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Genome assembly

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https://www.readbyqxmd.com/read/28938721/the-draft-genome-sequence-of-a-desert-tree-populus-pruinosa
#1
Wenlu Yang, Kun Wang, Jian Zhang, Jianchao Ma, Jianquan Liu, Tao Ma
Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation compared to its sister species, P. euphratica. Here we present a draft genome sequence for P. pruinosa and examine genomic variations between the 2 species. A total of 60 Gb of clean reads from whole-genome sequencing of a P. pruinosa individual were generated using the Illumina HiSeq2000 platform. The assembled genome is 479.3 Mb in length, with an N50 contig size of 14.0 kb and a scaffold size of 698...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938123/reconstructing-prehistoric-african-population-structure
#2
Pontus Skoglund, Jessica C Thompson, Mary E Prendergast, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Tasneem Salie, Nadin Rohland, Swapan Mallick, Alexander Peltzer, Anja Heinze, Iñigo Olalde, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica I Cerezo-Román, Chrissy Chiumia, Alison Crowther, Elizabeth Gomani-Chindebvu, Agness O Gidna, Katherine M Grillo, I Taneli Helenius, Garrett Hellenthal, Richard Helm, Mark Horton, Saioa López, Audax Z P Mabulla, John Parkington, Ceri Shipton, Mark G Thomas, Ruth Tibesasa, Menno Welling, Vanessa M Hayes, Douglas J Kennett, Raj Ramesar, Matthias Meyer, Svante Pääbo, Nick Patterson, Alan G Morris, Nicole Boivin, Ron Pinhasi, Johannes Krause, David Reich
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist...
September 21, 2017: Cell
https://www.readbyqxmd.com/read/28937999/structures-of-foot-and-mouth-disease-virus-pentamers-insight-into-capsid-dissociation-and-unexpected-pentamer-reassociation
#3
Nayab Malik, Abhay Kotecha, Sarah Gold, Amin Asfor, Jingshan Ren, Juha T Huiskonen, Tobias J Tuthill, Elizabeth E Fry, David I Stuart
Foot-and-mouth disease virus (FMDV) belongs to the aphthovirus genus of the Picornaviridae, a family of small, icosahedral, non-enveloped, single-stranded RNA viruses. It is a highly infectious pathogen and is one of the biggest hindrances to the international trade of animals and animal products. FMDV capsids (which are unstable below pH6.5) release their genome into the host cell from an acidic compartment, such as that of an endosome, and in the process dissociate into pentamers. Whilst other members of the family (enteroviruses) have been visualized to form an expanded intermediate capsid with holes from which inner capsid proteins (VP4), N-termini (VP1) and RNA can be released, there has been no visualization of any such state for an aphthovirus, instead the capsid appears to simply dissociate into pentamers...
September 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28937961/regulation-of-chromatin-assembly-and-cell-transformation-by-formaldehyde-exposure-in-human-cells
#4
Danqi Chen, Lei Fang, Shenglin Mei, Hongjie Li, Xia Xu, Thomas L Des Marais, Kun Lu, X Shirley Liu, Chunyuan Jin
BACKGROUND: Formaldehyde (FA) is an environmental and occupational chemical carcinogen. Recent studies have shown that exogenous FA causes only a modest increase in DNA adduct formation compared with the amount of adducts formed by endogenous FA, raising the possibility that epigenetic mechanisms may contribute to FA-mediated carcinogenicity. OBJECTIVES: We investigated the effects of FA exposure on histone modifications and chromatin assembly. We also examined the role of defective chromatin assembly in FA-mediated transcription and cell transformation...
September 21, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28935731/draft-genome-sequence-of-aspergillus-persii-nibrfgc000004109-which-has-antibacterial-activity-against-plant-pathogenic-bacteria
#5
Jung A Kim, Jongbum Jeon, Sook-Young Park, Ki-Tae Kim, Gobong Choi, Hoa Thi Nguyen, Sun Jeong Jeon, Hyang Burm Lee, Chang-Hwan Bae, Hee-Sun Yang, Joo-Hong Yeo, Jin-Cheol Kim, Yong-Hwan Lee, Soonok Kim
The fungus Aspergillus persii strain NIBRFGC000004109 is capable of producing penicillic acid and showed antibacterial activity against various plant-pathogenic bacteria, including Xanthomonas arboricola pv. pruni. Here, we report the first draft whole-genome sequence of A. persii The assembly comprises 38,414,373 bp, with 12 scaffolds.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935728/draft-genome-sequence-of-pantoea-agglomerans-jm1-a-strain-isolated-from-soil-polluted-by-industrial-production-of-beta-lactam-antibiotics-that-exhibits-valacyclovir-like-hydrolase-activity
#6
Jiří Zahradník, Martina Plačková, Andrea Palyzová, Helena Marešová, Eva Kyslíková, Pavel Kyslík
Strain Pantoea agglomerans JM1 was isolated from the soil of a microbiome that had been exposed to polluting pharmaceuticals. The bacterium exhibited enzymatic activities useful for the biotransformation of beta-lactams. The genome of the strain was assembled and described, and the gene encoding valacyclovir-like hydrolase was identified.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935727/complete-genome-sequences-of-lactobacillus-curvatus-kg6-l-curvatus-mrs6-and-lactobacillus-sakei-fam18311-isolated-from-fermented-meat-products
#7
Christoph Jans, Sandra Lagler, Christophe Lacroix, Leo Meile, Marc J A Stevens
The genomes of Lactobacillus curvatus KG6, L. curvatus MRS6, and Lactobacillus sakei FAM18311 were sequenced and assembled using PacBio single-molecule real-time (SMRT) technology. The strains were isolated from Swiss fermented meat products. Circular chromosomes were of 1.98 Mbp (KG6), 2.11 Mbp (MRS6), and 1.95 Mbp (FAM18311), with a G+C content of 41.3 to 42.0%.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28935722/genome-and-plasmid-sequences-of-escherichia-coli-kv7-an-extended-spectrum-%C3%AE-lactamase-isolate-derived-from-feces-of-a-healthy-pig
#8
Michael D Bateman, Stefan P W de Vries, Srishti Gupta, Luca Guardabassi, Lina M Cavaco, Andrew J Grant, Mark A Holmes
We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.
