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Genome assembly

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https://www.readbyqxmd.com/read/29351317/hafts-are-novel-lncrna-transcripts-from-aflatoxin-exposure
#1
B Alex Merrick, Justin S Chang, Dhiral P Phadke, Meredith A Bostrom, Ruchir R Shah, Xinguo Wang, Oksana Gordon, Garron M Wright
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5'- and 3'-RACE...
2018: PloS One
https://www.readbyqxmd.com/read/29351296/hybrid-genome-assembly-and-annotation-of-paenibacillus-pasadenensis-strain-r16-reveals-insights-on-endophytic-life-style-and-antifungal-activity
#2
Alessandro Passera, Luca Marcolungo, Paola Casati, Milena Brasca, Fabio Quaglino, Chiara Cantaloni, Massimo Delledonne
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one...
2018: PloS One
https://www.readbyqxmd.com/read/29350489/bioderived-dna-nanomachines-for-potential-uses-in-biosensing-diagnostics-and-therapeutic-applications
#3
REVIEW
Chava Angell, Mingxuan Kai, Sibai Xie, Xiangyi Dong, Yi Chen
Beside its genomic properties, DNA is also recognized as a novel material in the field of nanoengineering. The specific bonding of base pairs can be used to direct the assembly of highly structured materials with specific nanoscale features such as periodic 2D arrays, 3D nanostructures, assembly of nanomaterials, and DNA nanomachines. In recent years, a variety of DNA nanomachines are developed because of their many potential applications in biosensing, diagnostics, and therapeutic applications. In this review, the fuel-powered motors and secondary structure motors, whose working mechanisms are inspired or derived from natural phenomena and nanomachines, are discussed...
January 19, 2018: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29349107/draft-genome-sequence-of-xylaria-sp-the-causal-agent-of-taproot-decline-of-soybean-in-the-southern-united-states
#4
Sandeep Sharma, Alex Z Zaccaron, John B Ridenour, Tom W Allen, Kassie Conner, Vinson P Doyle, Trey Price, Edward Sikora, Raghuwinder Singh, Terry Spurlock, Maria Tomaso-Peterson, Tessie Wilkerson, Burton H Bluhm
The draft genome of Xylaria sp. isolate MSU_SB201401, causal agent of taproot decline of soybean in the southern U.S., is presented here. The genome assembly was 56.7 Mb in size with an L50 of 246. A total of 10,880 putative protein-encoding genes were predicted, including 647 genes encoding carbohydrate-active enzymes and 1053 genes encoding secreted proteins. This is the first draft genome of a plant-pathogenic Xylaria sp. associated with soybean. The draft genome of Xylaria sp. isolate MSU_SB201401 will provide an important resource for future experiments to determine the molecular basis of pathogenesis...
April 2018: Data in Brief
https://www.readbyqxmd.com/read/29348569/genomelandscaper-landscape-analysis-of-genome-fingerprints-maps-assessing-chromosome-architecture
#5
Hannan Ai, Yuncan Ai, Fanmei Meng
Assessing correctness of an assembled chromosome architecture is a central challenge. We create a geometric analysis method (called GenomeLandscaper) to conduct landscape analysis of genome-fingerprints maps (GFM), trace large-scale repetitive regions, and assess their impacts on the global architectures of assembled chromosomes. We develop an alignment-free method for phylogenetics analysis. The human Y chromosomes (GRCh.chrY, HuRef.chrY and YH.chrY) are analysed as a proof-of-concept study. We construct a galaxy of genome-fingerprints maps (GGFM) for them, and a landscape compatibility among relatives is observed...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348510/genome-and-secretome-analysis-of-pochonia-chlamydosporia-provide-new-insight-into-egg-parasitic-mechanisms
#6
Runmao Lin, Feifei Qin, Baoming Shen, Qianqian Shi, Chichuan Liu, Xi Zhang, Yang Jiao, Jun Lu, Yaoyao Gao, Marta Suarez-Fernandez, Federico Lopez-Moya, Luis Vicente Lopez-Llorca, Gang Wang, Zhenchuan Mao, Jian Ling, Yuhong Yang, Xinyue Cheng, Bingyan Xie
Pochonia chlamydosporia infects eggs and females of economically important plant-parasitic nematodes. The fungal isolates parasitizing different nematodes are genetically distinct. To understand their intraspecific genetic differentiation, parasitic mechanisms, and adaptive evolution, we assembled seven putative chromosomes of P. chlamydosporia strain 170 isolated from root-knot nematode eggs (~44 Mb, including 7.19% of transposable elements) and compared them with the genome of the strain 123 (~41 Mb) isolated from cereal cyst nematode...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348358/complete-genome-sequence-of-kyrpidia-sp-strain-ea-1-a-thermophilic-knallgas-bacterium-isolated-from-the-azores
#7
Johannes Eberhard Reiner, Christian Jonas Lapp, Boyke Bunk, Cathrin Spröer, Jörg Overmann, Johannes Gescher
Kyrpidia sp. strain EA-1 is a thermophilic hydrogen-oxidizing bacterium isolated from hydrothermal systems at São Miguel Island, Portugal. Here, we present the complete genome sequence of the strain assembled to a single circular chromosome. The genome spans 3,352,175 bp, with a GC content of 58.7%.
