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Fair M Vassoler, David J Oliver, Cristina Wyse, Ashley Blau, Michael Shtutman, Jill R Turner, Elizabeth M Byrnes
The United States is in the midst of an opiate epidemic, with abuse of prescription and illegal opioids increasing steadily over the past decade. While it is clear that there is a genetic component to opioid addiction, there is a significant portion of heritability that cannot be explained by genetics alone. The current study was designed to test the hypothesis that maternal exposure to opioids prior to pregnancy alters abuse liability in subsequent generations. Female adolescent Sprague Dawley rats were administered morphine at increasing doses (5-25 mg/kg, s...
October 8, 2016: Neuropharmacology
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
Sooyeon Lim, Dong-Ho Chang, Byoung-Chan Kim
Dermabacter vaginalis AD1-86(T) was isolated from the vaginal fluid of a Korean woman. Whole genome sequencing analysis was conducted using a PacBio RS II platform and annotated on RAST. The nucleotide sequence of this genome was deposited into DDBJ/EMBL/GenBank under the accession NZ_CP012117.
December 2016: Genomics Data
Qiongqiong Zhou, Wenjuan Sun, Xiyan Liu, Xiliang Wang, Yuncai Xiao, Dingren Bi, Jingdong Yin, Deshi Shi
AIM: Pig liver carboxylesterase (PLE) gene sequences in GenBank are incomplete, which has led to difficulties in studying the genetic structure and regulation mechanisms of gene expression of PLE family genes. The aim of this study was to obtain and analysis of complete gene sequences of PLE family by screening from a Rongchang pig BAC library and third-generation PacBio gene sequencing. METHODS: After a number of existing incomplete PLE isoform gene sequences were analysed, primers were designed based on conserved regions in PLE exons, and the whole pig genome used as a template for Polymerase chain reaction (PCR) amplification...
2016: PloS One
Denis Faure, Slimane Khayi, Jérémy Cigna, Teik Min Chong, Angélique Quêtu-Laurent, Kok Gan Chan, Valérie Hélias
Pectobacterium wasabiae was originally isolated from Japanese horseradish (Eutrema wasabi), but recently some Pectobacterium isolates collected from potato plants and tubers displaying blackleg and soft rot symptoms were also assigned to P. wasabiae. Here, combining genomic and phenotypical data, we reevaluated their taxonomical position. PacBio and Illumina technologies were used to complete the genome sequence of P. wasabiae CFBP 3304T and RNS 08-42-1A. MLSA showed that the Pectobacterium wasabiae strains RNS 08-42-1A, SCC3193, CFIA1002 and WPP163, which were collected from potato plant environment, constituted a separate clade from the originating Japanese horseradish P...
September 26, 2016: International Journal of Systematic and Evolutionary Microbiology
Sagar M Utturkar, Edward A Bayer, Ilya Borovok, Raphael Lamed, Richard A Hurt, Miriam L Land, Dawn M Klingeman, Dwayne Elias, Jizhong Zhou, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Steven D Brown
We and others have shown the utility of long sequence reads to improve genome assembly quality. In this study, we generated PacBio DNA sequence data to improve the assemblies of draft genomes for Clostridium thermocellum AD2, Clostridium thermocellum LQRI, and Pelosinus fermentans R7.
September 29, 2016: Genome Announcements
Dóra Tombácz, Zsolt Csabai, Péter Oláh, Zsolt Balázs, István Likó, Laura Zsigmond, Donald Sharon, Michael Snyder, Zsolt Boldogkői
Whole transcriptome studies have become essential for understanding the complexity of genetic regulation. However, the conventionally applied short-read sequencing platforms cannot be used to reliably distinguish between many transcript isoforms. The Pacific Biosciences (PacBio) RS II platform is capable of reading long nucleic acid stretches in a single sequencing run. The pseudorabies virus (PRV) is an excellent system to study herpesvirus gene expression and potential interactions between the transcriptional units...
2016: PloS One
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
Bayo Lau, Marghoob Mohiyuddin, John C Mu, Li Tai Fang, Narges Bani Asadi, Carolina Dallett, Hugo Y K Lam
: LongISLND is a software package designed to simulate sequencing data according to the characteristics of third generation, single-molecule sequencing technologies. The general software architecture is easily extendable, as demonstrated by the emulation of Pacific Biosciences (PacBio) multi-pass sequencing with P5 and P6 chemistries, producing data in FASTQ, H5, and the latest PacBio BAM format. We demonstrate its utility by downstream processing with consensus building and variant calling...
