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Genome assembly

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https://www.readbyqxmd.com/read/28731473/ninety-nine-de-novo-assembled-genomes-from-the-moose-alces-alces-rumen-microbiome-provide-new-insights-into-microbial-plant-biomass-degradation
#1
Olov Svartström, Johannes Alneberg, Nicolas Terrapon, Vincent Lombard, Ino de Bruijn, Jonas Malmsten, Ann-Marie Dalin, Emilie El Muller, Pranjul Shah, Paul Wilmes, Bernard Henrissat, Henrik Aspeborg, Anders F Andersson
The moose (Alces alces) is a ruminant that harvests energy from fiber-rich lignocellulose material through carbohydrate-active enzymes (CAZymes) produced by its rumen microbes. We applied shotgun metagenomics to rumen contents from six moose to obtain insights into this microbiome. Following binning, 99 metagenome-assembled genomes (MAGs) belonging to 11 prokaryotic phyla were reconstructed and characterized based on phylogeny and CAZyme profile. The taxonomy of these MAGs reflected the overall composition of the metagenome, with dominance of the phyla Bacteroidetes and Firmicutes...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28729714/maize-zea-mays-l-genome-size-indicated-by-180-bp-knob-abundance-is-associated-with-flowering-time
#2
Yinqiao Jian, Cheng Xu, Zifeng Guo, Shanhong Wang, Yunbi Xu, Cheng Zou
Flowering time is considered one of the most important agronomic traits in maize (Zea mays L.), and previous studies have indicated that this trait is correlated with genome size. We observed a significant difference in genome size between tropical and temperate inbred lines and a moderate positive correlation between genome size and 180-bp knob abundance determined by high-throughput sequencing in maize inbred lines in this study. We assembled the reads that were mapped to 180-bp knob sequences and found that the top ten abundant 180-bp knob sequences are highly variable...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729271/whole-genome-sequence-of-acinetobacter-pittii-humv-6483-isolated-from-human-urine
#3
Itziar Chapartegui-González, María Lázaro-Díez, Santiago Redondo-Salvo, Laura Alted-Pérez, Javier Gonzalo Ocejo-Vinyals, Jesús Navas, José Ramos-Vivas
Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28729267/draft-genome-sequence-of-the-blaoxa-436-and-blandm-1-harboring-shewanella-putrefaciens-sa70-isolate
#4
Robert F Potter, Alaric W D'Souza, Meghan A Wallace, Angela Shupe, Sanket Patel, Danish Gul, Jennie H Kwon, Saadia Andleeb, C A Burnham, Gautam Dantas
We sequenced a carbapenem-resistant Shewanella putrefaciens isolate cultured from the sink handle of a Pakistan hospital room. Assembly annotation indicates that the isolate has a chromosomal blaOXA-436 carbapenemase and a plasmid-borne blaNDM-1 gene. To our knowledge, this is the first report of a Shewanella species harboring blaNDM.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28728980/the-role-of-hexon-protein-as-a-molecular-mold-in-patterning-the-protein-ix-organization-in-human-adenoviruses
#5
Vijay S Reddy
Adenoviruses are respiratory, ocular and enteric pathogens that form complex capsids, which are assembled from seven different structural proteins and composed of several core proteins that closely interact with the packaged dsDNA genome. The recent near-atomic resolution structures revealed that the interlacing continuous hexagonal network formed by the protein IX (IX) molecules is conserved among different human adenoviruses (HAdVs), but not in non-human adenoviruses (non-HAdVs). In this report we propose a distinct role for the hexon protein as a "molecular mold" in enabling the formation of such hexagonal IX-network that has been shown to preserve the stability, infectivity of HAdVs...
July 17, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28726630/dissection-of-specific-binding-of-hiv-1-gag-to-the-packaging-signal-in-viral-rna
#6
Mauricio Comas-Garcia, Siddhartha Ak Datta, Laura Baker, Rajat Varma, Prabhakar R Gudla, Alan Rein
Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis-acting RNA element called the "packaging signal" (Ψ). However, the mechanism by which Ψ promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both Ψ-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength...
July 20, 2017: ELife
https://www.readbyqxmd.com/read/28725557/genome-assembly-of-chryseobacterium-sp-strain-ihbb-10212-from-glacier-top-surface-soil-in-the-indian-trans-himalayas-with-potential-for-hydrolytic-enzymes
#7
Mohinder Pal, Mohit Kumar Swarnkar, Hena Dhar, Sanjay Chhibber, Arvind Gulati
The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645 bp with an average 34.08% G + C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28725555/genome-sequence-of-the-type-strain-clib-1764-t-%C3%A2-cbs-14374-t-of-the-yeast-species-kazachstania-saulgeensis-isolated-from-french-organic-sourdough
#8
Véronique Sarilar, Lieven Sterck, Saki Matsumoto, Noémie Jacques, Cécile Neuvéglise, Colin R Tinsley, Delphine Sicard, Serge Casaregola
Kazachstania saulgeensis is a recently described species isolated from French organic sourdough. Here, we report the high quality genome sequence of a monosporic segregant of the type strain of this species, CLIB 1764(T) (= CBS 14374(T)). The genome has a total length of 12.9 Mb and contains 5326 putative protein-coding genes, excluding pseudogenes and transposons. The nucleotide sequences were deposited into the European Nucleotide Archive under the genome assembly accession numbers FXLY01000001-FXLY01000017...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28724762/stability-of-cucumber-necrosis-virus-at-the-quasi-six-fold-axis-affects-zoospore-transmission
#9
Michael B Sherman, Kishore Kakani, D'Ann Rochon, Wen Jiang, Neil R Voss, Thomas J Smith
Cucumber necrosis virus (CNV) is a member of the genus Tombusvirus and has a monopartite positive-sense RNA genome. CNV is transmitted in nature via zoospores of the fungus, Olpidium bornovanus As with other members of the Tombusvirus genus, the CNV capsid swells when exposed to alkaline pH and EDTA. We previously demonstrated that a P73G mutation blocks the virus from zoospore transmission while not significantly affecting replication in plants (1). P73 lies immediately adjacent to a putative zinc binding site (2) that is formed by three icosahedrally related His residues in the N-termini of the C subunit at the quasi 6-fold axes...
