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https://www.readbyqxmd.com/read/28811753/characterization-of-the-rosellinia-necatrix-transcriptome-and-genes-related-to-pathogenesis-by-single-molecule-mrna-sequencing
#1
Hyeongmin Kim, Seung Jae Lee, Ick-Hyun Jo, Jinsu Lee, Wonsil Bae, Hyemin Kim, Kyungho Won, Tae Kyung Hyun, Hojin Ryu
White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen...
August 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28802668/two-novel-lncrnas-discovered-in-human-mitochondrial-dna-using-pacbio-full-length-transcriptome-data
#2
Shan Gao, Xiaoxuan Tian, Hong Chang, Yu Sun, Zhenfeng Wu, Zhi Cheng, Pengzhi Dong, Qiang Zhao, Jishou Ruan, Wenjun Bu
In this study, we introduced a general framework to use PacBio full-length transcriptome sequencing for the investigation of mitochondrial RNAs. As a result, we produced the first full-length human mitochondrial transcriptome based on the public PacBio data and characterized the human mitochondrial transcriptome with more comprehensive and accurate information. Other results included the determination of the H-strand primary transcript, the identification of ND5/ND6AS/tRNA(Glu)AS, the discovery of palindrome small RNAs and the construction of "cleavage" model...
August 9, 2017: Mitochondrion
https://www.readbyqxmd.com/read/28798737/complete-genome-analysis-of-thermus-parvatiensis-and-comparative-genomics-of-thermus-spp-provide-insights-into-genetic-variability-and-evolution-of-natural-competence-as-strategic-survival-attributes
#3
Charu Tripathi, Harshita Mishra, Himani Khurana, Vatsala Dwivedi, Komal Kamra, Ram K Negi, Rup Lal
Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798190/draft-genome-sequence-of-thiohalobacter-thiocyanaticus-strain-fokn1-a-neutrophilic-halophile-capable-of-thiocyanate-degradation
#4
Mamoru Oshiki, Toshikazu Fukushima, Shuichi Kawano, Junichi Nakagawa
A draft genome sequence of a neutrophilic halophile capable of thiocyanate degradation, Thiohalobacter thiocyanaticus FOKN1, was determined using a PacBio RSII sequencer. A 3.23-Mb circular genome sequence was assembled, in which 3,026 gene-coding sequences, 45 tRNAs, and 1 rrn operon were annotated.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28798165/complete-genome-sequences-of-three-isolates-of-xanthomonas-fragariae-the-bacterium-responsible-for-angular-leaf-spots-on-strawberry-plants
#5
Michael Gétaz, Jan M van der Wolf, Jochen Blom, Joël F Pothier
Xanthomonas fragariae is a worldwide-spread plant bacterial disease causing angular leaf spots, thus reducing the yield of production for strawberry fruits. Three isolates with various geographic and time origins were sequenced with long-read technology (PacBio) to generate finished genome sequences of virulent strains and observe the variability in their contents.
August 10, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28794490/a-transcriptome-atlas-of-rabbit-revealed-by-pacbio-single-molecule-long-read-sequencing
#6
Shi-Yi Chen, Feilong Deng, Xianbo Jia, Cao Li, Song-Jia Lai
It is widely acknowledged that transcriptional diversity largely contributes to biological regulation in eukaryotes. Since the advent of second-generation sequencing technologies, a large number of RNA sequencing studies have considerably improved our understanding of transcriptome complexity. However, it still remains a huge challenge for obtaining full-length transcripts because of difficulties in the short read-based assembly. In the present study we employ PacBio single-molecule long-read sequencing technology for whole-transcriptome profiling in rabbit (Oryctolagus cuniculus)...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28769883/a-case-study-into-microbial-genome-assembly-gap-sequences-and-finishing-strategies
#7
Sagar M Utturkar, Dawn M Klingeman, Richard A Hurt, Steven D Brown
This study characterized regions of DNA which remained unassembled by either PacBio and Illumina sequencing technologies for seven bacterial genomes. Two genomes were manually finished using bioinformatics and PCR/Sanger sequencing approaches and regions not assembled by automated software were analyzed. Gaps present within Illumina assemblies mostly correspond to repetitive DNA regions such as multiple rRNA operon sequences. PacBio gap sequences were evaluated for several properties such as GC content, read coverage, gap length, ability to form strong secondary structures, and corresponding annotations...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28747380/identification-of-differentially-expressed-splice-variants-by-the-proteogenomic-pipeline-splicify
#8
Malgorzata A Komor, Thang Pham, Annemieke C Hiemstra, Sander R Piersma, Anne S Bolijn, Tim Schelfhorst, Pien M Delis-van Diemen, Marianne Tijssen, Robert P Sebra, Meredith Ashby, Gerrit A Meijer, Connie R Jimenez, Remond J A Fijneman
Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions...
