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https://www.readbyqxmd.com/read/28749613/linked-selection-demography-and-the-evolution-of-correlated-genomic-landscapes-in-birds-and-beyond
#1
Reto Burri
Selection has a deep impact on the distribution of genetic diversity and population differentiation along the genome (the genomic landscapes of diversity and differentiation), reducing diversity and elevating differentiation not only at the sites it targets, but also at linked neutral sites. Fuelled by the high-throughput sequencing revolution, these genomic footprints of selection have been extensively exploited over the past decade with the aim to identify genomic regions involved in adaptation and speciation...
August 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28749073/arranging-eukaryotic-nuclear-dna-polymerases-for-replication-specific-interactions-with-accessory-proteins-arrange-pols-%C3%AE-%C3%AE-and-%C3%AF%C2%B5-in-the-replisome-for-leading-strand-and-lagging-strand-dna-replication
#2
REVIEW
Thomas A Kunkel, Peter M J Burgers
Biochemical and cryo-electron microscopy studies have just been published revealing interactions among proteins of the yeast replisome that are important for highly coordinated synthesis of the two DNA strands of the nuclear genome. These studies reveal key interactions important for arranging DNA polymerases α, δ, and ϵ for leading and lagging strand replication. The CMG (Mcm2-7, Cdc45, GINS) helicase is central to this interaction network. These are but the latest examples of elegant studies performed in the recent past that lead to a much better understanding of how the eukaryotic replication fork achieves efficient DNA replication that is accurate enough to prevent diseases yet allows evolution...
August 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28748289/genetic-recombinational-events-in-prokaryotes-and-their-viruses-insight-into-the-study-of-evolution-and-biodiversity
#3
REVIEW
Jean-Pierre Gratia
The exact meaning of sexual reproduction and the precise evolutionary period at which recombination first took place remains the subject of intense debates. Despite some unity in biochemical organisation of genetic recombination, a plethora of mechanisms are found to exist in microbes and their viruses. Some routes used by viruses bypass barriers to genetic heterology and provide bacteria with genes conferring a selective advantage, and some contribute to genome enlargement. The present review aims at highlighting the diversity of such mechanisms with a particular focus on spontaneous zygogenesis (or Z-mating)...
July 26, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28747921/unreduced-megagametophyte-production-in-lemon-occurs-via-three-meiotic-mechanisms-predominantly-second-division-restitution
#4
Houssem Rouiss, José Cuenca, Luis Navarro, Patrick Ollitrault, Pablo Aleza
Unreduced (2n) gametes have played a pivotal role in polyploid plant evolution and are useful for sexual polyploid breeding in various species, particularly for developing new seedless citrus varieties. The underlying mechanisms of 2n gamete formation were recently revealed for Citrus reticulata but remain poorly understood for other citrus species, including lemon (C. limon [L.] Burm. f.). Here, we investigated the frequency and causal meiotic mechanisms of 2n megagametophyte production in lemon. We genotyped 48progeny plants of two lemon genotypes, "Eureka Frost" and "Fino", using 16 Simple Sequence Repeat (SSR) and 18 Single Nucleotide Polymorphism (SNP) markers to determine the genetic origin of the progenies and the underlying mechanisms for 2n gamete formation...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28747720/mitochondrial-genomes-of-two-bombycoidea-insects-and-implications-for-their-phylogeny
#5
Zhao-Zhe Xin, Yu Liu, Xiao-Yu Zhu, Ying Wang, Hua-Bin Zhang, Dai-Zhen Zhang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
The mitochondrial genome (mt genome) provides important information for understanding molecular evolution and phylogenetics. As such, the two complete mt genomes of Ampelophaga rubiginosa and Rondotia menciana were sequenced and annotated. The two circular genomes of A. rubiginosa and R. menciana are 15,282 and 15,636 bp long, respectively, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes and an A + T-rich region. The nucleotide composition of the A. rubiginosa mt genome is A + T rich (81...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747666/comparative-analysis-of-four-buckwheat-species-based-on-morphology-and-complete-chloroplast-genome-sequences
#6
Cheng-Long Wang, Meng-Qi Ding, Chen-Yan Zou, Xue-Mei Zhu, Yu Tang, Mei-Liang Zhou, Ji-Rong Shao
Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28747543/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#7
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN/CS) and normal populations (pN/pS). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
July 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/28747381/rapid-evolution-of-female-biased-genes-among-four-species-of-anopheles-malaria-mosquitoes
#8
Francesco Papa, Nikolai Windbichler, Robert M Waterhouse, Alessia Cagnetti, Rocco D'Amato, Tania Persampieri, Mara K N Lawniczak, Tony Nolan, Philippos A Papathanos
Understanding how phenotypic differences between males and females arise from the sex-biased expression of nearly identical genomes can reveal important insights into the biology and evolution of a species. Among Anopheles mosquito species, these phenotypic differences include vectorial capacity, as it is only females that blood feed and thus transmit human malaria. Here, we use RNA-seq data from multiple tissues of four vector species spanning the Anopheles phylogeny to explore the genomic and evolutionary properties of sex-biased genes...