July 19, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28724479/holocene-selection-for-variants-associated-with-general-cognitive-ability-comparing-ancient-and-modern-genomes
#10
Michael A Woodley, Shameem Younuskunju, Bipin Balan, Davide Piffer
Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (Fst = 0...
August 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28724409/hybrid-assembly-with-long-and-short-reads-improves-discovery-of-gene-family-expansions
#11
Jason R Miller, Peng Zhou, Joann Mudge, James Gurtowski, Hayan Lee, Thiruvarangan Ramaraj, Brian P Walenz, Junqi Liu, Robert M Stupar, Roxanne Denny, Li Song, Namrata Singh, Lyza G Maron, Susan R McCouch, W Richard McCombie, Michael C Schatz, Peter Tiffin, Nevin D Young, Kevin A T Silverstein
BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724357/genome-analysis-of-e-coli-isolated-from-crohn-s-disease-patients
#12
Daria V Rakitina, Alexander I Manolov, Alexandra V Kanygina, Sofya K Garushyants, Julia P Baikova, Dmitry G Alexeev, Valentina G Ladygina, Elena S Kostryukova, Andrei K Larin, Tatiana A Semashko, Irina Y Karpova, Vladislav V Babenko, Ruzilya K Ismagilova, Sergei Y Malanin, Mikhail S Gelfand, Elena N Ilina, Roman B Gorodnichev, Eugenia S Lisitsyna, Gennady I Aleshkin, Petr L Scherbakov, Igor L Khalif, Marina V Shapina, Igor V Maev, Dmitry N Andreev, Vadim M Govorun
BACKGROUND: Escherichia coli (E. coli) has been increasingly implicated in the pathogenesis of Crohn's disease (CD). The phylogeny of E. coli isolated from Crohn's disease patients (CDEC) was controversial, and while genotyping results suggested heterogeneity, the sequenced strains of E. coli from CD patients were closely related. RESULTS: We performed the shotgun genome sequencing of 28 E. coli isolates from ten CD patients and compared genomes from these isolates with already published genomes of CD strains and other pathogenic and non-pathogenic strains...
July 19, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28724077/physical-map-of-the-short-arm-of-bread-wheat-chromosome-3d
#13
Kateřina Holušová, Jan Vrána, Jan Šafář, Hana Šimková, Barbora Balcárková, Zeev Frenkel, Benoit Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
Bread wheat ( L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#14
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/28723901/2b-rad-genotyping-for-population-genomic-studies-of-chagas-disease-vectors-rhodnius-ecuadoriensis-in-ecuador
#15
Luis E Hernandez-Castro, Marta Paterno, Anita G Villacís, Björn Andersson, Jaime A Costales, Michele De Noia, Sofía Ocaña-Mayorga, Cesar A Yumiseva, Mario J Grijalva, Martin S Llewellyn
BACKGROUND: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses...
July 19, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28720894/coronavirus-nucleocapsid-proteins-assemble-constitutively-in-high-molecular-oligomers
#16
Yingying Cong, Franziska Kriegenburg, Cornelis A M de Haan, Fulvio Reggiori
Coronaviruses (CoV) are enveloped viruses and rely on their nucleocapsid N protein to incorporate the positive-stranded genomic RNA into the virions. CoV N proteins form oligomers but the mechanism and relevance underlying their multimerization remain to be fully understood. Using in vitro pull-down experiments and density glycerol gradients, we found that at least 3 regions distributed over its entire length mediate the self-interaction of mouse hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus (SARS-CoV) N protein...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720171/pacbio-assembly-of-a-plasmodium-knowlesi-genome-sequence-with-hi-c-correction-and-manual-annotation-of-the-sicavar-gene-family
#17
S A Lapp, J A Geraldo, J-T Chien, F Ay, S B Pakala, G Batugedara, J Humphrey, J D DeBARRY, K G Le Roch, M R Galinski, J C Kissinger
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features...
July 19, 2017: Parasitology
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#18
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28717250/plk1-phosphorylation-of-cap-h2-triggers-chromosome-condensation-by-condensin-ii-at-the-early-phase-of-mitosis
#19
Yuya Kagami, Masaya Ono, Kiyotsugu Yoshida
Condensin complexes play crucial roles in chromosome condensation that is a fundamental process to establish the "rod-like" shape of chromosome structure in mitosis. Failure of the chromosome assembly causes chromosome segregation errors and subsequent genomic instability. However, a molecular mechanism that controls condensin function for the chromosomal organization has not been fully understood. Here, we show that the abundance of CAP-H2, one of the condensin II subunits, is fluctuated during the cell cycle in accordance with Plk1 kinase activity...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717181/discovery-of-novel-human-gene-regulatory-modules-from-gene-co-expression-and-promoter-motif-analysis
#20
Shisong Ma, Michael Snyder, Savithramma P Dinesh-Kumar
Deciphering gene regulatory networks requires identification of gene expression modules. We describe a novel bottom-up approach to identify gene modules regulated by cis-regulatory motifs from a human gene co-expression network. Target genes of a cis-regulatory motif were identified from the network via the motif's enrichment or biased distribution towards transcription start sites in the promoters of co-expressed genes. A gene sub-network containing the target genes was extracted and used to derive gene modules...
July 17, 2017: Scientific Reports
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