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https://www.readbyqxmd.com/read/28438015/genome-characteristics-of-lactobacillus-fermentum-strain-jdfm216-for-application-as-probiotic-bacteria
#1
Sung Yong Jang, Jaeyoung Heo, Mi Ri Park, Min-Ho Song, Jong Nam Kim, Sung Ho Jo, Do-Youn Jeong, Hak Kyo Lee, Younghoon Kim, Sangnam Oh
Lactobacillus fermentum strain JDFM216, isolated from a Korean infant feces, possesses an enhancement of longevity and immune response on Caenorhabditis elegans host. To explore the molecular characteristics of strain JDFM216, we performed a whole-genome sequencing using PacBio system. The single circular DNA chromosome of 2,076,427 bp was completely assembled and 2,623 encoding sequences were predicted. Phylogenetically featured five genes possibly related to longevity and immune response of host were identified in L...
April 25, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28431028/hybrid-de-novo-genome-assembly-of-the-chinese-herbal-fleabane-erigeron-breviscapus
#2
Jing Yang, Guanghui Zhang, Jing Zhang, Hui Liu, Wei Chen, Xiao Wang, Yahe Li, Yang Dong, Shengchao Yang
Background: The plants in the Erigeron genus of the Compositae (Asteraceae) family are commonly called fleabanes, possibly due to the belief that certain chemicals in these plants repel fleas. In the traditional Chinese medicine, Erigeron breviscapus , which is native to China, was widely used in the treatment of cerebrovascular disease. A handful of bioactive compounds, including scutellarin, 3,5-dicaffeoylquinic acid, and 3,4-dicaffeoylquinic acid, have been isolated from the plant...
April 18, 2017: GigaScience
https://www.readbyqxmd.com/read/28430818/comparative-genomics-of-burkholderia-multivorans-a-ubiquitous-pathogen-with-a-highly-conserved-genomic-structure
#3
Charlotte Peeters, Vaughn S Cooper, Philip J Hatcher, Bart Verheyde, Aurélien Carlier, Peter Vandamme
The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B...
2017: PloS One
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#4
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28420692/an-improved-assembly-and-annotation-of-the-allohexaploid-wheat-genome-identifies-complete-families-of-agronomic-genes-and-provides-genomic-evidence-for-chromosomal-translocations
#5
Bernardo J Clavijo, Luca Venturini, Christian Schudoma, Gonzalo Garcia Accinelli, Gemy Kaithakottil, Jonathan Wright, Philippa Borrill, George Kettleborough, Darren Heavens, Helen Chapman, James Lipscombe, Tom Barker, Fu-Hao Lu, Neil McKenzie, Dina Raats, Ricardo H Ramirez-Gonzalez, Aurore Coince, Ned Peel, Lawrence Percival-Alwyn, Owen Duncan, Josua Trösch, Guotai Yu, Dan M Bolser, Guy Namaati, Arnaud Kerhornou, Manuel Spannagl, Heidrun Gundlach, Georg Haberer, Robert P Davey, Christine Fosker, Federica Di Palma, Andrew Phillips, A Harvey Millar, Paul J Kersey, Cristobal Uauy, Ksenia V Krasileva, David Swarbreck, Michael W Bevan, Matthew D Clark
Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data...
April 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28418097/genome-and-epigenome-of-a-novel-marine-thaumarchaeota-strain-suggest-viral-infection-phosphorothioation-dna-modification-and-multiple-restriction-systems
#6
Nathan A Ahlgren, Yangyang Chen, David M Needham, Alma E Parada, Rohan Sachdeva, Vicki Trinh, Ting Chen, Jed A Fuhrman
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes...
