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https://www.readbyqxmd.com/read/27912743/str-realigner-a-realignment-method-for-short-tandem-repeat-regions
#1
Kaname Kojima, Yosuke Kawai, Kazuharu Misawa, Takahiro Mimori, Masao Nagasaki
BACKGROUND: In the estimation of repeat numbers in a short tandem repeat (STR) region from high-throughput sequencing data, two types of strategies are mainly taken: a strategy based on counting repeat patterns included in sequence reads spanning the region and a strategy based on estimating the difference between the actual insert size and the insert size inferred from paired-end reads. The quality of sequence alignment is crucial, especially in the former approaches although usual alignment methods have difficulty in STR regions due to insertions and deletions caused by the variations of repeat numbers...
December 3, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27899577/a-comprehensive-approach-to-expression-of-l1-loci
#2
Prescott Deininger, Maria E Morales, Travis B White, Melody Baddoo, Dale J Hedges, Geraldine Servant, Sudesh Srivastav, Madison E Smither, Monica Concha, Dawn L DeHaro, Erik K Flemington, Victoria P Belancio
L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5' RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads...
November 28, 2016: Nucleic Acids 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/27882618/whole-genome-sequencing-analysis-of-the-cutaneous-pathogenic-yeast-malassezia-restricta-and-identification-of-the-major-lipase-expressed-on-the-scalp-of-patients-with-dandruff
#4
Minji Park, Yong-Joon Cho, Yang Won Lee, Won Hee Jung
Malassezia species are opportunistic pathogenic fungi that are frequently associated with seborrhoeic dermatitis, including dandruff. Most Malassezia species are lipid dependent, a property that is compensated by breaking down host sebum into fatty acids by lipases. In this study, we aimed to sequence and analyse the whole genome of Malassezia restricta KCTC 27527, a clinical isolate from a Korean patient with severe dandruff, to search for lipase orthologues and identify the lipase that is the most frequently expressed on the scalp of patients with dandruff...
November 24, 2016: Mycoses
https://www.readbyqxmd.com/read/27881545/complete-genome-sequence-of-the-probiotic-strain-lactobacillus-salivarius-lpm01
#5
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/27842515/evaluation-of-pacbio-sequencing-for-full-length-bacterial-16s-rrna-gene-classification
#6
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/27834701/complete-genome-sequence-of-brevibacterium-linens-smq-1335
#7
Alessandra G de Melo, Simon J Labrie, Jeannot Dumaresq, Richard J Roberts, Denise M Tremblay, Sylvain Moineau
Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.
November 10, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27831497/improved-assembly-of-noisy-long-reads-by-k-mer-validation
#8
Antonio Bernardo Carvalho, Eduardo G Dupim, Gabriel Goldstein
Genome assembly depends critically on read length. Two recent technologies, from Pacific Biosciences (PacBio) and Oxford Nanopore, produce read lengths >20 kb, which yield de novo genome assemblies with vastly greater contiguity than those based on Sanger, Illumina, or other technologies. However, the very high error rates of these two new technologies (∼15% per base) makes assembly imprecise at repeats longer than the read length and computationally expensive. Here we show that the contiguity and quality of the assembly of these noisy long reads can be significantly improved at a minimal cost, by leveraging on the low error rate and low cost of Illumina short reads...
October 7, 2016: Genome Research
https://www.readbyqxmd.com/read/27829352/short-tandem-repeats-segmental-duplications-gene-deletion-and-genomic-instability-in-a-rapidly-diversified-immune-gene-family
#9
Matan Oren, Megan A Barela Hudgell, Brian D'Allura, Jacob Agronin, Alexandra Gross, Daniele Podini, L Courtney Smith
BACKGROUND: Genomic regions with repetitive sequences are considered unstable and prone to swift DNA diversification processes. A highly diverse immune gene family of the sea urchin (Strongylocentrotus purpuratus), called Sp185/333, is composed of clustered genes with similar sequence as well as several types of repeats ranging in size from short tandem repeats (STRs) to large segmental duplications. This repetitive structure may have been the basis for the incorrect assembly of this gene family in the sea urchin genome sequence...