September 25, 2016: Bioinformatics
Naoya Shinzato, Hiroaki Aoyama, Seikoh Saitoh, Naruo Nikoh, Kazuma Nakano, Makiko Shimoji, Misuzu Shinzato, Kazuhito Satou, Kuniko Teruya, Takashi Hirano, Takanori Yamada, Masaru K Nobu, Hideyuki Tamaki, Yumi Shirai, Sanghwa Park, Takashi Narihiro, Wen-Tso Liu, Yoichi Kamagata
A free-living ciliate, Trimyema compressum, found in anoxic freshwater environments harbors methanogenic archaea and a bacterial symbiont named TC1 in its cytoplasm. Here, we report the complete genome sequence of the TC1 symbiont, consisting of a 1.59-Mb chromosome and a 35.8-kb plasmid, which was determined using the PacBio RSII sequencer.
2016: Genome Announcements
Hengyun Lu, Francesca Giordano, Zemin Ning
The revolution of genome sequencing is continuing after the successful second-generation sequencing (SGS) technology. The third-generation sequencing (TGS) technology, led by Pacific Biosciences (PacBio), is progressing rapidly, moving from a technology once only capable of providing data for small genome analysis, or for performing targeted screening, to one that promises high quality de novo assembly and structural variation detection for human-sized genomes. In 2014, the MinION, the first commercial sequencer using nanopore technology, was released by Oxford Nanopore Technologies (ONT)...
September 17, 2016: Genomics, Proteomics & Bioinformatics
Yasuhiro Uchimura, Madeleine Wyss, Sandrine Brugiroux, Julien P Limenitakis, Bärbel Stecher, Kathy D McCoy, Andrew J Macpherson
We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.
2016: Genome Announcements
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
Andrea Hahn, Amit Sanyal, Geovanny F Perez, Anamaris M Colberg-Poley, Joseph Campos, Mary C Rose, Marcos Pérez-Losada
BACKGROUND: Cystic fibrosis (CF) is an autosomal recessive disease characterized by recurrent lung infections. Studies of the lung microbiome have shown an association between decreasing diversity and progressive disease. 454 pyrosequencing has frequently been used to study the lung microbiome in CF, but will no longer be supported. We sought to identify the benefits and drawbacks of using two state-of-the-art next generation sequencing (NGS) platforms, MiSeq and PacBio RSII, to characterize the CF lung microbiome...
November 2016: Journal of Microbiological Methods
Xiaoting Hua, Yuejin Hua
The genome sequence of Deinococcus radiodurans R1 was published in 1999. We resequenced D. radiodurans R1 using PacBio and compared the sequence with the published one. Large insertions and single nucleotide polymorphisms (SNPs) were observed among the genome sequences. A more accurate genome sequence will be helpful to studies of D. radiodurans.
2016: Genome Announcements
Kazuma Nakano, Akino Shiroma, Hinako Tamotsu, Shun Ohki, Makiko Shimoji, Noriko Ashimine, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Chise Suzuki, Hiromi Kimoto-Nira, Miho Kobayashi, Koko Mizumachi, Reiji Aoki, Satoshi Miyata, Kazue Yamamoto, Yasuyuki Ohtake, Tomoko Eguchi-Ogawa, Naoko Moriya, Tatsuro Hagi, Masaru Nomura, Takashi Hirano
The first complete genome sequence of Lactobacillus curvatus was determined by PacBio RS II. The single circular chromosome (1,848,756 bp, G+C content of 42.1%) of L. curvatus FBA2, isolated from fermented vegetables, contained low G+C regions (26.9% minimum) and 43 sets of >1,000-bp identical sequence pairs. No plasmids were detected.
2016: Genome Announcements
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
Xiao-Heng Song, Hong-Xi Chen, Wang-Shu Zhou, Jiang-Bo Wang, Ma-Feng Liu, Ming-Shu Wang, An-Chun Cheng, Ren-Yong Jia, Shun Chen, Kun-Feng Sun, Qiao Yang, Ying Wu, Xiao-Yue Chen, De-Kang Zhu
Mycobacterium avium is an important pathogenic bacterium in birds and has never, to our knowledge, reported to be isolated from domestic ducks. We present here the complete genome sequence of a virulent strain of Mycobacterium avium, isolated from domestic Pekin ducks for the first time, which was determined by PacBio single-molecule real-time technology.
2016: Genome Announcements
Ehsan Haghshenas, Faraz Hach, S Cenk Sahinalp, Cedric Chauve
MOTIVATION: Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage...
September 1, 2016: Bioinformatics
Nan Du, Yanni Sun
MOTIVATION: Single-molecule, real-time sequencing (SMRT) developed by Pacific BioSciences produces longer reads than secondary generation sequencing technologies such as Illumina. The long read length enables PacBio sequencing to close gaps in genome assembly, reveal structural variations, and identify gene isoforms with higher accuracy in transcriptomic sequencing. However, PacBio data has high sequencing error rate and most of the errors are insertion or deletion errors. During alignment-based homology search, insertion or deletion errors in genes will cause frameshifts and may only lead to marginal alignment scores and short alignments...
September 1, 2016: Bioinformatics
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