July 26, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28747151/comparative-analysis-of-targeted-long-read-sequencing-approaches-for-characterization-of-a-plant-s-immune-receptor-repertoire
#9
Michael Giolai, Pirita Paajanen, Walter Verweij, Kamil Witek, Jonathan D G Jones, Matthew D Clark
BACKGROUND: The Oxford Nanopore Technologies MinION™ sequencer is a small, portable, low cost device that is accessible to labs of all sizes and attractive for in-the-field sequencing experiments. Selective breeding of crops has led to a reduction in genetic diversity, and wild relatives are a key source of new genetic resistance to pathogens, usually via NLR immune receptor-encoding genes. Recent studies have demonstrated how crop NLR repertoires can be targeted for sequencing on Illumina or PacBio (RenSeq) and the specific gene conveying pathogen resistance identified...
July 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28729278/high-quality-genome-sequence-of-the-highly-resistant-bacterium-staphylococcus-haemolyticus-isolated-from-a-neonatal-bloodstream-infection
#10
Farideh Hosseinkhani, Mohammad Emaneini, Willem van Leeuwen
Using Illumina HiSeq and PacBio technologies, we sequenced the genome of the multidrug-resistant bacterium Staphylococcus haemolyticus, originating from a bloodstream infection in a neonate. The sequence data can be used as an accurate reference sequence.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28729271/whole-genome-sequence-of-acinetobacter-pittii-humv-6483-isolated-from-human-urine
#11
Itziar Chapartegui-González, María Lázaro-Díez, Santiago Redondo-Salvo, Laura Alted-Pérez, Javier Gonzalo Ocejo-Vinyals, Jesús Navas, José Ramos-Vivas
Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly.
July 20, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28724921/saliva-and-tooth-biofilm-bacterial-microbiota-in-adolescents-in-a-low-caries-community
#12
Linda Eriksson, Pernilla Lif Holgerson, Ingegerd Johansson
The oral cavity harbours a complex microbiome that is linked to dental diseases and serves as a route to other parts of the body. Here, the aims were to characterize the oral microbiota by deep sequencing in a low-caries population with regular dental care since childhood and search for association with caries prevalence and incidence. Saliva and tooth biofilm from 17-year-olds and mock bacteria communities were analysed using 16S rDNA Illumina MiSeq (v3-v4) and PacBio SMRT (v1-v8) sequencing including validity and reliability estimates...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720171/pacbio-assembly-of-a-plasmodium-knowlesi-genome-sequence-with-hi-c-correction-and-manual-annotation-of-the-sicavar-gene-family
#13
S A Lapp, J A Geraldo, J-T Chien, F Ay, S B Pakala, G Batugedara, J Humphrey, J D DeBARRY, K G Le Roch, M R Galinski, J C Kissinger
Plasmodium knowlesi has risen in importance as a zoonotic parasite that has been causing regular episodes of malaria throughout South East Asia. The P. knowlesi genome sequence generated in 2008 highlighted and confirmed many similarities and differences in Plasmodium species, including a global view of several multigene families, such as the large SICAvar multigene family encoding the variant antigens known as the schizont-infected cell agglutination proteins. However, repetitive DNA sequences are the bane of any genome project, and this and other Plasmodium genome projects have not been immune to the gaps, rearrangements and other pitfalls created by these genomic features...
