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https://www.readbyqxmd.com/read/27904456/methylome-analysis-of-two-xanthomonas-spp-using-single-molecule-real-time-sequencing
#1
Hoon Je Seong, Hye-Jee Park, Eunji Hong, Sung Chul Lee, Woo Jun Sul, Sang-Wook Han
Single-molecule real-time (SMRT) sequencing allows identification of methylated DNA bases and methylation patterns/motifs at the genome level. Using SMRT sequencing, diverse bacterial methylomes including those of Helicobacter pylori, Lactobacillus spp., and Escherichia coli have been determined, and previously unreported DNA methylation motifs have been identified. However, the methylomes of Xanthomonas species, which belong to the most important plant pathogenic bacterial genus, have not been documented. Here, we report the methylomes of Xanthomonas axonopodis pv...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27895111/discovery-and-genotyping-of-structural-variation-from-long-read-haploid-genome-sequence-data
#2
John Huddleston, Mark Jp Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David S Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. Using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF >1%)...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27891183/complete-genome-of-vibrio-parahaemolyticus-forc014-isolated-from-the-toothfish
#3
Sojin Ahn, Han Young Chung, Sooyeon Lim, Kwondo Kim, Suyeon Kim, Eun Jung Na, Kelsey Caetano-Anolles, Ju-Hoon Lee, Sangryeol Ryu, Sang Ho Choi, Heebal Kim
BACKGROUND: Foodborne illness can occur due to various pathogenic bacteria such as Staphylococcus aureus, Escherichia coli and Vibrio parahaemolyticus, and can cause severe gastroenteritis symptoms. In this study, we completed the genome sequence of a foodborne pathogen V. parahaemolyticus FORC_014, which was isolated from suspected contaminated toothfish from South Korea. Additionally, we extended our knowledge of genomic characteristics of the FORC_014 strain through comparative analysis using the complete sequences of other V...
2016: Gut Pathogens
https://www.readbyqxmd.com/read/27891116/complete-genome-sequence-of-clostridium-estertheticum-dsm-8809-a-microbe-identified-in-spoiled-vacuum-packed-beef
#4
Zhongyi Yu, Lynda Gunn, Evan Brennan, Rachael Reid, Patrick G Wall, Peadar Ó Gaora, Daniel Hurley, Declan Bolton, Séamus Fanning
Blown pack spoilage (BPS) is a major issue for the beef industry. Etiological agents of BPS involve members of a group of Clostridium species, including Clostridium estertheticum which has the ability to produce gas, mostly carbon dioxide, under anaerobic psychotrophic growth conditions. This spore-forming bacterium grows slowly under laboratory conditions, and it can take up to 3 months to produce a workable culture. These characteristics have limited the study of this commercially challenging bacterium. Consequently information on this bacterium is limited and no effective controls are currently available to confidently detect and manage this production risk...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27885609/methods-for-genome-wide-methylome-profiling-of-campylobacter-jejuni
#5
Kathy T Mou, Tyson A Clark, Usha K Muppirala, Andrew J Severin, Paul J Plummer
Methylation has a profound role in the regulation of numerous biological processes in bacteria including virulence. The study of methylation in bacteria has greatly advanced thanks to next-generation sequencing technologies. These technologies have expedited the process of uncovering unique features of many bacterial methylomes such as characterizing previously uncharacterized methyltransferases, cataloging genome-wide DNA methylations in bacteria, identifying the frequency of methylation at particular genomic loci, and revealing regulatory roles of methylation in the biology of various bacterial species...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27881545/complete-genome-sequence-of-the-probiotic-strain-lactobacillus-salivarius-lpm01
#6
Empar Chenoll, Francisco M Codoñer, Juan F Martinez-Blanch, Marcelo Acevedo-Piérart, M Loreto Ormeño, Daniel Ramón, Salvador Genovés
Lactobacillus salivarius LPM01 (DSM 22150) is a probiotic strain able to improve health status in immunocompromised people. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insights into its functional activity and safety assessment.