November 9, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27822864/full-length-mitochondrial-dna-sequencing-on-the-pacbio-rsii
#10
Rolf H A M Vossen, Henk P J Buermans
Conventional mitochondrial-DNA (MT DNA) sequencing approaches use Sanger sequencing of 20-40 partially overlapping PCR fragments per individual, which is a time- and resource-consuming process. We have developed a high-throughput, accurate, fast, and cost-effective human MT DNA sequencing approach. In this setup we first generate long-range PCR products for two partially overlapping 7.7 and 9.2 kb MT DNA-specific amplicons, add sample-specific barcodes, and sequence these on the PacBio RSII system to obtain full-length MT DNA sequences for genotyping/haplotyping purposes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27821852/bac-pool-sequencing-and-analysis-confirms-growth-associated-qtls-in-the-asian-seabass-genome
#11
Xueyan Shen, Si Yan Ngoh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, Pranjali Bhandare, Andy Wee Kiat Tan, Gui Quan Tan, Siddharth Singh, Norman Chun Han Phua, Shubha Vij, László Orbán
The Asian seabass is an important marine food fish that has been cultured for several decades in Asia Pacific. However, the lack of a high quality reference genome has hampered efforts to improve its selective breeding. A 3D BAC pool set generated in this study was screened using 22 SSR markers located on linkage group 2 which contains a growth-related QTL region. Seventy-two clones corresponding to 22 FPC contigs were sequenced by Illumina MiSeq technology. We co-assembled the MiSeq-derived scaffolds from each FPC contig with error-corrected PacBio reads, resulting in 187 sequences covering 9...
November 8, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27803027/quantum-changes-in-helicobacter-pylori-gene-expression-accompany-host-adaptation
#12
Eng-Guan Chua, Michael J Wise, Yalda Khosravi, Shih-Wee Seow, Arlaine A Amoyo, Sven Pettersson, Fanny Peters, Chin-Yen Tay, Timothy T Perkins, Mun-Fai Loke, Barry J Marshall, Jamuna Vadivelu
Helicobacter pylori is a highly successful gastric pathogen. High genomic plasticity allows its adaptation to changing host environments. Complete genomes of H. pylori clinical isolate UM032 and its mice-adapted serial derivatives 298 and 299, generated using both PacBio RS and Illumina MiSeq sequencing technologies, were compared to identify novel elements responsible for host-adaptation. The acquisition of a jhp0562-like allele, which encodes for a galactosyltransferase, was identified in the mice-adapted strains...
November 1, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/27799338/assessing-the-gene-content-of-the-megagenome-sugar-pine-pinus-lambertiana
#13
Daniel Gonzalez-Ibeas, Pedro J Martinez-Garcia, Randi A Famula, Annette Delfino-Mix, Kristian A Stevens, Carol A Loopstra, Charles H Langley, David B Neale, Jill L Wegrzyn
Sugar pine (Pinus lambertiana Douglas) is within the subgenus Strobus with an estimated genome size of 31 Gbp. Transcriptomic resources are of particular interest in conifers due to the challenges presented in their megagenomes for gene identification. In this study, we present the first comprehensive survey of the P. lambertiana transcriptome through deep sequencing of a variety of tissue types to generate more than 2.5 billion short reads. Third generation, long reads generated through PacBio Iso-Seq has been included for the first time in conifers to combat the challenges associated with de novo transcriptome assembly...
October 31, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27797956/a-portrait-of-ribosomal-dna-contacts-with-hi-c-reveals-5s-and-45s-rdna-anchoring-points-in-the-folded-human-genome
#14
Shoukai Yu, Bernardo Lemos
Ribosomal rRNAs account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, while the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs)...
October 25, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27793962/incfiik-plasmid-harbouring-an-amplification-of-16s-rrna-methyltransferase-encoding-gene-rmth-associated-with-mobile-element-iscr2
#15
Racha Beyrouthy, Frederic Robin, Monzer Hamze, Richard Bonnet
OBJECTIVES: To investigate the resistance mechanisms and genetic support underlying the high resistance level of the Klebsiella pneumoniae strain CMUL78 to aminoglycoside and β-lactam antibiotics. METHODS: Antibiotic susceptibility was assessed by the disc diffusion method and MICs were determined by the microdilution method. Antibiotic resistance genes and their genetic environment were characterized by PCR and Sanger sequencing. Plasmid contents were analysed in the clinical strain and transconjugants obtained by mating-out assays...
October 28, 2016: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/27729240/transgenerational-attenuation-of-opioid-self-administration-as-a-consequence-of-adolescent-morphine-exposure
#16
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
https://www.readbyqxmd.com/read/27725207/complete-genome-sequence-of-plant-growth-promoting-bacterium-leifsonia-xyli-se134-a-possible-gibberellin-and-auxin-producer
#17
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/27722089/whole-genome-sequence-of-dermabacter-vaginalis-ad1-86-t-isolated-from-vaginal-fluid-of-korean-woman
#18
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
https://www.readbyqxmd.com/read/27695062/third-generation-sequencing-and-analysis-of-four-complete-pig-liver-esterase-gene-sequences-in-clones-identified-by-screening-bac-library
#19
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
https://www.readbyqxmd.com/read/27692046/transfer-of-the-potato-plant-isolates-of-pectobacterium-wasabiae-to-pectobacterium-parmentieri-sp-nov
#20
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
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