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https://www.readbyqxmd.com/read/29773637/complete-genome-sequence-of-celeribacter-baekdonensis-strain-lh4-a-thiosulfate-oxidizing-alphaproteobacterial-isolate-from-gulf-of-mexico-continental-slope-sediments
#1
Beverly E Flood, Dalton Leprich, Jake V Bailey
We report here the closed genome sequences of Celeribacter baekdonensis strain LH4 and five unnamed plasmids obtained through PacBio sequencing with 99.99% consensus concordance. The genomes contained several distinctive features not found in other published Celeribacter genomes, including the potential to aerobically degrade styrene and other phenolic compounds.
May 17, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29767360/transcript-profiling-using-long-read-sequencing-technologies
#2
Anthony Bayega, Yu Chang Wang, Spyros Oikonomopoulos, Haig Djambazian, Somayyeh Fahiminiya, Jiannis Ragoussis
RNA sequencing using next-generation sequencing (NGS, RNA-Seq) technologies is currently the standard approach for gene expression profiling, particularly for large-scale high-throughput studies. NGS technologies comprise short-read RNA-Seq (dominated by Illumina) and long-read RNA-Seq technologies provided by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Although short-read sequencing technologies are the most widely used, long-read technologies are increasingly becoming the standard approach for de novo transcriptome assembly and isoform expression quantification due to the complex nature of the transcriptome which consists of variable lengths of transcripts and multiple alternatively spliced isoforms for most genes...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29762659/independent-assessment-and-improvement-of-wheat-genome-sequence-assemblies-using-fosill-jumping-libraries
#3
Fu-Hao Lu, Neil McKenzie, George Kettleborough, Darren Heavens, Matthew D Clark, Michael W Bevan
Background: The accurate sequencing and assembly of very large, often polyploid, genomes remain a challenging task, limiting long-range sequence information and phased sequence variation for applications such as plant breeding. The 15 Gb hexaploid bread wheat genome has been particularly challenging to sequence, and several different approaches have recently generated long-range assemblies. Mapping and understanding the types of assembly errors is important for optimising future sequencing and assembly approaches and for comparative genomics...
May 11, 2018: GigaScience
https://www.readbyqxmd.com/read/29761214/analysis-of-resistance-genes-of-clinical-pannonibacter-phragmitetus-strain-31801-by-complete-genome-sequencing
#4
De-Song Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the resistance mechanisms of Pannonibacter phragmitetus 31801, isolated from the blood of a liver abscess patient, at the genomic level, we performed whole genomic sequencing using a PacBio RS II single-molecule real-time long-read sequencer. Bioinformatic analysis of the resulting sequence was then carried out to identify any possible resistance genes. Analyses included Basic Local Alignment Search Tool searches against the Antibiotic Resistance Genes Database, ResFinder analysis of the genome sequence, and Resistance Gene Identifier analysis within the Comprehensive Antibiotic Resistance Database...
May 14, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29757469/soil-microclimate-changes-affect-soil-fungal-communities-in-a-mediterranean-pine-forest
#5
Carles Castaño, Björn D Lindahl, Josu G Alday, Andreas Hagenbo, Juan Martínez de Aragón, Javier Parladé, Joan Pera, José Antonio Bonet
Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated the spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature. Fungal communities in 336 soil samples collected monthly over 1 year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol...
May 14, 2018: New Phytologist
https://www.readbyqxmd.com/read/29757382/de-novo-genome-assembly-of-the-red-silk-cotton-tree-bombax-ceiba
#6
Yong Gao, Haibo Wang, Chao Liu, Honglong Chu, Dongqin Dai, Shengnan Song, Long Yu, Lihong Han, Yi Fu, Bin Tian, Lizhou Tang
Background: Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia, and northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate the further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. Findings: We assembled a relatively intact genome of B...
May 10, 2018: GigaScience
https://www.readbyqxmd.com/read/29753477/using-pacbio-sequencing-to-investigate-the-bacterial-microbiota-of-traditional-buryatian-cottage-cheese-and-comparison-with-italian-and-kazakhstan-artisanal-cheeses
#7
Hao Jin, Lanxin Mo, Lin Pan, Qaingchaun Hou, Chuanjuan Li, Iaptueva Darima, Jie Yu
Traditional fermented dairy foods including cottage cheese have been major components of the Buryatia diet for centuries. Buryatian cheeses have maintained not only their unique taste and flavor but also their rich natural lactic acid bacteria (LAB) content. However, relatively few studies have described their microbial communities or explored their potential to serve as LAB resources. In this study, the bacterial microbiota community of 7 traditional artisan cheeses produced by local Buryatian families was investigated using single-molecule, real-time sequencing...
