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Genome assembly

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https://www.readbyqxmd.com/read/28088723/discovery-and-metagenomic-analysis-of-an-anammox-bacterial-enrichment-related-to-candidatus-brocadia-caroliniensis-in-a-full-scale-glycerol-fed-nitritation-denitritation-separate-centrate-treatment-process
#1
Hongkeun Park, Ariane C Brotto, Mark C M van Loosdrecht, Kartik Chandran
A distinctive red biofilm was observed in a glycerol-fed digester liquid effluent treatment process coupling partial nitrification (nitritation) and partial denitrification (denitritation) processes. Based on initial phylogenetic screening using 16S rRNA clone libraries and quantitative polymerase chain reaction, the biofilm was enriched in novel anaerobic ammonium oxidizing bacteria (AMX/anammox) closely related to Candidatus "Brocadia caroliniensis". The metabolic functionality of the C. "Brocadia caroliniensis" enrichment was further explored using high-throughput sequencing and de novo metagenome assembly...
January 6, 2017: Water Research
https://www.readbyqxmd.com/read/28087768/the-rice-paradox-multiple-origins-but-single-domestication-in-asian-rice
#2
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087711/ctcf-mediated-topological-boundaries-during-development-foster-appropriate-gene-regulation
#3
Varun Narendra, Milica Bulajić, Job Dekker, Esteban O Mazzoni, Danny Reinberg
The genome is organized into repeating topologically associated domains (TADs), each of which is spatially isolated from its neighbor by poorly understood boundary elements thought to be conserved across cell types. Here, we show that deletion of CTCF (CCCTC-binding factor)-binding sites at TAD and sub-TAD topological boundaries that form within the HoxA and HoxC clusters during differentiation not only disturbs local chromatin domain organization and regulatory interactions but also results in homeotic transformations typical of Hox gene misregulation...
December 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/28087693/de-novo-genome-and-transcriptome-assembly-of-the-canadian-beaver-castor-canadensis
#4
Si Lok, Tara A Paton, Zhuozhi Wang, Gaganjot Kaur, Susan Walker, Ryan K C Yuen, Wilson W L Sung, Joseph Whitney, Janet A Buchanan, Brett Trost, Naina Singh, Beverly Apresto, Nan Chen, Matthew Coole, Travis J Dawson, Karen Y Ho, Zhizhou Hu, Sanjeev Pullenayegum, Kozue Samler, Arum Shipstone, Fiona Tsoi, Ting Wang, Sergio L Pereira, Pirooz Rostami, Carol Ann Ryan, Amy Hin Yan Tong, Karen Ng, Yogi Sundaravadanam, Jared T Simpson, Burton K Lim, Mark D Engstrom, Christopher J Dutton, Kevin C R Kerr, Maria Franke, William Rapley, Richard F Wintle, Stephen W Scherer
The Canadian beaver (Castor canadensis) is the largest indigenous rodent in North America. We report a draft annotated assembly of the beaver genome, the first for a large rodent and the first mammalian genome assembled directly from uncorrected and moderate coverage (< 30 ×) long-reads generated by single-molecule sequencing. The genome size is 2.7 Gb estimated by k-mer analysis. We assembled the beaver genome using the new Canu assembler optimized for noisy reads. The resulting assembly was refined using Pilon supported by shortreads (80 ×) and checked for accuracy by congruency against an independent short-read assembly...
January 13, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#5
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28086790/rna-sequencing-for-global-gene-expression-associated-with-muscle-growth-in-a-single-male-modern-broiler-line-compared-to-a-foundational-barred-plymouth-rock-chicken-line
#6
Byung-Whi Kong, Nicholas Hudson, Dongwon Seo, Seok Lee, Bhuwan Khatri, Kentu Lassiter, Devin Cook, Alissa Piekarski, Sami Dridi, Nicholas Anthony, Walter Bottje
BACKGROUND: Modern broiler chickens exhibit very rapid growth and high feed efficiency compared to unselected chicken breeds. The improved production efficiency in modern broiler chickens was achieved by the intensive genetic selection for meat production. This study was designed to investigate the genetic alterations accumulated in modern broiler breeder lines during selective breeding conducted over several decades. METHODS: To identify genes important in determining muscle growth and feed efficiency in broilers, RNA sequencing (RNAseq) was conducted with breast muscle in modern pedigree male (PeM) broilers (n = 6 per group), and with an unselected foundation broiler line (Barred Plymouth Rock; BPR)...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28086783/de-novo-transcriptome-analysis-of-rose-scented-geranium-provides-insights-into-the-metabolic-specificity-of-terpene-and-tartaric-acid-biosynthesis
#7
Lokesh K Narnoliya, Girija Kaushal, Sudhir P Singh, Rajender S Sangwan
BACKGROUND: Rose-scented geranium (Pelargonium sp.) is a perennial herb that produces a high value essential oil of fragrant significance due to the characteristic compositional blend of rose-oxide and acyclic monoterpenoids in foliage. Recently, the plant has also been shown to produce tartaric acid in leaf tissues. Rose-scented geranium represents top-tier cash crop in terms of economic returns and significance of the plant and plant products. However, there has hardly been any study on its metabolism and functional genomics, nor any genomic expression dataset resource is available in public domain...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28081303/the-novel-fusion-transcript-nr5a2-klhl29ft-is-generated-by-an-insertion-at-the-klhl29-locus
#8
Zhenguo Sun, Xiquan Ke, Steven L Salzberg, Daehwan Kim, Valentin Antonescu, Yulan Cheng, Binbin Huang, Jee Hoon Song, John M Abraham, Sariat Ibrahim, Hui Tian, Stephen J Meltzer
BACKGROUND: Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. METHODS: RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement...
