae, thus increasing the chance of being horizontally transmitted...
January 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28087686/amoebozoans-are-secretly-but-ancestrally-sexual-evidence-for-sex-genes-and-potential-novel-crossover-pathways-in-diverse-groups-of-amoebae
#2
Yonas I Tekle, Fiona C Wood, Laura A Katz, Mario A Cerón-Romero, Lydia A Gorfu
Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade...
January 13, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082609/variation-in-the-intensity-of-selection-on-codon-bias-over-time-causes-contrasting-patterns-of-base-composition-evolution-in-drosophila
#3
Benjamin C Jackson, José L Campos, Penelope R Haddrill, Brian Charlesworth, Kai Zeng
Four-fold degenerate coding sites form a major component of the genome, and are often used to make inferences about selection and demography, so that understanding their evolution is important. Despite previous efforts, many questions regarding the causes of base composition changes at these sites in Drosophila remain unanswered. To shed further light on this issue, we obtained a new whole-genome polymorphism dataset from D. simulans We analysed samples from the putatively ancestral range of D. simulans, as well as an existing polymorphism dataset from an African population of D...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082608/the-conservation-of-the-germline-multipotency-program-from-sponges-to-vertebrates-a-stepping-stone-to-understanding-the-somatic-and-germline-origins
#4
Laura Fierro-Constaín, Quentin Schenkelaars, Eve Gazave, Anne Haguenauer, Caroline Rocher, Alexander Ereskovsky, Carole Borchiellini, Emmanuelle Renard
The germline definition in metazoans was first based on few bilaterian models. As a result, gene function interpretations were often based on phenotypes observed in those models and led to the definition of a set of genes, considered as specific of the germline, named the "germline core". However, some of these genes were shown to also be involved in somatic stem cells, thus leading to the notion of germline multipotency program (GMP). Because Porifera and Ctenophora are currently the best candidates to be the sister-group to all other animals, the comparative analysis of gene contents and functions between these phyla, Cnidaria and Bilateria is expected to provide clues on early animal evolution and on the links between somatic and germ lineages...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082607/2b-or-not-2b-experimental-evolution-of-functional-exogenous-sequences-in-a-plant-rna-virus
#5
Anouk Willemsen, Mark P Zwart, Silvia Ambrós, José L Carrasco, Santiago F Elena
Horizontal gene transfer (HGT) is pervasive in viruses, and thought to be a key mechanism in their evolution. On the other hand, strong selective constraints against increasing genome size are an impediment for HGT, rapidly purging horizontally transferred sequences and thereby potentially hindering evolutionary innovation. Here we explore experimentally the evolutionary fate of viruses with simulated HGT events, using the plant RNA virus Tobacco etch virus (TEV), by separately introducing two functional, exogenous sequences to its genome...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082606/support-for-lungfish-as-the-closest-relative-of-tetrapods-by-using-slowly-evolving-ray-finned-fish-as-the-outgroup
#6
LETTER
Naoko Takezaki, Hidenori Nishihara
In a previous analysis of the phylogenetic relationships of coelacanths, lungfishes and tetrapods, using cartilaginous fish as the outgroup, the sister relationship of lungfishes and tetrapods was constructed with high statistical support. However, using as the outgroup ray-finned fish, which are more taxonomically closely related to the three lineages than cartilaginous fish, the sister relationship of coelacanths and tetrapods was most often constructed depending on the methods and the data sets, but the statistical support was generally low except in the cases in which the data set including a small number of species was analyzed...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082605/molecular-evolution-of-piggybac-superfamily-from-selfishness-to-domestication
#7
Maryem Bouallègue, Jacques-Deric Rouault, Aurélie Hua-Van, Mohamed Makni, Pierre Capy
The piggyBac transposable element was originally isolated from the cabbage looper moth, Trichoplusia ni, in the 1980s. Despite its early discovery and specificity compared to the other Class II elements, the diversity and evolution of this superfamily have been only partially analyzed. Two main types of elements can be distinguished: the piggyBac-like elements (PBLE) with terminal inverted repeats (TIR), UTR and an ORF encoding a transposase, and the piggyBac-derived sequences (PGBD), containing a sequence derived from a piggyBac transposase, and which correspond to domesticated elements...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082604/landscape-of-fluid-sets-of-hairpin-derived-21-24-nt-long-small-rnas-at-seed-set-uncovers-special-epigenetic-features-in-picea-glauca
#8
Yang Liu, Yousry A El-Kassaby