April 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28417959/genome-sequence-of-plasmopara-viticola-and-insight-into-the-pathogenic-mechanism
#7
Ling Yin, Yunhe An, Junjie Qu, Xinlong Li, Yali Zhang, Ian Dry, Huijuan Wu, Jiang Lu
Plasmopara viticola causes downy mildew disease of grapevine which is one of the most devastating diseases of viticulture worldwide. Here we report a 101.3 Mb whole genome sequence of P. viticola isolate 'JL-7-2' obtained by a combination of Illumina and PacBio sequencing technologies. The P. viticola genome contains 17,014 putative protein-coding genes and has ~26% repetitive sequences. A total of 1,301 putative secreted proteins, including 100 putative RXLR effectors and 90 CRN effectors were identified in this genome...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28408691/whole-genome-sequence-of-staphylococcus-hominis-strain-j31-isolated-from-healthy-human-skin
#8
Rosanna Coates-Brown, Malcolm J Horsburgh
We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.
April 13, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28405230/lorte-detecting-transposon-induced-genomic-variants-using-low-coverage-pacbio-long-read-sequences
#9
Eric Disdero, Jonathan Filée
BACKGROUND: Population genomic analysis of transposable elements has greatly benefited from recent advances of sequencing technologies. However, the short size of the reads and the propensity of transposable elements to nest in highly repeated regions of genomes limits the efficiency of bioinformatic tools when Illumina or 454 technologies are used. Fortunately, long read sequencing technologies generating read length that may span the entire length of full transposons are now available...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28400415/recombination-dependent-replication-and-gene-conversion-homogenize-repeat-sequences-and-diversify-plastid-genome-structure
#10
Tracey A Ruhlman, Jin Zhang, John C Blazier, Jamal S M Sabir, Robert K Jansen
PREMISE OF THE STUDY: There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements...
April 11, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28385004/molecular-and-genomic-features-of-mycobacterium-bovis-strain-1595-isolated-from-korean-cattle
#11
Narae Kim, Yunho Jang, Jin Kyoung Kim, Soyoon Ryoo, Ka Hee Kwon, Miso Kim, Shin Seok Kang, Hyeon Seop Byeon, Hee Soo Lee, Young-Hee Lim, Jae-Myung Kim
The aim of this study was to investigate the molecular characteristics and conduct a comparative genomic analysis for Mycobacterium bovis strain 1595 isolated from a native Korean cow. Molecular typing showed that M. bovis 1595 has spoligotype SB0140 with mycobacterial interspersed repetitive units-variable number of tandem repeats typing of 4-2-5-3-2-7-5-5-4-3-4-3-4-3, representing the most common type of M. bovis in Korea. The complete genome sequence of strain 1595 was determined using Illumina MiSeq and PacBio single-molecule real-time technology, which showed a genome of 4,351,712 bp in size with a 65...
April 6, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28381259/halc-high-throughput-algorithm-for-long-read-error-correction
#12
Ergude Bao, Lingxiao Lan
BACKGROUND: The third generation PacBio SMRT long reads can effectively address the read length issue of the second generation sequencing technology, but contain approximately 15% sequencing errors. Several error correction algorithms have been designed to efficiently reduce the error rate to 1%, but they discard large amounts of uncorrected bases and thus lead to low throughput. This loss of bases could limit the completeness of downstream assemblies and the accuracy of analysis. RESULTS: Here, we introduce HALC, a high throughput algorithm for long read error correction...
April 5, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28373483/single-molecule-sequencing-resolves-the-detailed-structure-of-complex-satellite-dna-loci-in-drosophila-melanogaster
#13
Daniel E Khost, Danna G Eickbush, Amanda M Larracuente
Highly repetitive satellite DNA (satDNA) repeats are found in most eukaryotic genomes. SatDNAs are rapidly evolving and have roles in genome stability and chromosome segregation. Their repetitive nature poses a challenge for genome assembly and makes progress on the detailed study of satDNA structure difficult. Here, we use single-molecule sequencing long reads from Pacific Biosciences (PacBio) to determine the detailed structure of all major autosomal complex satDNA loci in Drosophila melanogaster, with a particular focus on the 260-bp and Responder satellites...
April 3, 2017: Genome Research
https://www.readbyqxmd.com/read/28364362/advantages-of-genome-sequencing-by-long-read-sequencer-using-smrt-technology-in-medical-area
#14
REVIEW
Kazuma Nakano, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Shun Ohki, Misuzu Shinzato, Maiko Minami, Tetsuhiro Nakanishi, Kuniko Teruya, Kazuhito Satou, Takashi Hirano
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions...