July 26, 2017: Genome Research
https://www.readbyqxmd.com/read/28747239/palaeoparasitology-and-palaeogenetics-review-and-perspectives-for-the-study-of-ancient-human-parasites
#9
Nathalie M-L Côté, Matthieu LE Bailly
While some species of parasites can be identified to species level from archaeological remains using microscopy (i.e. Enterobius vermicularis, Clonorchis sinensis), others can only be identified to family or genus level as different species produce eggs with similar morphology (i.e. Tænia sp. and Echinococcus sp.). Molecular and immunological approaches offer the possibility to provide more precise determination at the species level. They can also identify taxa when classic parasite markers such as eggs or cysts have been destroyed over time...
July 27, 2017: Parasitology
https://www.readbyqxmd.com/read/28746838/whole-genome-characterization-of-a-novel-porcine-reproductive-and-respiratory-syndrome-virus-1-isolate-genetic-evidence-for-recombination-between-amervac-vaccine-and-circulating-strains-in-mainland-china
#10
Nanhua Chen, Qiaorong Liu, Mingming Qiao, Xiaoyu Deng, Xizhao Chen, Ming Sun
Genotype 1 porcine reproductive and respiratory syndrome virus (PRRSV 1) have been continuously isolated in China in recent years. Complete genome sequences of these isolates are important to investigate the prevalence and evolution of Chinese PRRSV 1. Herein, we describe the isolation of a novel PRRSV 1 isolate, denominated HLJB1, in the Heilongjiang province of China. Complete genome sequencing of HLJB1 showed that it shares 90.66% and 58.21% nucleotide identities with PRRSV 1 and 2 prototypic strains Lelystad virus and ATCC VR-2332, respectively...
July 23, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28746449/gut-transcriptome-analysis-on-females-of-ornithodoros-mimon-acari-argasidae-and-phylogenetic-inference-of-ticks
#11
Gabriel Alves Landulfo, José Salvatore Leister Patané, Dalton Giovanni Nogueira da Silva, Inácio Loiola Meirelles Junqueira-de-Azevedo, Ronaldo Zucatelli Mendonca, Simone Michaela Simons, Eneas de Carvalho, Darci Moraes Barros-Battesti
Ornithodoros mimon is an argasid tick that parasitizes bats, birds and opossums and is also harmful to humans. Knowledge of the transcripts present in the tick gut helps in understanding the role of vital molecules in the digestion process and parasite-host relationship, while also providing information about the evolution of arthropod hematophagy. Thus, the present study aimed to know and ascertain the main molecules expressed in the gut of argasid after their blood meal, through analysis on the gut transcriptome of engorged females of O...
April 2017: Revista Brasileira de Parasitologia Veterinária, Brazilian Journal of Veterinary Parasitology
https://www.readbyqxmd.com/read/28746337/genome-wide-analysis-of-ivermectin-response-by-onchocerca-volvulus-reveals-that-genetic-drift-and-soft-selective-sweeps-contribute-to-loss-of-drug-sensitivity
#12
Stephen R Doyle, Catherine Bourguinat, Hugues C Nana-Djeunga, Jonas A Kengne-Ouafo, Sébastien D S Pion, Jean Bopda, Joseph Kamgno, Samuel Wanji, Hua Che, Annette C Kuesel, Martin Walker, Maria-Gloria Basáñez, Daniel A Boakye, Mike Y Osei-Atweneboana, Michel Boussinesq, Roger K Prichard, Warwick N Grant
BACKGROUND: Treatment of onchocerciasis using mass ivermectin administration has reduced morbidity and transmission throughout Africa and Central/South America. Mass drug administration is likely to exert selection pressure on parasites, and phenotypic and genetic changes in several Onchocerca volvulus populations from Cameroon and Ghana-exposed to more than a decade of regular ivermectin treatment-have raised concern that sub-optimal responses to ivermectin's anti-fecundity effect are becoming more frequent and may spread...
July 26, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28745717/evolution-and-conservation-of-characidium-sex-chromosomes
#13
R Utsunomia, P C Scacchetti, M Hermida, R Fernández-Cebrián, X Taboada, C Fernández, M Bekaert, N J Mendes, D Robledo, J E Mank, J B Taggart, C Oliveira, F Foresti, P Martínez
Fish species exhibit substantial variation in the degree of genetic differentiation between sex chromosome pairs, and therefore offer the opportunity to study the full range of sex chromosome evolution. We used restriction-site associated DNA sequencing (RAD-seq) to study the sex chromosomes of Characidium gomesi, a species with conspicuous heteromorphic ZW/ZZ sex chromosomes. We screened 9863 single-nucleotide polymorphisms (SNPs), corresponding to ~1 marker/100 kb distributed across the genome for sex-linked variation...
