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Genome evolution

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https://www.readbyqxmd.com/read/29792772/genome-sequence-resources-for-the-wheat-stripe-rust-pathogen-puccinia-striiformis-f-sp-tritici-and-the-barley-stripe-rust-pathogen-puccinia-striiformis-f-sp-hordei
#1
Chongjing Xia, Meinan Wang, Chuntao Yin, Omar E Cornejo, Scot Hulbert, Xianming Chen
Puccinia striiformis f. sp. tritici (Pst) causes devastating stripe (yellow) rust on wheat and P. striiformis f. sp. hordei (Psh) causes stripe rust on barley. Several Pst genomes are available, but no Psh genome is available. More genomes of Pst and Psh are needed to understand the genome evolution and molecular mechanisms of their pathogenicity. We sequenced Pst isolate 93-210 and Psh isolate 93TX-2 using PacBio and Illumina technologies, and RNA sequencing. Their genomic sequences were assembled to contigs with high continuity and showed significant structural differences...
May 24, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29792159/on-the-possibility-of-death-of-new-genes-evidence-from-the-deletion-of-de-novo-micrornas
#2
Guang-An Lu, Yixin Zhao, Zhongqi Liufu, Chung-I Wu
BACKGROUND: New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death. RESULTS: In this study, we discover a Drosophila-specific de novo miRNA (mir-977) that may be facing impending death...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791254/a-genome-wide-mirna-screen-identifies-regulators-of-tetraploid-cell-proliferation
#3
Marc A Vittoria, Elizabeth M Shenk, Kevin P O'Rourke, Amanda F Bolgioni, Sanghee Lim, Victoria Kacprzak, Ryan J Quinton, Neil J Ganem
Tetraploid cells, which are most commonly generated by errors in cell division, are genomically unstable and have been shown to promote tumorigenesis. Recent genomic studies have estimated that ∼40% of all solid tumors have undergone a genome-doubling event during their evolution, suggesting a significant role for tetraploidy in driving the development of human cancers. To safeguard against the deleterious effects of tetraploidy, non transformed cells that fail mitosis and become tetraploid activate both the Hippo and p53 tumor suppressor pathways to restrain further proliferation...
May 23, 2018: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/29790967/common-genetic-basis-of-eye-and-pigment-loss-in-two-distinct-cave-populations-of-the-isopod-crustacean-asellus-aquaticus
#4
Cassandra Re, Žiga Fišer, Justin Perez, Allyson Tacdol, Peter Trontelj, Meredith E Protas
Repeated evolution of similar phenotypes is a widespread phenomenon found throughout the living world and it can proceed through the same or different genetic mechanisms. Cave animals with their convergent traits such as eye and pigment loss, as well as elongated appendages, are a striking example of the evolution of similar phenotypes. Yet, few cave species are amenable to genetic crossing and mapping techniques making it challenging to determine the genetic mechanisms causing their similar phenotypes. To address this limitation, we have been developing Asellus aquaticus, a freshwater isopod crustacean, as a genetic model...
May 21, 2018: Integrative and Comparative Biology
https://www.readbyqxmd.com/read/29790943/mutalisk-a-web-based-somatic-mutation-analyis-toolkit-for-genomic-transcriptional-and-epigenomic-signatures
#5
Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790939/nextstrain-real-time-tracking-of-pathogen-evolution
#6
James Hadfield, Colin Megill, Sidney M Bell, John Huddleston, Barney Potter, Charlton Callender, Pavel Sagulenko, Trevor Bedford, Richard A Neher
Summary: Understanding the spread and evolution of pathogens is important for effective public health measures and surveillance. Nextstrain consists of a database of viral genomes, a bioinformatics pipeline for phylodynamics analysis, and an interactive visualisation platform. Together these present a real-time view into the evolution and spread of a range of viral pathogens of high public health importance. The visualization integrates sequence data with other data types such as geographic information, serology, or host species...
May 22, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29790926/bathyarchaeota-globally-distributed-metabolic-generalists-in-anoxic-environments
#7
Zhichao Zhou, Jie Pan, Fengping Wang, Ji-Dong Gu, Meng Li
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundant archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to the marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-CoA centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, (v) and/or potentially other organic matter...