November 23, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27856253/discovery-of-high-affinity-bcl6-binding-peptide-and-its-structure-activity-relationship
#7
Kotaro Sakamoto, Satoshi Sogabe, Yusuke Kamada, Nozomu Sakai, Kouhei Asano, Mie Yoshimatsu, Kou Ida, Yasuhiro Imaeda, Jun-Ichi Sakamoto
B cell lymphoma 6 (BCL6) is a transcriptional repressor that interacts with its corepressors BcoR and SMRT. Since this protein-protein interaction (PPI) induces activation and differentiation of B lymphocytes, BCL6 has been an attractive drug target for potential autoimmune disease treatments. Here we report a novel BCL6 inhibitory peptide, F1324 (Ac-LWYTDIRMSWRVP-OH), which we discovered using phage display technology; we also discuss this peptide's structure-activity relationship (SAR). For BCL6(5-129) binding, KD and IC50 values of F1324 were 0...
November 14, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27842515/evaluation-of-pacbio-sequencing-for-full-length-bacterial-16s-rrna-gene-classification
#8
Josef Wagner, Paul Coupland, Hilary P Browne, Trevor D Lawley, Suzanna C Francis, Julian Parkhill
BACKGROUND: Currently, bacterial 16S rRNA gene analyses are based on sequencing of individual variable regions of the 16S rRNA gene (Kozich, et al Appl Environ Microbiol 79:5112-5120, 2013).This short read approach can introduce biases. Thus, full-length bacterial 16S rRNA gene sequencing is needed to reduced biases. A new alternative for full-length bacterial 16S rRNA gene sequencing is offered by PacBio single molecule, real-time (SMRT) technology. The aim of our study was to validate PacBio P6 sequencing chemistry using three approaches: 1) sequencing the full-length bacterial 16S rRNA gene from a single bacterial species Staphylococcus aureus to analyze error modes and to optimize the bioinformatics pipeline; 2) sequencing the full-length bacterial 16S rRNA gene from a pool of 50 different bacterial colonies from human stool samples to compare with full-length bacterial 16S rRNA capillary sequence; and 3) sequencing the full-length bacterial 16S rRNA genes from 11 vaginal microbiome samples and compare with in silico selected bacterial 16S rRNA V1V2 gene region and with bacterial 16S rRNA V1V2 gene regions sequenced using the Illumina MiSeq...
November 14, 2016: BMC Microbiology
https://www.readbyqxmd.com/read/27829364/lscplus-a-fast-solution-for-improving-long-read-accuracy-by-short-read-alignment
#9
Ruifeng Hu, Guibo Sun, Xiaobo Sun
BACKGROUND: The single molecule, real time (SMRT) sequencing technology of Pacific Biosciences enables the acquisition of transcripts from end to end due to its ability to produce extraordinarily long reads (>10 kb). This new method of transcriptome sequencing has been applied to several projects on humans and model organisms. However, the raw data from SMRT sequencing are of relatively low quality, with a random error rate of approximately 15 %, for which error correction using next-generation sequencing (NGS) short reads is typically necessary...
November 9, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27825778/control-of-viral-replication-and-transcription-by-the-papillomavirus-e8-e2-protein
#10
REVIEW
Marcel Dreer, Saskia van de Poel, Frank Stubenrauch
Human papillomaviruses have adjusted their replication levels to the differentiation state of the infected keratinocyte. PV genomes replicate in undifferentiated cells at low levels and to high levels in differentiated cells. Genome replication requires the viral E1 helicase and the viral E2 transcription/replication activator. The limited replication in undifferentiated cells is predominantly due to the expression of the highly conserved E8^E2 viral repressor protein, which is a fusion between E8 and the C-terminal half of the E2 protein...
November 4, 2016: Virus Research
https://www.readbyqxmd.com/read/27796642/genomic-analysis-of-the-multi-drug-resistant-clinical-isolate-myroides-odoratimimus-pr63039
#11
Shaohua Hu, Tao Jiang, Yajun Zhou, Desong Ming, Hongzhi Gao, Mingxi Wang
Myroides odoratimimus (M. odoratimimus) has been gradually implicated as an important nosocomial pathogen that poses a serious health threat to immunocompromised patients owing to its multi-drug resistance. However, the resistance mechanism is currently unclear. To clarify the antibiotic resistance and infectivity mechanisms of M. odoratimimus, whole genome sequencing was performed on the multi-drug-resistant M. odoratimimus strain PR63039. The genome sequence was completed with single molecule real-time (SMRT) technologies...
