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https://www.readbyqxmd.com/read/28729554/comparison-of-traditional-and-new-generation-dna-markers-declares-high-genetic-diversity-and-differentiated-population-structure-of-wild-almond-species
#1
Karim Sorkheh, Mehrana Koohi Dehkordi, Sezai Ercisli, Attila Hegedus, Júlia Halász
Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28725045/genomic-epidemiology-of-global-klebsiella-pneumoniae-carbapenemase-kpc-producing-escherichia-coli
#2
N Stoesser, A E Sheppard, G Peirano, L W Anson, L Pankhurst, R Sebra, H T T Phan, A Kasarskis, A J Mathers, T E A Peto, P Bradford, M R Motyl, A S Walker, D W Crook, J D Pitout
The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#3
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28722229/a-transposon-directed-epigenetic-change-in-zmcct-underlies-quantitative-resistance-to-gibberella-stalk-rot-in-maize
#4
Chao Wang, Qin Yang, Weixiang Wang, Yipu Li, Yanling Guo, Dongfeng Zhang, Xuena Ma, Wei Song, Jiuran Zhao, Mingliang Xu
A major resistance quantitative trait locus, qRfg1, significantly enhances maize resistance to Gibberella stalk rot, a devastating disease caused by Fusarium graminearum. However, the underlying molecular mechanism remains unknown. We adopted a map-based cloning approach to identify the resistance gene at qRfg1 and examined the dynamic epigenetic changes during qRfg1-mediated maize resistance to the disease. A CCT domain-containing gene, ZmCCT, is the causal gene at the qRfg1 locus and a polymorphic CACTA-like transposable element (TE1) c...
July 19, 2017: New Phytologist
https://www.readbyqxmd.com/read/28721856/repeat-induced-point-mutation-and-other-genome-defense-mechanisms-in-fungi
#5
Eugene Gladyshev
Transposable elements have colonized the genomes of nearly all organisms, including fungi. Although transposable elements may sometimes provide beneficial functions to their hosts their overall impact is considered deleterious. As a result, the activity of transposable elements needs to be counterbalanced by the host genome defenses. In fungi, the primary genome defense mechanisms include repeat-induced point mutation (RIP) and methylation induced premeiotically, meiotic silencing by unpaired DNA, sex-induced silencing, cosuppression (also known as somatic quelling), and cotranscriptional RNA surveillance...
July 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28715998/detection-of-active-transposable-elements-in-arabidopsis-thaliana-using-oxford-nanopore-sequencing-technology
#6
Emilie Debladis, Christel Llauro, Marie-Christine Carpentier, Marie Mirouze, Olivier Panaud
BACKGROUND: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV)...
July 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28715472/a-novel-isoform-of-il-33-revealed-by-screening-for-transposable-element-promoted-genes-in-human-colorectal-cancer
#7
Frances E Lock, Artem Babaian, Ying Zhang, Liane Gagnier, Sabrina Kuah, Antonia Weberling, Mohammad M Karimi, Dixie L Mager
Remnants of ancient transposable elements (TEs) are abundant in mammalian genomes. These sequences contain multiple regulatory motifs and hence are capable of influencing expression of host genes. TEs are known to be released from epigenetic repression and can become transcriptionally active in cancer. Such activation could also lead to lineage-inappropriate activation of oncogenes, as previously described in lymphomas. However, there are few reports of this mechanism occurring in non-blood cancers. Here, we re-analyzed whole transcriptome data from a large cohort of patients with colon cancer, compared to matched normal colon control samples, to detect genes or transcripts ectopically expressed through activation of TE promoters...
2017: PloS One
https://www.readbyqxmd.com/read/28711973/piwi-interacting-rnas-as-novel-regulators-of-pancreatic-beta-cell-function
#8
Imène Sarah Henaoui, Cécile Jacovetti, Inês Guerra Mollet, Claudiane Guay, Jonathan Sobel, Lena Eliasson, Romano Regazzi
AIMS/HYPOTHESIS: P-element induced Wimpy testis (PIWI)-interacting RNAs (piRNAs) are small non-coding RNAs that interact with PIWI proteins and guide them to silence transposable elements. They are abundantly expressed in germline cells and play key roles in spermatogenesis. There is mounting evidence that piRNAs are also present in somatic cells, where they may accomplish additional regulatory tasks. The aim of this study was to identify the piRNAs expressed in pancreatic islets and to determine whether they are involved in the control of beta cell activities...