May 21, 2018: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29789962/genome-based-identification-and-analysis-of-ionotropic-receptors-in-spodoptera-litura
#8
Jia-Ying Zhu, Zhi-Wen Xu, Xin-Min Zhang, Nai-Yong Liu
The ability to sense and recognize various classes of compounds is of particular importance for survival and reproduction of insects. Ionotropic receptor (IR), a sub-family of the ionotropic glutamate receptor family, has been identified as one of crucial chemoreceptor super-families, which mediates the sensing of odors and/or tastants, and serves as non-chemosensory functions. Yet, little is known about IR characteristics, evolution, and functions in Lepidoptera. Here, we identify the IR gene repertoire from a destructive polyphagous pest, Spodoptera litura...
May 22, 2018: Die Naturwissenschaften
https://www.readbyqxmd.com/read/29789590/heterozygous-diploid-and-interspecies-scrambleing
#9
Michael J Shen, Yi Wu, Kun Yang, Yunxiang Li, Hui Xu, Haoran Zhang, Bing-Zhi Li, Xia Li, Wen-Hai Xiao, Xiao Zhou, Leslie A Mitchell, Joel S Bader, Yingjin Yuan, Jef D Boeke
SCRaMbLE (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution) is a genome restructuring technique that can be used in synthetic genomes such as that of Sc2.0, the synthetic yeast genome, which contains hundreds to thousands of strategically positioned loxPsym sites. SCRaMbLE has been used to induce rearrangements in yeast strains harboring one or more synthetic chromosomes, as well as plasmid DNA in vitro and in vivo. Here we describe a collection of heterozygous diploid strains produced by mating haploid semisynthetic Sc2...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789561/l-scramble-as-a-tool-for-light-controlled-cre-mediated-recombination-in-yeast
#10
Lena Hochrein, Leslie A Mitchell, Karina Schulz, Katrin Messerschmidt, Bernd Mueller-Roeber
The synthetic yeast genome constructed by the International Synthetic Yeast Sc2.0 consortium adds thousands of loxPsym recombination sites to all 16 redesigned chromosomes, allowing the shuffling of Sc2.0 chromosome parts by the Cre-loxP recombination system thereby enabling genome evolution experiments. Here, we present L-SCRaMbLE, a light-controlled Cre recombinase for use in the yeast Saccharomyces cerevisiae. L-SCRaMbLE allows tight regulation of recombinase activity with up to 179-fold induction upon exposure to red light...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789384/mutations-in-eid1-and-lnk2-caused-light-conditional-clock-deceleration-during-tomato-domestication
#11
Niels A Müller, Lei Zhang, Maarten Koornneef, José M Jiménez-Gómez
Circadian period and phase of cultivated tomato ( Solanum lycopersicum ) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1 , the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps...
May 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29788479/repeated-cis-regulatory-tuning-of-a-metabolic-bottleneck-gene-during-evolution
#12
Meihua Christina Kuang, Jacek Kominek, William G Alexander, Jan-Fang Cheng, Russell L Wrobel, Chris Todd Hittinger
Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788292/biological-processes-modulating-longevity-across-primates-a-phylogenetic-genome-phenome-analysis
#13
Gerard Muntané, Xavier Farré, Juan Antonio Rodríguez, Cinta Pegueroles, David A Hughes, João Pedro de Magalhães, Toni Gabaldón, Arcadi Navarro
Aging is a complex process affecting different species and individuals in different ways. Comparing genetic variation across species with their aging phenotypes will help understanding the molecular basis of aging and longevity. Although most studies on aging have so far focused on short-lived model organisms, recent comparisons of genomic, transcriptomic, and metabolomic data across lineages with different lifespans are unveiling molecular signatures associated with longevity. Here, we examine the relationship between genomic variation and maximum lifespan (MLS) across primate species...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29788052/fast-evolution-and-lineage-specific-gene-family-expansions-of-aphid-salivary-effectors-driven-by-interactions-with-host-plants
#14
Hélène Boulain, Fabrice Legeai, Endrick Guy, Stéphanie Morlière, Nadine E Douglas, Jonghee Oh, Marimuthu Murugan, Michael Smith, Julie Jaquiéry, Jean Peccoud, Frank F White, James C Carolan, Jean-Christophe Simon, Akiko Sugio
Effector proteins play crucial roles in plant-parasite interactions by suppressing plant defenses and hijacking plant physiological responses to facilitate parasite invasion and propagation. Although effector proteins have been characterized in many microbial plant pathogens, their nature and role in adaptation to host plants are largely unknown in insect herbivores. Aphids rely on salivary effector proteins injected into the host plants to promote phloem sap uptake. Therefore, gaining insight into the repertoire and evolution of aphid effectors is key to unveiling the mechanisms responsible for aphid virulence and host plant specialization...