September 21, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28934976/desman-a-new-tool-for-de-novo-extraction-of-strains-from-metagenomes
#9
Christopher Quince, Tom O Delmont, Sébastien Raguideau, Johannes Alneberg, Aaron E Darling, Gavin Collins, A Murat Eren
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain...
September 21, 2017: Genome Biology
https://www.readbyqxmd.com/read/28934590/the-relationship-between-the-human-genome-and-microbiome-comes-into-view
#10
Julia K Goodrich, Emily R Davenport, Andrew G Clark, Ruth E Ley
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28934323/identification-chromosomal-arrangements-and-expression-analyses-of-the-evolutionarily-conserved-prmt1-gene-in-chicken-in-comparison-with-its-vertebrate-paralogue-prmt8
#11
Yi-Chun Wang, Chien-Wen Wang, Wen-Chang Lin, Yun-Jung Tsai, Chien-Ping Chang, Yu-Jen Lee, Min-Jon Lin, Chuan Li
Nine protein arginine methyltransferases (PRMTs) are conserved in mammals and fish. Among these, PRMT1 is the major type I PRMT for asymmetric dimethylarginine (ADMA) formation and is the most conserved and widely distributed one. Two chicken prmt1 splicing variants were assembled and confirmed by RT-PCR experiments. However, only two scaffolds containing single separate prmt1 exon with high GC contents are present in the current chicken genome assembly. Besides, prmt1 exons are scattered in separate small scaffolds in most avian species...
2017: PloS One
https://www.readbyqxmd.com/read/28934256/transcriptome-analysis-of-sex-related-genes-in-the-blood-clam-tegillarca-granosa
#12
Heng Chen, Guoqiang Xiao, Xueliang Chai, Xingguan Lin, Jun Fang, Shuangshuang Teng
BACKGROUND: Blood clams (Tegillarca granosa) are one of the most commercial shellfish in China and South Asia with wide distribution in Indo-Pacific tropical to temperate estuaries. However, recent data indicate a decline in the germplasm of this species. Furthermore, the molecular mechanisms underpinning reproductive regulation remain unclear and information regarding genetic diversity is limited. Understanding the reproductive biology of shellfish is important in interpreting their embryology development, reproduction and population structure...
2017: PloS One
https://www.readbyqxmd.com/read/28933082/-transcriptome-characterization-of-ephedra-sinica-with-454-ests
#13
Hai-Xia Yan, Hong-Mei Luo, Ying Li, Yong-Zhen Sun, Chao Sun, Zhong-Zhi Qian, Shi-Lin Chen
Using the latest 454 GS FLX platform and Titanium regent, a substantial expressed sequence tag (ESTs) dataset of Ephedra sinica was produced, and the profile of gene expression and function gene of which were investigated. A total of 48 389 reads with an average length of 373 bp were generated. These 454 reads were assembled into 18 801 unigenes, which were all 454 sequencing identified. A total number of 10 531 unigenes(56.0%) were annotated using BLAST searches (E-value≤1×10⁻⁵) against the Nr, Nt, TAIR, SwissProt and KEGG databases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28933075/-key-technologies-in-synthetic-biology-of-natural-products
#14
Xue-Jun Kuang, Li-Qiu Zou, Ying Li, Chao Sun, Shi-Lin Chen
Natural products with complex and diverse structures are the major sources of new drugs. The biosynthesis of natural products is considered to be one of the best ways to solve the problems of complex and scarce natural products. DNA assembly technology and genome editing technology are two key technologies in the emerging interdisciplinary field of synthetic biology. A number of novel DNA assembly methods developed in the last few years have paved the way for the engineering of high molecular weight DNA molecules, including whole genomes, hence, it can realize the reconstruction of the metabolic pathways and speed up optimization process...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932346/insights-from-the-draft-genome-into-the-pathogenicity-of-a-clinical-isolate-of-elizabethkingia-meningoseptica-em3
#15
Shicheng Chen, Marty Soehnlen, Frances P Downes, Edward D Walker
Elizabethkingia meningoseptica is an emerging, healthcare-associated pathogen causing a high mortality rate in immunocompromised patients. We report the draft genome sequence of E. meningoseptica Em3, isolated from sputum from a patient with multiple underlying diseases. The genome has a length of 4,037,922 bp, a GC-content 36.4%, and 3673 predicted protein-coding sequences. Average nucleotide identity analysis (>95%) assigned the bacterium to the species E. meningoseptica. Genome analysis showed presence of the curli formation and assembly operon and a gene encoding hemagglutinins, indicating ability to form biofilm...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28931599/mrpl35-a-mitospecific-component-of-mitoribosomes-plays-a-key-role-in-cytochrome-c-oxidase-assembly