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348357/draft-genome-sequence-of-bacillus-subtilis-2c-9b-a-strain-with-biocontrol-potential-against-chili-pepper-root-pathogens-and-tolerance-to-pb-and-zn
#8
Claudia Y Muñoz-Moreno, Yumiko De La Cruz-Rodríguez, Julio Vega-Arreguín, Miguel Alvarado-Rodríguez, José Manuel Gómez-Soto, Alejandro Alvarado-Gutiérrez, Saúl Fraire-Velázquez
Bacillus subtilis 2C-9B, obtained from the rhizosphere of wild grass, exhibits inhibition against root rot causal pathogens in Capsicum annuum, Pb and Zn tolerance, and plant growth promotion in medium supplemented with Pb. The genome of B. subtilis 2C-9B was sequenced and the draft genome assembled, with a length of 4,215,855 bp and 4,723 coding genes.
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348347/completed-genome-sequences-of-strains-from-36-serotypes-of-salmonella
#9
James Robertson, Catherine Yoshida, Simone Gurnik, John H E Nash
We report here the completed closed genome sequences of strains representing 36 serotypes of Salmonella These genome sequences will provide useful references for understanding the genetic variation between serotypes, particularly as references for mapping of raw reads or to create assemblies of higher quality, as well as to aid in studies of comparative genomics of Salmonella.
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348336/nine-whole-genome-assemblies-of-yersinia-pestis-subsp-microtus-bv-altaica-strains-isolated-from-the-altai-mountain-natural-plague-focus-no-36-in-russia
#10
Angelina A Kislichkina, Alexandr G Bogun, Lidiya A Kadnikova, Nadezhda V Maiskaya, Viktor I Solomentsev, Svetlana V Dentovskaya, Sergey V Balakhonov, Andrey P Anisimov
We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica strains isolated from the Altai Mountain plague focus (no. 36), which represent the 0.PE4 phylogroup circulating in populations of Mongolian pika (Ochotona pallasi).
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348174/oligomer-formation-and-g-quadruplex-binding-by-purified-murine-rif1-protein-a-key-organizer-of-higher-order-chromatin-architecture
#11
Kenji Moriyama, Naoko Yoshizawa-Sugata, Hisao Masai
Rap1-interacting protein 1(Rif1) regulates telomere length in budding yeast. We previously reported that, in metazoans and fission yeast, Rif1 also plays pivotal roles in controlling genome-wide DNA replication timing. We proposed that Rif1 may assemble chromatin compartments that contain specific replication-timing domains by promoting chromatin loop formation. Rif1 also is involved in DNA lesion repair, restart after replication fork collapse, anti-apoptosis activities, replicative senescence, and transcriptional regulation...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29347977/expansion-of-cytochrome-p450-and-cathepsin-genes-in-the-generalist-herbivore-brown-marmorated-stink-bug
#12
Raman Bansal, Andy Michel
BACKGROUND: The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347966/reprdb-and-pandb-minimalist-databases-with-maximal-microbial-representation
#13
Wei Zhou, Nicole Gay, Julia Oh
BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes...
January 18, 2018: Microbiome
https://www.readbyqxmd.com/read/29346644/genome-wide-analysis-of-disease-progression-in-age-related-macular-degeneration
#14
Qi Yan, Ying Ding, Yi Liu, Tao Sun, Lars G Fritsche, Traci Clemons, Rinki Ratnapriya, Michael L Klein, Richard J Cook, Yu Liu, Ruzong Fan, Lai Wei, Gonçalo R Abecasis, Anand Swaroop, Emily Y Chew, Daniel E Weeks, Wei Chen
Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related Macular Degeneration (AMD), one of the first batch and most successful examples of genome-wide association study (GWAS). However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization [CNV] or geographic atrophy [GA]). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2,721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346625/complete-genomic-and-transcriptional-landscape-analysis-using-third-generation-sequencing-a-case-study-of-saccharomyces-cerevisiae-cen-pk113-7d
#15
Piroon Jenjaroenpun, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W Ussery, Jens Nielsen, Intawat Nookaew
Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of second-generation sequencing. Saccharomyces cerevisiae strain CEN.PK113-7D, widely used as a model organism and a cell factory, was selected for this study to demonstrate the superior capability of very long sequence reads for de novo genome assembly. We generated long reads using two common third-generation sequencing technologies (Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)) and used short reads obtained using Illumina sequencing for error correction...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#16
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346504/baum-improving-genome-assembly-by-adaptive-unique-mapping-and-local-overlap-layout-consensus-approach
#17
Anqi Wang, Zhanyu Wang, Zheng Li, Lei M Li
Motivation: It is highly desirable to assemble genomes of high continuity and consistency at low cost. The current bottleneck of draft genome continuity using the Second Generation Sequencing (SGS) reads is primarily caused by uncertainty among repetitive sequences. Even though the Single-Molecule Real-Time sequencing technology is very promising to overcome the uncertainty issue, its relatively high cost and error rate add burden on budget or computation. Many long-read assemblers take the overlap-layout-consensus (OLC) paradigm, which is less sensitive to sequencing errors, heterozygosity and variability of coverage...
January 15, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29346292/isoform-sequencing-and-state-of-art-applications-for-unravelling-complexity-of-plant-transcriptomes
#18
REVIEW
Dong An, Hieu X Cao, Changsheng Li, Klaus Humbeck, Wenqin Wang
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications...
January 18, 2018: Genes
https://www.readbyqxmd.com/read/29343494/uncovering-genomic-regions-associated-with-trypanosoma-infections-in-wild-populations-of-the-tsetse-fly-glossina-fuscipes
#19
Andrea Gloria-Soria, W Augustine Dunn, Xiaoqing Yu, Aurélien Vigneron, Kuang-Yao Lee, Mo Li, Brian L Weiss, Hongyu Zhao, Serap Aksoy, Adalgisa Caccone
Vector-borne diseases are responsible for more than one million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ~73,000 polymorphic sites distributed across the genome...
January 17, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#20
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
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