October 28, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27784934/high-throughput-sequencing-an-overview-of-sequencing-chemistry
#12
REVIEW
Sheetal Ambardar, Rikita Gupta, Deepika Trakroo, Rup Lal, Jyoti Vakhlu
In the present century sequencing is to the DNA science, what gel electrophoresis was to it in the last century. From 1977 to 2016 three generation of the sequencing technologies of various types have been developed. Second and third generation sequencing technologies referred commonly to as next generation sequencing technology, has evolved significantly with increase in sequencing speed, decrease in sequencing cost, since its inception in 2004. GS FLX by 454 Life Sciences/Roche diagnostics, Genome Analyzer, HiSeq, MiSeq and NextSeq by Illumina, Inc...
December 2016: Indian Journal of Microbiology
https://www.readbyqxmd.com/read/27765811/genomic-analyses-of-multidrug-resistant-pseudomonas-aeruginosa-pa1-resequenced-by-single-molecule-real-time-sequencing
#13
Gang Li, Mengyu Shen, Shuai Le, Yinling Tan, Ming Li, Xia Zhao, Wei Shen, Yuhui Yang, Jing Wang, Hongbin Zhu, Shu Li, Xiancai Rao, Fuquan Hu, Shuguang Lu
As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin-antitoxin (T-A) pairs and genomic islands...
December 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27730570/comprehensive-genomic-and-phenotypic-metal-resistance-profile-of-pseudomonas-putida-strain-s13-1-2-isolated-from-a-vineyard-soil
#14
Teik Min Chong, Wai-Fong Yin, Jian-Woon Chen, Samuel Mondy, Catherine Grandclément, Denis Faure, Yves Dessaux, Kok-Gan Chan
Trace metals are required in many cellular processes in bacteria but also induce toxic effects to cells when present in excess. As such, various forms of adaptive responses towards extracellular trace metal ions are essential for the survival and fitness of bacteria in their environment. A soil Pseudomonas putida, strain S13.1.2 has been isolated from French vineyard soil samples, and shown to confer resistance to copper ions. Further investigation revealed a high capacity to tolerate elevated concentrations of various heavy metals including nickel, cobalt, cadmium, zinc and arsenic...
December 2016: AMB Express
https://www.readbyqxmd.com/read/27725207/complete-genome-sequence-of-plant-growth-promoting-bacterium-leifsonia-xyli-se134-a-possible-gibberellin-and-auxin-producer
#15
Sang-Mo Kang, Sajjad Asaf, Sang-Jun Kim, Byung-Wook Yun, In-Jung Lee
Leifsonia xyli SE134 is a potential plant growth-promoting bacterium isolated from a soil in Daegu, Republic of Korea, which produces large amounts of gibberellin (GA) and indole acetic acid (IAA). In this study, we sequenced the complete genome of L. xyli SE134 by the Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. The genome of L. xyli SE134 contains a single chromosome that is 3,596,761bp in length, with 70.2% G+C content. The genome contains 3466 protein-coding genes (CDSs) and 51 rRNA- and 46 tRNA-coding genes...
October 7, 2016: Journal of Biotechnology
https://www.readbyqxmd.com/read/27684375/alternative-isoform-analysis-of-ttc8-expression-in-the-rat-pineal-gland-using-a-multi-platform-sequencing-approach-reveals-neural-regulation
#16
Stephen W Hartley, James C Mullikin, David C Klein, Morgan Park, Steven L Coon
Alternative isoform regulation (AIR) vastly increases transcriptome diversity and plays an important role in numerous biological processes and pathologies. However, the detection and analysis of isoform-level differential regulation is difficult, particularly in the face of complex and incompletely-annotated transcriptomes. Here we have used Illumina short-read/high-throughput RNA-Seq to identify 55 genes that exhibit neurally-regulated AIR in the pineal gland, and then used two other complementary experimental platforms to further study and characterize the Ttc8 gene, which is involved in Bardet-Biedl syndrome and non-syndromic retinitis pigmentosa...