Conifers' exceptionally large genome (20-30 Gb) is scattered with 60% retrotransposon (RT) components and we have little knowledge on their origin and evolutionary implications. RTs may impede the expression of flanking genes and provide sources of the formation of novel small RNA (sRNAs) populations to constrain events of transposon (TE) proliferation/transposition. Here we show a declining expression of 24-nt-long sRNAs and low expression levels of their key processing gene, pgRTL2 (RNASE THREE LIKE 2) at seed set in Picea glauca The sRNAs in 24-nt size class are significantly less enriched in type and read number than 21-nt sRNAs and have not been documented in other species...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082603/analysis-of-three-sugarcane-homo-homeologous-regions-suggests-independent-polyploidization-events-of-saccharum-officinarum-and-saccharum-spontaneum
#9
Mariane de Mendonça Vilela, Luiz-Eduardo Del-Bem, Marie-Anne Van Sluys, Nathalia de Setta, João Paulo Kitajima, Guilherme Marcelo Queiroga Cruz, Danilo Augusto Sforça, Anete Pereira de Souza, Paulo Cavalcanti Gomes Ferreira, Clícia Grativol, Claudio Benicio Cardoso-Silva, Renato Vicentini, Michel Vincentz
Whole genome duplication has played an important role in plant evolution and diversification. Sugarcane is an important crop with a complex hybrid polyploid genome, for which the process of adaptation to polyploidy is still poorly understood. In order to improve our knowledge about sugarcane genome evolution and the homo/homeologous gene expression balance, we sequenced and analyzed 27 BACs (Bacterial Artificial Chromosome) of sugarcane R570 cultivar, containing the putative single-copy genes LFY (seven haplotypes), PHYC (four haplotypes) and TOR (seven haplotypes)...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082602/a-snp-enabled-assessment-of-genetic-diversity-evolutionary-relationships-and-the-identification-of-candidate-genes-in-chrysanthemum
#10
Xinran Chong, Fei Zhang, Yangyang Wu, Xiaodong Yang, Nan Zhao, Haibin Wang, Zhiyong Guan, Weimin Fang, Fadi Chen
Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. A set of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082601/genomic-characterization-of-the-evolutionary-potential-of-the-sea-urchin-strongylocentrotus-droebachiensis-facing-ocean-acidification
#11
Daniel E Runcie, Narimane Dorey, David A Garfield, Meike Stumpp, Sam Dupont, Gregory A Wray
Ocean acidification (OA) is increasing due to anthropogenic CO2 emissions, and poses a threat to marine species and communities worldwide. To better project the effects of acidification on organisms' health and persistence an understanding is needed of (1) the mechanisms underlying developmental and physiological tolerance, and (2) the potential populations have for rapid evolutionary adaptation. This is especially challenging in non-model species where targeted assays of metabolism and stress physiology may not be available or economical for large-scale assessments of genetic constraints...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082600/evolution-of-chaperonin-gene-duplication-in-stigonematalean-cyanobacteria-subsection-v
#12
Julia Weissenbach, Judith Ilhan, David Bogumil, Nils Hülter, Karina Stucken, Tal Dagan
Chaperonins promote protein folding and are known to play a role in the maintenance of cellular stability under stress conditions. The group I bacterial chaperonin complex comprises GroEL, that forms a barrel-like oligomer, and GroES that forms the lid. In most eubacteria the GroES/GroEL chaperonin is encoded by a single-copy bicistronic operon, whereas in cyanobacteria up to three groES/groEL paralogs have been documented. Here we study the evolution and functional diversification of chaperonin paralogs in the heterocystous, multi-seriate filament forming cyanobacterium Chlorogloeopsis fritschii PCC 6912...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28082599/hsp90-and-physiological-stress-are-linked-to-autonomous-transposon-mobility-and-heritable-genetic-change-in-nematodes
#13
Calen P Ryan, Jeremy C Brownlie, Steve Whyard
Transposable elements (TEs) have been recognized as potentially powerful drivers of genomic evolutionary change, but factors affecting their mobility and regulation remain poorly understood. Chaperones such as Hsp90 buffer environmental perturbations by regulating protein conformation, but are also part of the PIWI-interacting RNA pathway, which regulates genomic instability arising from mobile TEs in the germline. Stress-induced mutagenesis from TE movement could thus arise from functional trade-offs in the dual roles of Hsp90...
January 12, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28069829/genomic-insights-into-a-sustained-national-outbreak-of-yersinia-pseudotuberculosis
#14
Deborah A Williamson, Sarah L Baines, Glen Carter, Anders Gonçalves da Silva, Xiaoyun Ren, Jill Sherwood, Muriel Dufour, Mark B Schultz, Nigel P French, Torsten Seemann, Timothy P Stinear, Benjamin P Howden
In 2014, a sustained outbreak of yersiniosis due to Yersinia pseudotuberculosis occurred across all major cities in New Zealand (NZ), with a total of 220 laboratory-confirmed cases, representing one of the largest ever reported outbreaks of Y. pseudotuberculosis Here, we performed whole genome sequencing of outbreak-associated isolates to produce the largest population analysis to date of Y. pseudotuberculosis, giving us unprecedented capacity to understand the emergence and evolution of the outbreak clone...