January 12, 2017: Cancer
https://www.readbyqxmd.com/read/28079247/dynamic-location-changes-of-bub1-phosphorylated-h2athr133-with-cenh3-nucleosome-in-maize-centromeric-regions
#9
Handong Su, Yalin Liu, Qianhua Dong, Chao Feng, Jing Zhang, Yang Liu, James A Birchler, Fangpu Han
The genomic stability of all organisms requires precise cell division with proper chromosome orientation. The Bub1-H2Aph-Sgo1 pathway and spindle assembly checkpoint (SAC) components have been identified in yeast and mammals that are important for sister centromere orientation and chromosome segregation. However, their roles in plants are not clear. Maize meiotic mutants and minichromosomes were used to study the role of H2AThr133 phosphorylation and SAC components in sister centromere orientation and chromosome segregation...
January 12, 2017: New Phytologist
https://www.readbyqxmd.com/read/28079141/development-of-a-690%C3%A2-k-snp-array-in-catfish-and-its-application-for-genetic-mapping-and-validation-of-the-reference-genome-sequence
#10
Qifan Zeng, Qiang Fu, Yun Li, Geoff Waldbieser, Brian Bosworth, Shikai Liu, Yujia Yang, Lisui Bao, Zihao Yuan, Ning Li, Zhanjiang Liu
Single nucleotide polymorphisms (SNPs) are capable of providing the highest level of genome coverage for genomic and genetic analysis because of their abundance and relatively even distribution in the genome. Such a capacity, however, cannot be achieved without an efficient genotyping platform such as SNP arrays. In this work, we developed a high-density SNP array with 690,662 unique SNPs (herein 690 K array) that were relatively evenly distributed across the entire genome, and covered 98.6% of the reference genome sequence...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078516/dense-gene-physical-maps-of-the-non-model-species-drosophila-subobscura
#11
Dorcas J Orengo, Eva Puerma, Montserrat Papaceit, Carmen Segarra, Montserrat Aguadé
The comparative analysis of genetic and physical maps as well as of whole genome sequences had revealed that in the Drosophila genus, most structural rearrangements occurred within chromosomal elements as a result of paracentric inversions. Genome sequence comparison would seem the best method to estimate rates of chromosomal evolution, but the high-quality reference genomes required for this endeavor are still scanty. Here, we have obtained dense physical maps for Muller elements A, C, and E of Drosophila subobscura, a species with an extensively studied rich and adaptive chromosomal polymorphism...
January 11, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28077638/a-conserved-glycine-residue-is-required-for-proper-functioning-of-a-baculovirus-vp39-protein
#12
Susumu Katsuma, Ryuhei Kokusho
: The baculovirus VP39 is a major nucleocapsid protein essential for viral propagation. However, the critical domains or residues of the VP39 protein have not yet been identified. Here, we performed mutagenesis experiments of Bombyx mori nucleopolyhedrovirus (BmNPV) using 5-bromo-2' -deoxyuridine and isolated a BmNPV mutant that produced fewer occlusion bodies than the wild-type virus. This mutant also produced fewer infectious budded viruses (BVs), when compared with the wild-type virus in both cultured cells and B...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077567/farme-db-a-functional-antibiotic-resistance-element-database
#13
James C Wallace, Jesse A Port, Marissa N Smith, Elaine M Faustman
Antibiotic resistance (AR) is a major global public health threat but few resources exist that catalog AR genes outside of a clinical context. Current AR sequence databases are assembled almost exclusively from genomic sequences derived from clinical bacterial isolates and thus do not include many microbial sequences derived from environmental samples that confer resistance in functional metagenomic studies. These environmental metagenomic sequences often show little or no similarity to AR sequences from clinical isolates using standard classification criteria...
2017: Database: the Journal of Biological Databases and Curation
https://www.readbyqxmd.com/read/28077444/protein-interactions-during-the-flavivirus-and-hepacivirus-life-cycle
#14
Gisa Gerold, Janina Bruening, Bettina Weigel, Thomas Pietschmann
Protein-protein interactions govern biological functions in cells, in the extracellular milieu and at the border between cells and extracellular space. Viruses are small intracellular parasites and thus rely on protein interactions to produce progeny inside host cells and to spread from cell to cell. Usage of host proteins by viruses can have severe consequences e.g. apoptosis, metabolic disequilibria or altered cell proliferation and mobility. Understanding protein interactions during virus infection can thus educate us on viral infection and pathogenesis mechanisms...