March 31, 2017: Human Cell
https://www.readbyqxmd.com/read/28361880/genomic-structure-of-the-horse-major-histocompatibility-complex-class-ii-region-resolved-using-pacbio-long-read-sequencing-technology
#15
Agnese Viļuma, Sofia Mikko, Daniela Hahn, Loren Skow, Göran Andersson, Tomas F Bergström
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region...
March 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28360165/complete-genome-sequence-of-lactobacillus-fermentum-mtcc-25067-formerly-tds030603-a-viscous-exopolysaccharide-producing-strain-isolated-from-indian-fermented-milk
#16
Ni Putu Desy Aryantini, Jashbhai B Prajapati, Tadasu Urashima, Kenji Fukuda
Lactobacillus fermentum MTCC 25067 (formerly TDS030603) is capable of producing a highly viscous slime exopolysaccharide. We report here the complete genome sequence of the strain, which was deciphered by using PacBio single-molecule real-time sequencing technology.
March 30, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28344744/automation-of-pacbio-smrtbell-ngs-library-preparation-for-bacterial-genome-sequencing
#17
Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, Bart C Weimer
BACKGROUND: The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library. FINDINGS: The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28336594/first-report-on-the-complete-genome-sequence-of-lactobacillus-crustorum-mn047-a-potent-probiotic-strain-isolated-from-koumiss-in-china
#18
Lanhua Yi, Xing Guo, Lian Liu, Chunge Shao, Xin Lü
The complete genome sequence of Lactobacillus crustorum deciphered by PacBio RS II and Illumina HiSeq 4000 sequencing was first reported with one chromosome and two plasmids. Sequence analysis of L. crustorum MN047 showed probiotic characteristics.
March 23, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28327967/genome-sequence-of-pacific-abalone-haliotis-discus-hannai-the-first-draft-genome-in-family-haliotidae
#19
Bo-Hye Nam, Woori Kwak, Young-Ok Kim, Dong-Gyun Kim, Hee Jeong Kong, Woo-Jin Kim, Jeong-Ha Kang, Jung Youn Park, Cheul Min An, Ji-Young Moon, Choul Ji Park, Jae Woong Yu, Joon Yoon, Minseok Seo, Kwondo Kim, Duk Kyung Kim, SaetByeol Lee, Samsun Sung, Chul Lee, Younhee Shin, Myunghee Jung, Byeong-Chul Kang, Shin Ga-Hee, Sojeong Ka, Kelsey Caetano-Anolles, Seoae Cho, Heebal Kim
Background: Abalones are large marine snails in the family Haliotidae and the genus Haliotis belonging to the class Gastropoda of the phylum Mollusca. The family Haliotidae contains only one genus, Haliotis, and this single genus is known to contain several species of abalone. With 18 additional subspecies, the most comprehensive treatment of Haliotidae considers 56 species valid [1]. Abalone is an economically important fishery and aquaculture animal which is considered a highly-prized seafood delicacy...
March 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28316149/detecting-alternatively-spliced-transcript-isoforms-from-single-molecule-long-read-sequences-without-a-reference-genome
#20
Xiaoxian Liu, Wenbin Mei, Pamela S Soltis, Douglas E Soltis, W Brad Barbazuk
Alternative splicing (AS) is a major source of transcript and proteome diversity, but examining AS in species without well-annotated reference genomes remains difficult. Research on both human and mouse has demonstrated the advantages of using Iso-Seq(™) data for isoform-level transcriptome analysis, including the study of AS and gene fusion. We applied Iso-Seq(™) to investigate AS in Amborella trichopoda, a phylogenetically pivotal species that is sister to all other living angiosperms. Our data show that, compared with RNA-Seq data, the Iso-Seq(™) platform provides better recovery on large transcripts, new gene locus identification, and gene model correction...
March 18, 2017: Molecular Ecology Resources
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