July 16, 2017: Diabetologia
https://www.readbyqxmd.com/read/28695823/pervasive-epigenetic-effects-of-drosophila-euchromatic-transposable-elements-impact-their-evolution
#9
Yuh Chwen G Lee, Gary H Karpen
Transposable elements (TEs) are widespread genomic parasites, and their evolution has remained a critical question in evolutionary genomics. Here, we study the relatively unexplored epigenetic impacts of TEs and provide the first genome-wide quantification of such effects in D. melanogaster and D. simulans. Surprisingly, the spread of repressive epigenetic marks (histone H3K9me2) to nearby DNA occurs at >50% of euchromatic TEs, and can extend up to 20 kb. This results in differential epigenetic states of genic alleles and, in turn, selection against TEs...
July 11, 2017: ELife
https://www.readbyqxmd.com/read/28683794/genome-wide-analysis-of-wox-genes-in-upland-cotton-and-their-expression-pattern-under-different-stresses
#10
Zhaoen Yang, Qian Gong, Wenqiang Qin, Zuoren Yang, Yuan Cheng, Lili Lu, Xiaoyang Ge, Chaojun Zhang, Zhixia Wu, Fuguang Li
BACKGROUND: WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton. RESULTS: In this study, we identified 21, 20, and 38 WOX genes in Gossypium arboreum (2n = 26, A2), G. raimondii (2n = 26, D5), and G...
July 6, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28683762/segmental-duplications-evolution-and-impact-among-the-current-lepidoptera-genomes
#11
Qian Zhao, Dongna Ma, Liette Vasseur, Minsheng You
BACKGROUND: Structural variation among genomes is now viewed to be as important as single nucleoid polymorphisms in influencing the phenotype and evolution of a species. Segmental duplication (SD) is defined as segments of DNA with homologous sequence. RESULTS: Here, we performed a systematic analysis of segmental duplications (SDs) among five lepidopteran reference genomes (Plutella xylostella, Danaus plexippus, Bombyx mori, Manduca sexta and Heliconius melpomene) to understand their potential impact on the evolution of these species...
July 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28681105/chimeras-linked-to-tandem-repeats-and-transposable-elements-in-tetraploid-hybrid-fish
#12
Lihai Ye, Ni Jiao, Xiaojun Tang, Yiyi Chen, Xiaolan Ye, Li Ren, Fangzhou Hu, Shi Wang, Ming Wen, Chun Zhang, Min Tao, Shaojun Liu
The formation of the allotetraploid hybrid lineage (4nAT) encompasses both distant hybridization and polyploidization processes. The allotetraploid offspring have two sets of sub-genomes inherited from both parental species, and therefore, it is important to explore its genetic structure. Herein, we construct a bacterial artificial chromosome library of allotetraploids, and then sequence and analyze the full-length sequences of 19 bacterial artificial chromosomes. Sixty-eight DNA chimeras are identified, which are divided into four models according to the distribution of the genomic DNA derived from the parents...
July 5, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/28678163/genome-sequences-of-marine-shrimp-exopalaemon-carinicauda-holthuis-provide-insights-into-genome-size-evolution-of-caridea
#13
Jianbo Yuan, Yi Gao, Xiaojun Zhang, Jiankai Wei, Chengzhang Liu, Fuhua Li, Jianhai Xiang
Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemoncarinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions...
July 5, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28674418/commensal-to-pathogen-transition-one-single-transposon-insertion-results-in-two-pathoadaptive-traits-in-escherichia-coli-macrophage-interaction
#14
João T Proença, Duarte C Barral, Isabel Gordo
Escherichia coli is both a harmless commensal in the intestines of many mammals, as well as a dangerous pathogen. The evolutionary paths taken by strains of this species in the commensal-to-pathogen transition are complex and can involve changes both in the core genome, as well in the pan-genome. One way to understand the likely paths that a commensal strain of E. coli takes when evolving pathogenicity is through experimentally evolving the strain under the selective pressures that it will have to withstand as a pathogen...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28673235/comparative-analysis-of-lincrna-in-insect-species
#15
Alberto Lopez-Ezquerra, Mark C Harrison, Erich Bornberg-Bauer
BACKGROUND: The ever increasing availability of genomes makes it possible to investigate and compare not only the genomic complements of genes and proteins, but also of RNAs. One class of RNAs, the long noncoding RNAs (lncRNAs) and, in particular, their subclass of long intergenic noncoding RNAs (lincRNAs) have recently gained much attention because of their roles in regulation of important biological processes such as immune response or cell differentiation and as possible evolutionary precursors for protein coding genes...