January 11, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28076891/comparative-genomics-of-mortierella-elongata-and-its-bacterial-endosymbiont-mycoavidus-cysteinexigens
#15
J Uehling, A Gryganskyi, K Hameed, T Tschaplinski, P K Misztal, S Wu, A Desirò, N Vande Pol, Z Du, A Zienkiewicz, K Zienkiewicz, E Morin, E Tisserant, R Splivallo, M Hainaut, B Henrissat, R Ohm, A Kuo, J Yan, A Lipzen, M Nolan, K LaButti, K Barry, A H Goldstein, J Labbé, C Schadt, G Tuskan, I Grigoriev, F Martin, R Vilgalys, G Bonito
Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants, and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. We sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within in a lineage of endofungal symbionts that are sister clade to Burkholderia...
January 11, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28074246/draft-genome-of-scalindua-rubra-obtained-from-the-interface-above-the-discovery-deep-brine-in-the-red-sea-sheds-light-on-potential-salt-adaptation-strategies-in-anammox-bacteria
#16
Daan R Speth, Ilias Lagkouvardos, Yong Wang, Pei-Yuan Qian, Bas E Dutilh, Mike S M Jetten
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua...
January 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28074120/complete-genome-sequence-of-the-heavy-metal-resistant-bacterium-agromyces-aureus-ar33-t-and-comparison-with-related-actinobacteria
#17
Erika Corretto, Livio Antonielli, Angela Sessitsch, Stéphane Compant, Christoph Höfer, Markus Puschenreiter, Günter Brader
Agromyces aureus AR33(T) is a Gram-positive, rod-shaped and motile bacterium belonging to the Microbacteriaceae family in the phylum Actinobacteria that was isolated from a former zinc/lead mining and processing site in Austria. In this study, the whole genome was sequenced and assembled combining sequences obtained from Illumina MiSeq and Sanger sequencing. The assembly resulted in the complete genome sequence which is 4,373,124 bp long and has a GC content of 70.1%. Furthermore, we performed a comparative genomic analysis with other related organisms: 6 Agromyces spp...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28073968/variants-of-abgri3-carrying-the-arma-gene-in-extensively-antibiotic-resistant-acinetobacter-baumannii-from-singapore
#18
Grace A Blackwell, Kathryn E Holt, Stephen D Bentley, Li Yang Hsu, Ruth M Hall
OBJECTIVES: To investigate the context of the ribosomal RNA methyltransferase gene armA in carbapenem-resistant global clone 2 (GC2) Acinetobacter baumannii isolates from Singapore. METHODS: Antibiotic resistance was determined using disc diffusion; PCR was used to identify resistance genes. Whole genome sequences were determined and contigs were assembled and ordered using PCR. Resistance regions in unsequenced isolates were mapped. RESULTS: Fifteen GC2 A...
January 10, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28073912/auxiliary-metabolic-genes-distinct-features-of-cyanophage-encoded-t-type-phycobiliprotein-lyase-%C3%AE-cpet
#19
Raphael Gasper, Julia Schwach, Jana Hartmann, Andrea Holtkamp, Jessica Wiethaus, Natascha Riedel, Eckhard Hofmann, Nicole Frankenberg-Dinkel
Auxiliary metabolic genes (AMG) are commonly found in the genomes of phages that infect cyanobacteria and increase cyanophage's fitness. AMGs are often homologs of host genes, and also typically related to photosynthesis. For example, the θcpeT gene in the cyanophage P-HM1 encodes a putative phycobiliprotein lyase related to cyanobacterial T-type lyases, which facilitate attachment of linear tetrapyrrole chromophores to Cys-155 of phycobiliprotein β-subunits, suggesting that θCpeT may also help assemble light-harvesting phycobiliproteins during infection...
January 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28073664/extract-of-bulbus-fritillaria-cirrhosa-perturbs-spindle-assembly-checkpoint-induces-mitotic-aberrations-and-genomic-instability-in-human-colon-epithelial-cell-line
#20
Xihan Guo, Juan Ni, Jinglun Xue, Xu Wang
BACKGROUND: Bulbus Fritillaria cirrhosa D. Don (BFC) has been used in China as a folk medicine for the treatment of cough and asthma for more than 2000 years. The antitussive and antiasthmatic effects of BFC have been reported before, nevertheless its toxicity and safety have not been documented. This study investigated the possible effects of BFC on spindle assembly checkpoint (SAC), mitotic fidelity and genomic stability in human NCM460 colon epithelial cells. METHODS: Cells were treated with BFC (0, 20, 40, 80 and 160μg/ml) for 24, 48 and 72h and harvested differently according to the biomarkers observed...
January 7, 2017: Experimental and Toxicologic Pathology: Official Journal of the Gesellschaft Für Toxikologische Pathologie
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