May 18, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29787822/the-complete-plastome-sequence-of-rubus-takesimensis-endemic-to-ulleung-island-korea-insights-into-molecular-evolution-of-anagenetically-derived-species-in-rubus-rosaceae
#15
Ji Young Yang, Jae-Hong Pak, Seung-Chul Kim
Previous phylogenetic studies have suggested that Rubus takesimensis (Rosaceae), which is endemic to Ulleung Island, Korea, is closely related to R. crataegifolius, which is broadly distributed across East Asia. A recent phylogeographic study also suggested the possible polyphyletic origins of R. takesimensis from multiple source populations of its continental progenitor R. crataegifolius in China, Japan, Korea, and the Russian Far East. However, even though the progenitor-derivative relationship between R...
May 19, 2018: Gene
https://www.readbyqxmd.com/read/29787745/modeling-transposable-element-dynamics-with-fragmentation-equations
#16
Mario Banuelos, Suzanne Sindi
Transposable elements (TEs), segments of DNA capable of self-replication, are abundant in the genomes of most organisms and thus serve as a record of past mutational events. While some work suggests TEs may serve a regulatory function for the host, most empirical and theoretical studies have shown that TEs often have deleterious effects on a host. Because they are not essential, the host genome consists of both full-length (actively replicating) and partial length (inactive remnant) copies of TEs. We developed a novel mathematical formulation of TE dynamics by modeling the density of full and partial length copies resulting from mutations (insertions and deletions) and TE replication within the host genome...
May 19, 2018: Mathematical Biosciences
https://www.readbyqxmd.com/read/29787621/recent-evolution-of-the-human-skin-barrier
#17
REVIEW
Erin A Brettmann, Cristina de Guzman Strong
The skin is the first line of defense against the environment, with the epidermis as the outermost tissue providing much of the barrier function. Given its direct exposure to and encounters with the environment, the epidermis must evolve to provide an optimal barrier for the survival of an organism. Recent advances in genomics have identified a number of genes for the human skin barrier that have undergone evolutionary changes since humans diverged from chimpanzees. Here we highlight a selection of key and innovative genetic findings for skin barrier evolution in our divergence from our primate ancestors and among modern human populations...
May 22, 2018: Experimental Dermatology
https://www.readbyqxmd.com/read/29787233/controlling-the-replication-of-a-genomically-recoded-hiv-1-with-a-functional-quadruplet-codon-in-mammalian-cells
#18
Yan Chen, Yanmin Wan, Nanxi Wang, Zhe Yuan, Wei Niu, Qingsheng Li, Jiantao Guo
Large efforts have been devoted to the genetic code engineering in the past decade, aiming for unnatural amino acid mutagenesis. Recently, an increasing number of studies were reported to employ quadruplet codons to encode unnatural amino acids. We and others have demonstrated that the quadruplet decoding efficiency could be significantly enhanced by an extensive engineering of tRNAs bearing an extra nucleotide in their anticodon loops. In this work, we report the identification of tRNA mutants derived from directed evolution to efficiently decode a UAGA quadruplet codon in mammalian cells...
May 22, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29785946/-crispr-cas-systems-in-genome-engineering-of-bacteriophages
#19
Cai Jiao Liang, Fan Mei Meng, Yun Can Ai
Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785877/hepatitis-b-virus-lymphotropism-emerging-details-and-challenges
#20
Shivali S Joshi, Carla S Coffin
The hepatitis B virus (HBV) is predominantly a hepatotropic virus but also infects cells of the lymphatic system. HBV genomes (DNA, messenger (m)RNA, covalently closed circular (ccc) DNA) and proteins have been found in extrahepatic sites such as peripheral blood mononuclear cells (PBMC), lymph nodes, spleen, bone marrow and cerebrospinal fluid. HBV entry into hepatocytes occurs by binding of the HBV preS1 surface protein to its specific receptor, the bile acid transporter, sodium taurocholate co-transporting polypeptide (NTCP)...
May 22, 2018: Biotechnology & Genetic Engineering Reviews
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