July 19, 2017: Parasitology
https://www.readbyqxmd.com/read/28720120/interrogating-the-unsequenceable-genomic-trinucleotide-repeat-disorders-by-long-read-sequencing
#14
Qian Liu, Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28711667/identification-of-three-homologous-latex-clearing-protein-lcp-genes-from-the-genome-of-streptomyces-sp-strain-cfmr-7
#15
Jayaram Nanthini, Su Yean Ong, Kumar Sudesh
Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28711373/comparative-genomic-and-phylogenetic-analysis-of-a-toxigenic-clinical-isolate-of-corynebacterium-diphtheriae-strain-b-d-16-78-from-malaysia
#16
Kar-Wai Hong, A W Asmah Hani, C A Nurul Aina Murni, R R Pusparani, Chee Kheong Chong, Khebir Verasahib, Wan Noraini W Yusoff, Noorliza M Noordin, Kok Keng Tee, Wai-Fong Yin, Choo Yee Yu, Geik Yong Ang, Kok-Gan Chan
In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile...
July 12, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28701704/concatseq-a-method-for-increasing-throughput-of-single-molecule-sequencing-by-concatenating-short-dna-fragments
#17
Ulrich Schlecht, Janine Mok, Carolina Dallett, Jan Berka
Single molecule sequencing (SMS) platforms enable base sequences to be read directly from individual strands of DNA in real-time. Though capable of long read lengths, SMS platforms currently suffer from low throughput compared to competing short-read sequencing technologies. Here, we present a novel strategy for sequencing library preparation, dubbed ConcatSeq, which increases the throughput of SMS platforms by generating long concatenated templates from pools of short DNA molecules. We demonstrate adaptation of this technique to two target enrichment workflows, commonly used for oncology applications, and feasibility using PacBio single molecule real-time (SMRT) technology...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28701143/smrt-gate-a-method-for-validation-of-synthetic-constructs-on-pacific-biosciences-sequencing-platforms
#18
Rosalinda D'Amore, James Johnson, Sam Haldenby, Neil Hall, Margaret Hughes, Ryan Joynson, John G Kenny, Nicola Patron, Christiane Hertz-Fowler, Anthony Hall
Current DNA assembly methods are prone to sequence errors, requiring rigorous quality control (QC) to identify incorrect assemblies or synthesized constructs. Such errors can lead to misinterpretation of phenotypes. Because of this intrinsic problem, routine QC analysis is generally performed on three or more clones using a combination of restriction endonuclease assays, colony PCR, and Sanger sequencing. However, as new automation methods emerge that enable high-throughput assembly, QC using these techniques has become a major bottleneck...
July 1, 2017: BioTechniques
https://www.readbyqxmd.com/read/28696923/whole-genome-sequence-of-the-heterozygous-clinical-isolate-candida-krusei-81-b-5
#19
Christina A Cuomo, Terrance Shea, Bo Yang, Reeta Rao, Anja Forche
Candida krusei is a diploid, heterozygous yeast that is an opportunistic fungal pathogen in immunocompromised patients. This species also is utilized for fermenting cocoa beans during chocolate production. One major concern in the clinical setting is the innate resistance of this species to the most commonly used antifungal drug fluconazole. Here we report a high-quality genome sequence and assembly for the first clinical isolate of C. krusei, strain 81-B-5, into 11 scaffolds generated with PacBio sequencing technology...
July 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28696422/metagenomic-binning-of-a-marine-sponge-microbiome-reveals-unity-in-defense-but-metabolic-specialization
#20
Beate M Slaby, Thomas Hackl, Hannes Horn, Kristina Bayer, Ute Hentschel
Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts...
July 11, 2017: ISME Journal
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