January 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062756/phylogenetic-origin-and-diversification-of-rnai-pathway-genes-in-insects
#15
Daniel Dowling, Thomas Pauli, Alexander Donath, Karen Meusemann, Lars Podsiadlowski, Malte Petersen, Ralph S Peters, Christoph Mayer, Shanlin Liu, Xin Zhou, Bernhard Misof, Oliver Niehuis
RNA interference (RNAi) refers to the set of molecular processes found in eukaryotic organisms in which small RNA molecules mediate the silencing or down-regulation of target genes. In insects, RNAi serves a number of functions, including regulation of endogenous genes, anti-viral defense, and defense against transposable elements. Despite being well studied in model organisms, such as Drosophila, the distribution of core RNAi pathway genes and their evolution in insects is not well understood. Here we present the most comprehensive overview of the distribution and diversity of core RNAi pathway genes across 100 insect species, encompassing all currently recognized insect orders...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062755/evolutionary-conservation-and-divergence-of-gene-coexpression-networks-in-gossypium-cotton-seeds
#16
Guanjing Hu, Ran Hovav, Corrinne E Grover, Adi Faigenboim-Doron, Noa Kadmon, Justin T Page, Joshua A Udall, Jonathan F Wendel
The cotton genus (Gossypium) provides a superior system for the study of diversification, genome evolution, polyploidization, and human-mediated selection. To gain insight into phenotypic diversification in cotton seeds, we conducted coexpression network analysis of developing seeds from diploid and allopolyploid cotton species and explored network properties. Key network modules and functional associations were identified related to seed oil content and seed weight. We compared species-specific networks to reveal topological changes, including rewired edges and differentially coexpressed genes, associated with speciation, polyploidy, and cotton domestication...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062754/mycobacterium-tuberculosis-complex-exhibits-lineage-specific-variations-affecting-protein-ductility-and-epitope-recognition
#17
Inmaculada Yruela, Bruno Contreras-Moreira, Carlos Magalhães, Nuno S Osório, Jesús Gonzalo-Asensio
The advent of whole-genome sequencing has provided an unprecedented detail about the evolution and genetic significance of species-specific variations across the whole Mycobacterium tuberculosis Complex. However, little attention has been focused on understanding the functional roles of these variations in the protein coding sequences. In this work, we compare the coding sequences from 74 sequenced mycobacterial species including M. africanum, M. bovis, M. canettii, M. caprae, M. orygis, and M. tuberculosis Results show that albeit protein variations affect all functional classes, those proteins involved in lipid and intermediary metabolism and respiration have accumulated mutations during evolution...
January 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28062753/standard-codon-substitution-models-overestimate-purifying-selection-for-non-stationary-data
#18
Benjamin D Kaehler, Von Bing Yap, Gavin A Huttley
Estimation of natural selection on protein-coding sequences is a key comparative genomics approach for de novo prediction of lineage-specific adaptations. Selective pressure is measured on a per-gene basis by comparing the rate of non-synonymous substitutions to the rate of synonymous substitutions. All published codon substitution models have been time-reversible and thus assume that sequence composition does not change over time. We previously demonstrated that if time-reversible DNA substitution models are applied in the presence of changing sequence composition, the number of substitutions is systematically biased towards overestimation...
January 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28057732/satellite-dna-and-transposable-elements-in-seabuckthorn-hippophae-rhamnoides-a-dioecious-plant-with-small-y-and-large-x-chromosomes
#19
Janka Puterova, Olga Razumova, Tomas Martinek, Oleg Alexandrov, Mikhail Divashuk, Zdenek Kubat, Roman Hobza, Gennady Karlov, Eduard Kejnovsky
Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28057731/extremely-low-genomic-diversity-of-rickettsia-japonica-distributed-in-japan
#20
Arzuba Akter, Tadasuke Ooka, Yasuhiro Gotoh, Seigo Yamamoto, Hiromi Fujita, Fumio Terasoma, Kouji Kida, Masakatsu Taira, Fumiko Nakadouzono, Mutsuyo Gokuden, Manabu Hirano, Mamoru Miyashiro, Kouichi Inari, Yukie Shimazu, Kenji Tabara, Atsushi Toyoda, Dai Yoshimura, Takehiko Itoh, Tomokazu Kitano, Mitsuhiko P Sato, Keisuke Katsura, Shakhinur Islam Mondal, Yoshitoshi Ogura, Shuji Ando, Tetsuya Hayashi
Rickettsiae are obligate intracellular bacteria that have small genomes as a result of reductive evolution. Many Rickettsia species of the spotted fever group (SFG) cause tick-borne diseases known as "spotted fevers." The life cycle of SFG rickettsiae is closely associated with that of the tick, which is generally thought to act as a bacterial vector and reservoir that maintains the bacterium through transstadial and transovarial transmission. Each SFG member is thought to have adapted to a specific tick species, thus restricting the bacterial distribution to a relatively limited geographic region...
January 4, 2017: Genome Biology and Evolution
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