July 3, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28672159/viruses-as-vectors-of-horizontal-transfer-of-genetic-material-in-eukaryotes
#16
REVIEW
Clément Gilbert, Richard Cordaux
Horizontal transfer (HT) of genetic material, mainly transposable elements, is increasingly recognized as an important factor shaping eukaryote genomes. Yet our understanding of the mechanisms and vectors underpinning these transfers is still limited. It has been proposed that such transfers may be facilitated by viruses, because they typically inject their genomes into host cells to replicate and they can be horizontally transmitted between their hosts. Recent evidence from high throughput sequencing of viral populations and paleovirology shows that both virus-to-host and host-to-virus gene flow can be common in a variety of eukaryote lineages...
June 30, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28667117/reduced-mutation-rate-and-increased-transformability-of-transposon-free-acinetobacter-baylyi-adp1-isx
#17
Gabriel A Suárez, Brian A Renda, Aurko Dasgupta, Jeffrey E Barrick
The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction...
June 30, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28664720/resistance-to-the-tetracyclines-and-macrolide-lincosamide-streptogramin-group-of-antibiotics-and-its-genetic-linkage-a-review
#18
REVIEW
Durdica Marosevic, Marija Kaevska, Zoran Jaglic
An excessive use of antimicrobial agents poses a risk for the selection of resistant bacteria. Of particular interest are antibiotics that have large consumption rates in both veterinary and human medicine, such as the tetracyclines and macrolide-lincosamide-streptogramin (MLS) group of antibiotics. A high load of these agents increases the risk of transmission of resistant bacteria and/or resistance determinants to humans, leading to a subsequent therapeutic failure. An increasing incidence of bacteria resistant to both tetracyclines and MLS antibiotics has been recently observed...
June 12, 2017: Annals of Agricultural and Environmental Medicine: AAEM
https://www.readbyqxmd.com/read/28662628/diversity-and-evolution-of-mariner-like-elements-in-aphid-genomes
#19
Maryem Bouallègue, Jonathan Filée, Imen Kharrat, Maha Mezghani-Khemakhem, Jacques-Deric Rouault, Mohamed Makni, Pierre Capy
BACKGROUND: Although transposons have been identified in almost all organisms, genome-wide information on mariner elements in Aphididae remains unknown. Genomes of Acyrthosiphon pisum, Diuraphis noxia and Myzus persicae belonging to the Macrosiphini tribe, actually available in databases, have been investigated. RESULTS: A total of 22 lineages were identified. Classification and phylogenetic analysis indicated that they were subdivided into three monophyletic groups, each of them containing at least one putative complete sequence, and several non-autonomous sublineages corresponding to Miniature Inverted-Repeat Transposable Elements (MITE), probably generated by internal deletions...
June 29, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28660784/the-novel-pseudomonas-putida-plasmid-p12969-2-harbors-an-in127-carrying-multidrug-resistant-region
#20
Yang Xu, Yong Niu, Fengjun Sun, Ying Yang, Wenbo Luo, Zhe Wang
AIM: This study aims to characterize a multidrug-resistant (MDR) plasmid p12969-2 coexistent with the previously reported one p12969-DIM in clinical Pseudomonas putida. MATERIALS & METHODS: The complete sequence of p12969-2 was determined using next-generation sequencing technology. RESULTS: p12969-2 contains a 29.2 kb MDR region, which carries In127 harboring three resistance genes aadA2, qacED1 and sul1. The MDR region is derived from the connection of Tn5041D and Tn5045, which is facilitated by two copies of miniature inverted-repeat transposable element...
June 29, 2017: Future Microbiology
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