2016: PloS One
https://www.readbyqxmd.com/read/27673566/next-generation-sequencing-data-of-a-defined-microbial-mock-community
#17
Esther Singer, Bill Andreopoulos, Robert M Bowers, Janey Lee, Shweta Deshpande, Jennifer Chiniquy, Doina Ciobanu, Hans-Peter Klenk, Matthew Zane, Christopher Daum, Alicia Clum, Jan-Fang Cheng, Alex Copeland, Tanja Woyke
Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of new genome sequence analysis methods, including assembly and binning tools. Moreover the validation of new sequencing library protocols and platforms to assess critical components such as sequencing errors and biases relies on such datasets. We here report the next generation metagenomic sequence data of a defined mock community (Mock Bacteria ARchaea Community; MBARC-26), composed of 23 bacterial and 3 archaeal strains with finished genomes...
September 27, 2016: Scientific Data
https://www.readbyqxmd.com/read/27672193/implementation-and-data-analysis-of-tn-seq-whole-genome-resequencing-and-single-molecule-real-time-sequencing-for-bacterial-genetics
#18
Peter E Burby, Taylor M Nye, Jeremy W Schroeder, Lyle A Simmons
Few discoveries have been more transformative to the biological sciences than the development of DNA sequencing technologies. The rapid advancement of sequencing and bioinformatics tools has revolutionized bacterial genetics, deepening our understanding of model and clinically relevant organisms. Although application of newer sequencing technologies to studies in bacterial genetics is increasing, the implementation of DNA sequencing technologies and development of the bioinformatics tools required for analyzing the large data sets generated remains a challenge for many...
September 26, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27622467/building-two-indica-rice-reference-genomes-with-pacbio-long-read-and-illumina-paired-end-sequencing-data
#19
COMMENT
Jianwei Zhang, Ling-Ling Chen, Shuai Sun, Dave Kudrna, Dario Copetti, Weiming Li, Ting Mu, Wen-Biao Jiao, Feng Xing, Seunghee Lee, Jayson Talag, Jia-Ming Song, Bogu Du, Weibo Xie, Meizhong Luo, Carlos Ernesto Maldonado, Jose Luis Goicoechea, Lizhong Xiong, Changyin Wu, Yongzhong Xing, Dao-Xiu Zhou, Sibin Yu, Yu Zhao, Gongwei Wang, Yeisoo Yu, Yijie Luo, Beatriz Elena Padilla Hurtado, Ann Danowitz, Rod A Wing, Qifa Zhang
Over the past 30 years, we have performed many fundamental studies on two Oryza sativa subsp. indica varieties, Zhenshan 97 (ZS97) and Minghui 63 (MH63). To improve the resolution of many of these investigations, we generated two reference-quality reference genome assemblies using the most advanced sequencing technologies. Using PacBio SMRT technology, we produced over 108 (ZS97) and 174 (MH63) Gb of raw sequence data from 166 (ZS97) and 209 (MH63) pools of BAC clones, and generated ~97 (ZS97) and ~74 (MH63) Gb of paired-end whole-genome shotgun (WGS) sequence data with Illumina sequencing technology...
2016: Scientific Data
https://www.readbyqxmd.com/read/27587810/high-quality-genome-assembly-and-annotation-for-plasmodium-coatneyi-generated-using-single-molecule-real-time-pacbio-technology
#20
Jung-Ting Chien, Suman B Pakala, Juliana A Geraldo, Stacey A Lapp, Jay C Humphrey, John W Barnwell, Jessica C Kissinger, Mary R Galinski
Plasmodium coatneyi is a protozoan parasite species that causes simian malaria and is an excellent model for studying disease caused by the human malaria parasite, P. falciparum Here we report the complete (nontelomeric) genome sequence of P. coatneyi Hackeri generated by the application of only Pacific Biosciences RS II (PacBio RS II) single-molecule real-time (SMRT) high-resolution sequence technology and assembly using the Hierarchical Genome Assembly Process (HGAP). This is the first Plasmodium genome sequence reported to use only PacBio technology...
2016: Genome Announcements
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