#16
Jodie M Box, Jasvinder Kaur, Rosemary A Stuart
Mitoribosomes perform the synthesis of the core components of the oxidative phosphorylation (OXPHOS) system encoded by the mitochondrial genome. We provide evidence that MrpL35 (mL38), a mitospecific component of the yeast mitoribosomal central protuberance, assembles into a subcomplex with MrpL7 (uL5), Mrp7 (bL27) and MrpL36 (bL31) and mitospecific proteins MrpL17 (mL46) and MrpL28 (mL40). We isolated respiratory defective mrpL35 mutant yeast strains, which do not display an overall inhibition in mitochondrial protein synthesis, but rather have a problem in cytochrome c oxidase complex (COX) assembly...
September 20, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28931373/improving-contig-binning-of-metagenomic-data-using-formula-see-text-oligonucleotide-frequency-dissimilarity
#17
Ying Wang, Kun Wang, Yang Young Lu, Fengzhu Sun
BACKGROUND: Metagenomics sequencing provides deep insights into microbial communities. To investigate their taxonomic structure, binning assembled contigs into discrete clusters is critical. Many binning algorithms have been developed, but their performance is not always satisfactory, especially for complex microbial communities, calling for further development. RESULTS: According to previous studies, relative sequence compositions are similar across different regions of the same genome, but they differ between distinct genomes...
September 20, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28931057/challenges-and-advances-for-transcriptome-assembly-in-non-model-species
#18
Arnaud Ungaro, Nicolas Pech, Jean-François Martin, R J Scott McCairns, Jean-Philippe Mévy, Rémi Chappaz, André Gilles
Analyses of high-throughput transcriptome sequences of non-model organisms are based on two main approaches: de novo assembly and genome-guided assembly using mapping to assign reads prior to assembly. Given the limits of mapping reads to a reference when it is highly divergent, as is frequently the case for non-model species, we evaluate whether using blastn would outperform mapping methods for read assignment in such situations (>15% divergence). We demonstrate its high performance by using simulated reads of lengths corresponding to those generated by the most common sequencing platforms, and over a realistic range of genetic divergence (0% to 30% divergence)...
2017: PloS One
https://www.readbyqxmd.com/read/28930672/histone-h3-methylated-at-arginine-17-is-essential-for-reprogramming-the-paternal-genome-in-zygotes
#19
Yuki Hatanaka, Takeshi Tsusaka, Natsumi Shimizu, Kohtaro Morita, Takehiro Suzuki, Shinichi Machida, Manabu Satoh, Arata Honda, Michiko Hirose, Satoshi Kamimura, Narumi Ogonuki, Toshinobu Nakamura, Kimiko Inoue, Yoshihiko Hosoi, Naoshi Dohmae, Toru Nakano, Hitoshi Kurumizaka, Kazuya Matsumoto, Yoichi Shinkai, Atsuo Ogura
At fertilization, the paternal genome undergoes extensive reprogramming through protamine-histone exchange and active DNA demethylation, but only a few maternal factors have been defined in these processes. We identified maternal Mettl23 as a protein arginine methyltransferase (PRMT), which most likely catalyzes the asymmetric dimethylation of histone H3R17 (H3R17me2a), as indicated by in vitro assays and treatment with TBBD, an H3R17 PRMT inhibitor. Maternal histone H3.3, which is essential for paternal nucleosomal assembly, is unable to be incorporated into the male pronucleus when it lacks R17me2a...
September 19, 2017: Cell Reports
https://www.readbyqxmd.com/read/28930579/using-comparative-genomics-to-decode-the-genetics-of-acaricide-resistance
#20
Janice P Van Zee, Catherine A Hill
The availability of genome assemblies and other genomic resources is facilitating investigations of complex genetic traits for several species of ticks. Understanding the genetics of acaricide resistance is a priority for tick and tick-borne disease control. The synaptic enzyme acetylcholinesterase (ACE) is recognized as the target of organophosphates (OPs) and carbamates, and mutations in ACE have been tied to resistance. Multiple studies support three ACE (ace) loci in R. microplus but the molecular basis of OP-resistance in this tick remains elusive...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
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