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https://www.readbyqxmd.com/read/29679645/sequencing-of-pt5282-ctxm-p13190-kpc-and-p30860-nr-and-comparative-genomics-analysis-of-incx8-plasmids
#1
Haihong Fang, Jiao Feng, Yuanhong Xu, Ying Zhang, Zhe Zhan, Zhe Yin, Xiongbo Duan, Bo Gao, Yigang Tong, Jinglin Wang, Yanping Luo, Erhei Dai, Dongsheng Zhou
This study proposed a replicon-based scheme for typing IncX into nine separately clustering subgroups, including IncX1α, IncX1β and IncX2-8. The complete nucleotide sequences of three IncX8 plasmids, namely pT5282-CTXM and p30860-NR from Enterobacter cloacae and p13190-KPC from Klebsiella pneumoniae, were determined and compared with all the other two previously sequenced IncX8 plasmids pCAV1043-58 and pCAV1741-16. These five plasmids possessed conserved IncX8 backbones with limited genetic variations with respect to gene content and organization, and each of them carried one or three accessory modules that harbored resistance markers and metabolic gene clusters as well as transposons, insertion sequence (IS)-based transposition units and miniature inverted repeat transposable elements, indicating that the relatively small IncX8 backbones were able to integrate various foreign genetic contents...
April 18, 2018: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/29678924/sirnas-and-pirnas-collaborate-for-transposon-control-in-the-two-spotted-spider-mite
#2
Mosharrof Mondal, Kody Mansfield, Alex Flynt
RNAi has revolutionized genetic research, and is being commercialized as an insect pest control technology. Mechanisms exploited for this purpose are antiviral and therefore rapidly evolving. Ideally, RNAi will also be used for non-insect pests, however, differences in RNAi biology makes this uncertain. Tetranychus urticae (two-spotted spider mite) is a destructive non-insect pest, which has a proclivity to develop pesticide resistance. Here we provide a comprehensive study of the endogenous RNAi pathways of spider mites to inform design of exogenous RNAi triggers...
April 20, 2018: RNA
https://www.readbyqxmd.com/read/29675466/parallel-evolution-of-batesian-mimicry-supergene-in-two-papilio-butterflies-p-polytes-and-p-memnon
#3
Takuro Iijima, Rei Kajitani, Shinya Komata, Chung-Ping Lin, Teiji Sota, Takehiko Itoh, Haruhiko Fujiwara
Batesian mimicry protects animals from predators when mimics resemble distasteful models. The female-limited Batesian mimicry in Papilio butterflies is controlled by a supergene locus switching mimetic and nonmimetic forms. In Papilio polytes , recent studies revealed that a highly diversified region (HDR) containing doublesex ( dsx -HDR) constitutes the supergene with dimorphic alleles and is likely maintained by a chromosomal inversion. In the closely related Papilio memnon , which exhibits a similar mimicry polymorphism, we performed whole-genome sequence analyses in 11 butterflies, which revealed a nearly identical dsx -HDR containing three genes ( dsx , Nach-like , and UXT ) with dimorphic sequences strictly associated with the mimetic/nonmimetic phenotypes...
April 2018: Science Advances
https://www.readbyqxmd.com/read/29674435/phylogenetic-and-phylogenomic-definition-of-rhizopus-species
#4
Andrii P Gryganskyi, Jacob Golan, Somayeh Dolatabadi, Stephen Mondo, Sofia Robb, Alexander Idnurm, Anna Muszewska, Kamil Steczkiewicz, Sawyer Masonjones, Hui-Ling Liao, Michael T Gajdeczka, Felicia Anike, Antonina Vuek, Iryna M Anishchenko, Kerstin Voigt, G Sybren de Hoog, Matthew E Smith, Joseph Heitman, Rytas Vilgalys, Jason E Stajich
Phylogenomic approaches have the potential to improve confidence about the inter-relationships of species in the order Mucorales within the fungal tree of life. Rhizopus species are especially important as plant and animal pathogens and bioindustrial fermenters for food and metabolite production. A dataset of 192 orthologous genes was used to construct a phylogenetic tree of 21 Rhizopus strains, classified into four species isolated from habitats of industrial, medical and environmental importance. The phylogeny indicates that the genus Rhizopus consists of three major clades, with R...