July 26, 2017: Heredity
https://www.readbyqxmd.com/read/28745003/an-evolutionary-perspective-on-the-systems-of-adaptive-immunity
#14
Viktor Müller, Rob J de Boer, Sebastian Bonhoeffer, Eörs Szathmáry
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback...
July 26, 2017: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/28744786/genetic-basis-of-exploiting-ecological-opportunity-during-the-long-term-diversification-of-a-bacterial-population
#15
Jessika Consuegra, Jessica Plucain, Joël Gaffé, Thomas Hindré, Dominique Schneider
Adaptive diversification is an essential evolutionary process, one that produces phenotypic innovations including the colonization of available ecological niches. Bacteria can diverge in sympatry when ecological opportunities allow, but the underlying genetic mechanisms are often unknown. Perhaps, the longest-lasting adaptive diversification seen in the laboratory occurred during the long-term evolution experiment, in which 12 populations of Escherichia coli have been evolving independently for more than 65,000 generations from a common ancestor...
July 25, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28743997/high-throughput-analysis-of-the-satellitome-revealed-enormous-diversity-of-satellite-dnas-in-the-neo-y-chromosome-of-the-cricket-eneoptera-surinamensis
#16
Octavio Manuel Palacios-Gimenez, Guilherme Borges Dias, Leonardo Gomes de Lima, Gustavo Campos E Silva Kuhn, Érica Ramos, Cesar Martins, Diogo Cavalcanti Cabral-de-Mello
Satellite DNAs (satDNAs) constitute large portion of eukaryote genomes, comprising non-protein-coding sequences tandemly repeated. They are mostly found in heterochromatic regions of chromosomes such as around centromere or near telomeres, in intercalary heterochromatin, and often in non-recombining segments of sex chromosomes. We examined the satellitome in the cricket Eneoptera surinamensis (2n = 9, neo-X1X2Y, males) to characterize the molecular evolution of its neo-sex chromosomes. To achieve this, we analyzed illumina reads using graph-based clustering and complementary analyses...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743951/genome-wide-analysis-and-expression-divergence-of-the-trihelix-family-in-brassica-rapa-insight-into-the-evolutionary-patterns-in-plants
#17
Wenli Wang, Peng Wu, TongKong Liu, Haibo Ren, Ying Li, Xilin Hou
Trihelix gene family is an important transcription factor (TF) family involved in plants' growth and development. This extensive study of trihelix genes from Arabidopsis thaliana to Brassica rapa could shed light on the evolution in plants and support crop breeding. In this study, a total of 52 trihelix genes were identified in B.rapa. Whole-genome annotation, molecular-evolution and gene-expression analyses of all known trihelix genes were conducted. By statistics of the number of trihelix genes in each species, we found the expansion of trihelix gene family started with angiosperm evolution...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743766/the-evolution-of-duplicate-gene-expression-in-mammalian-organs
#18
Katerina Guschanski, Maria Warnefors, Henrik Kaessmann
Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs...
July 25, 2017: Genome Research
https://www.readbyqxmd.com/read/28743759/anatolian-origins-and-diversification-of-aethionema-the-sister-lineage-of-the-core-brassicaceae
#19
Setareh Mohammadin, Kim Peterse, Sara J van de Kerke, Lars W Chatrou, Ali A Dönmez, Klaus Mummenhoff, J Chris Pires, Patrick P Edger, Ihsan A Al-Shehbaz, M Eric Schranz
PREMISE OF THE STUDY: The Irano-Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano-Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time-calibrated phylogenetic tree and biogeographical history of the genus is needed...
July 25, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28743260/molecular-evolution-of-two-asymptomatic-echovirus-6-strains-that-constitute-a-novel-branch-of-recently-epidemic-echovirus-6-in-china
#20
Hao Sun, Xiaoqin Huang, Keqin Lin, Kai Huang, Jiayou Chu, Zhaoqing Yang, Shaohui Ma
BACKGROUND: Echovirus 6 (E6) infections are associated with aseptic meningitis and acute flaccid paralysis (AFP). But some infections, sometimes most of them, are asymptomatic. The mechanism of E6 virulence is unknown. Analyses of the molecular evolution of asymptomatic E6 may help understand why the infections show different manifestations. METHODS: Ninety-six stool samples of healthy children in Yunnan, China were collected and two E6 strains were isolated from them...
July 25, 2017: Virology Journal
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