April 19, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29673330/modular-assembly-of-transposable-element-arrays-by-microsatellite-targeting-in-the-guayule-and-rice-genomes
#5
José A Valdes Franco, Yi Wang, Naxin Huo, Grisel Ponciano, Howard A Colvin, Colleen M McMahan, Yong Q Gu, William R Belknap
BACKGROUND: Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. RESULTS: The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50  = 22 kb), maps > 95% of the shotgun reads and is essentially complete...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29670042/long-non-coding-rnas-in-neuronal-aging
#6
REVIEW
Diana Pereira Fernandes, Mainá Bitar, Frank M J Jacobs, Guy Barry
The expansion of long non-coding RNAs (lncRNAs) in organismal genomes has been associated with the emergence of sophisticated regulatory networks that may have contributed to more complex neuronal processes, such as higher-order cognition. In line with the important roles of lncRNAs in the normal functioning of the human brain, dysregulation of lncRNA expression has been implicated in aging and age-related neurodegenerative disorders. In this paper, we discuss the function and expression of known neuronal-associated lncRNAs, their impact on epigenetic changes, the contribution of transposable elements to lncRNA expression, and the implication of lncRNAs in maintaining the 3D nuclear architecture in neurons...
April 18, 2018: Non-Coding RNA
https://www.readbyqxmd.com/read/29664234/characterization-of-maize-leaf-pyruvate-orthophosphate-dikinase-using-high-throughput-sequencing
#7
Yuling Zhang, Rita Giuliani, Youjun Zhang, Yang Zhang, Wagner Luiz Araujo, Baichen Wang, Peng Liu, Qi Sun, Asaph Cousins, Gerald Edwards, Alisdair Fernie, Thomas P Brutnell, Pinghua Li
In C4 photosynthesis, pyruvate orthophosphate dikinase (PPDK) catalyzes the regeneration of phosphoenolpyruvate in the carbon shuttle pathway. Although the biochemical function of PPDK in maize is well characterized, a genetic analysis of PPDK has not been reported. In this study, we utilize the maize transposable elements Mutator and Ds to generate multiple mutant alleles of PPDK. Loss-of-function mutants are seedling lethal even when plants were grown under 2% CO2 , and they show very low capacity for CO2 assimilation indicating C4 photosynthesis is essential in maize...
April 17, 2018: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29659815/plant-lineage-specific-amplification-of-transcription-factor-binding-motifs-by-miniature-inverted-repeat-transposable-elements-mites
#8
Jordi Morata, Fatima Marín, Jordi Payet, Josep M Casacuberta
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. Transposons have been show to contain transcription factor binding sites that can be mobilized upon transposition with the potential to integrate new genes into transcriptional networks. MITEs are a type of non-coding DNA transposons that could be particularly suited as a vector to mobilize transcription factor binding sites and modify transcriptional networks during evolution...
April 5, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29651164/genome-wide-analysis-of-the-transition-to-pathogenic-lifestyles-in-magnaporthales-fungi
#9
Ning Zhang, Guohong Cai, Dana C Price, Jo Anne Crouch, Pierre Gladieux, Bradley Hillman, Chang Hyun Khang, Marc-Henri LeBrun, Yong-Hwan Lee, Jing Luo, Huan Qiu, Daniel Veltri, Jennifer H Wisecaver, Jie Zhu, Debashish Bhattacharya
The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis...
April 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29648536/silencing-of-transposable-elements-may-not-be-a-major-driver-of-regulatory-evolution-in-primate-ipscs
#10
Michelle C Ward, Siming Zhao, Kaixuan Luo, Bryan J Pavlovic, Mohammad M Karimi, Matthew Stephens, Yoav Gilad
Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly-evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from ten human and seven chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3...
April 12, 2018: ELife
https://www.readbyqxmd.com/read/29642859/identification-of-novel-mites-miniature-inverted-repeat-transposable-elements-in-coxiella-burnetii-implications-for-protein-and-small-rna-evolution
#11
Shaun Wachter, Rahul Raghavan, Jenny Wachter, Michael F Minnick
BACKGROUND: Coxiella burnetii is a Gram-negative gammaproteobacterium and zoonotic agent of Q fever. C. burnetii's genome contains an abundance of pseudogenes and numerous selfish genetic elements. MITEs (miniature inverted-repeat transposable elements) are non-autonomous transposons that occur in all domains of life and are thought to be insertion sequences (ISs) that have lost their transposase function. Like most transposable elements (TEs), MITEs are thought to play an active role in evolution by altering gene function and expression through insertion and deletion activities...
April 11, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29625540/the-role-of-transposable-elements-in-emergence-of-metazoa
#12
REVIEW
R N Mustafin, E K Khusnutdinova
Systems initially emerged for protecting genomes against insertions of transposable elements and represented by mechanisms of splicing regulation, RNA-interference, and epigenetic factors have played a key role in the evolution of animals. Many studies have shown inherited transpositions of mobile elements in embryogenesis and preservation of their activities in certain tissues of adult organisms. It was supposed that on the emergence of Metazoa the self-regulation mechanisms of transposons related with the gene networks controlling their activity could be involved in intercellular cell coordination in the cascade of successive divisions with differentiated gene expression for generation of tissues and organs...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625109/generation-of-splice-switching-oligonucleotides-targeting-the-cockayne-syndrome-group-b-gene-product-in-order-to-change-the-diseased-cell-state
#13
Yooksil Sin, Futaba Makimura, Masafumi Saijo, Satoshi Obika
Cockayne syndrome (CS) is a severe disorder with no effective treatment. The Cockayne syndrome group B (CSB) gene is one gene responsible for CS and also causes UV sensitive syndrome (UVS S), a disorder that causes mild symptoms. How the CSB gene determines a patient's fate is unknown, but one intriguing point is that in UVS S patient cell, there are nonsense mutations in both alleles at the same position in each upstream region of the PiggyBac transposable element derived 3 (PGBD3) inserted region. In contrast, in CS patient cells, there is at least one allele with several mutations downstream of the PGBD3 inserted region, or there are homozygous mutations in exon 1...
April 3, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29624899/phylogenetic-distribution-of-roseobacticides-in-the-roseobacter-group-and-their-effect-on-microalgae
#14
Eva C Sonnenschein, Christopher Broughton William Phippen, Mikkel Bentzon-Tilia, Silas Anselm Rasmussen, Kristian Fog Nielsen, Lone Gram
The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P...
April 6, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29624756/sex-chromosome-repeats-tip-the-balance-towards-speciation
#15
Michael J O'Neill, Rachel J O'Neill
Because sex chromosomes, by definition, carry genes that determine sex, mutations that alter their structural and functional stability can have immediate consequences for the individual by reducing fertility, but also for a species by altering the sex ratio. Moreover, the sex-specific segregation patterns of heteromorphic sex chromosomes make them havens for selfish genetic elements that not only create sub-optimal sex ratios, but can also foster sexual antagonism. Compensatory mutations to mitigate antagonism or return sex ratios to a Fisherian optimum can create hybrid incompatibility and establish reproductive barriers leading to species divergence...
April 6, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29621231/house-dust-mites-use-a-plant-like-sirna-pathway-to-silence-transposable-elements
#16
Lichao Li, Weifeng Gu
No abstract text is available yet for this article.
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29618487/integrated-analysis-sheds-light-on-evolutionary-trajectories-of-young-transcription-start-sites-in-the-human-genome
#17
Cai Li, Boris Lenhard, Nicholas M Luscombe
Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription Start Sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed ~200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage...
April 4, 2018: Genome Research
https://www.readbyqxmd.com/read/29617829/genetic-environment-of-cry1-genes-indicates-their-common-origin
#18
Krzysztof Fiedoruk, Tamara Daniluk, Jacques Mahillon, Katarzyna Leszczynska, Izabela Swiecicka
Although in Bacillus thuringiensis the cry genes coding for the insecticidal crystal proteins are plasmid-borne and are usually associated with mobile genetic elements, several aspects related to their genomic organization, diversification, and transmission remain to be elucidated. Plasmids of B. thuringiensis and other members of the Bacillus cereus group (n = 364) deposited in GenBank were screened for the presence of cry1 genes, and their genetic environment was analyzed using a comparative bioinformatic approach...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29615117/arabidopsis-mutants-may-represent-recombinant-introgression-lines
#19
Narendra Singh Yadav, Janardan Khadka, Gideon Grafi
OBJECTIVES: It is a common practice in Arabidopsis to transfer a mutation generated in one genetic background to other genetic background via crossing. However, the drawback of this methodology is unavoidable presence of genomic fragments from the donor parent being often replacing desirable genomic fragments of the recurrent parent. Here, we highlighted problem of Arabidopsis mutants being recombinant introgression lines that can lead to unreliable and misinterpreted results. RESULTS: We studied the regulation of low copy number transposable elements Tag1 and Evelknievel (EK), located at the end of the bottom arm of chromosome 1 and both are present in the Arabidopsis Landsberg erecta (Ler) but not in Columbia (Col) ecotype...
April 3, 2018: BMC Research Notes
https://www.readbyqxmd.com/read/29608716/modeling-interactions-between-transposable-elements-and-the-plant-epigenetic-response-a-surprising-reliance-on-element-retention
#20
Kyria Roessler, Alexandros Bousios, Esteban Meca, Brandon S Gaut
Transposable elements (TEs) compose the majority of angiosperm DNA. Plants counteract TE activity by silencing them epigenetically. One form of epigenetic silencing requires 21-22 nt small interfering RNAs that act to degrade TE mRNA and may also trigger DNA methylation. DNA methylation is reinforced by a second mechanism, the RNA-dependent DNA methylation (RdDM) pathway. RdDM relies on 24 nt small interfering RNAs and ultimately establishes TEs in a quiescent state. These host factors interact at a systems level, but there have been no system level analyses of their interactions...
March 1, 2018: Genome Biology and Evolution
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