May 9, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29748405/high-quality-whole-genome-sequences-for-77-shiga-toxin-producing-escherichia-coli-strains-generated-with-pacbio-sequencing
#8
Pooja N Patel, Rebecca L Lindsey, Lisley Garcia-Toledo, Lori A Rowe, Dhwani Batra, Samuel W Whitley, Daniel Drapeau, Devon Stoneburg, Haley Martin, Phalasy Juieng, Vladimir N Loparev, Nancy Strockbine
Shiga toxin-producing Escherichia coli (STEC) is an enteric foodborne pathogen that can cause mild to severe illness. Here, we report the availability of high-quality whole-genome sequences for 77 STEC strains generated using the PacBio sequencing platform.
May 10, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29740915/analysis-of-recombinational-switching-at-the-antigenic-variation-locus-of-the-lyme-spirochete-using-a-novel-pacbio-sequencing-pipeline
#9
Theodore B Verhey, Mildred Castellanos, George Chaconas
No abstract text is available yet for this article.
May 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29730772/genome-annotation-and-comparative-genomic-analysis-of-bacillus-subtilis-mj01-a-new-bio-degradation-strain-isolated-from-oil-contaminated-soil
#10
Touraj Rahimi, Ali Niazi, Tahereh Deihimi, Seyed Mohsen Taghavi, Shahab Ayatollahi, Esmaeil Ebrahimie
One of the main challenges in elimination of oil contamination from polluted environments is improvement of biodegradation by highly efficient microorganisms. Bacillus subtilis MJ01 has been evaluated as a new resource for producing biosurfactant compounds. This bacterium, which produces surfactin, is able to enhance bio-accessibility to oil hydrocarbons in contaminated soils. The genome of B. subtilis MJ01 was sequenced and assembled by PacBio RS sequencing technology. One big contig with a length of 4,108,293 bp without any gap was assembled...
May 5, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29725120/long-read-sequencing-data-analysis-for-yeasts
#11
Jia-Xing Yue, Gianni Liti
Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process...
June 2018: Nature Protocols
https://www.readbyqxmd.com/read/29724849/complete-genome-sequence-of-petrimonas-sp-strain-ibaraki-assembled-from-the-metagenome-data-of-a-culture-containing-dehalococcoides-spp
#12
Kentaro Ikegami, Yuto Aita, Akino Shiroma, Makiko Shimoji, Hinako Tamotsu, Noriko Ashimine, Misuzu Shinzato, Shun Ohki, Kazuma Nakano, Kuniko Teruya, Kazuhito Satou, Takashi Hirano, Masafumi Yohda
The complete genome sequence of Petrimonas sp. strain IBARAKI in a Dehalococcoides -containing culture was determined using the PacBio RS II platform. The genome is a single circular chromosome of 3,693,233 nucleotides (nt), with a GC content of 44%. This is the first genome sequence of a Petrimonas species.
May 3, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29721151/strategies-for-high-altitude-adaptation-revealed-from-high-quality-draft-genome-of-non-violacein-producing-janthinobacterium-lividum-ergs5-01
#13
Rakshak Kumar, Vishal Acharya, Dharam Singh, Sanjay Kumar
A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29720989/molecular-mechanisms-of-acclimatization-to-phosphorus-starvation-and-recovery-underlying-full-length-transcriptome-profiling-in-barley-hordeum-vulgare-l
#14
Panrong Ren, Yaxiong Meng, Baochun Li, Xiaole Ma, Erjing Si, Yong Lai, Juncheng Wang, Lirong Yao, Ke Yang, Xunwu Shang, Huajun Wang
A lack of phosphorus (P) in plants can severely constrain growth and development. Barley, one of the earliest domesticated crops, is extensively planted in poor soil around the world. To date, the molecular mechanisms of enduring low phosphorus, at the transcriptional level, in barley are still unclear. In the present study, two different barley genotypes (GN121 and GN42)-with contrasting phosphorus efficiency-were used to reveal adaptations to low phosphorus stress, at three time points, at the morphological, physiological, biochemical, and transcriptome level...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29716534/comparative-genomics-of-cocci-shaped-sporosarcina-strains-with-diverse-spatial-isolation
#15
Andrew Oliver, Matthew Kay, Kerry K Cooper
BACKGROUND: Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. RESULTS: For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world...
May 2, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29708767/a-fast-approximate-algorithm-for-mapping-long-reads-to-large-reference-databases
#16
Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M Phillippy
Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision...
April 30, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29708484/expanding-an-expanded-genome-long-read-sequencing-of-trypanosoma-cruzi
#17
Luisa Berná, Matias Rodriguez, María Laura Chiribao, Adriana Parodi-Talice, Sebastián Pita, Gastón Rijo, Fernando Alvarez-Valin, Carlos Robello
Although the genome of Trypanosoma cruzi, the causative agent of Chagas disease, was first made available in 2005, with additional strains reported later, the intrinsic genome complexity of this parasite (the abundance of repetitive sequences and genes organized in tandem) has traditionally hindered high-quality genome assembly and annotation. This also limits diverse types of analyses that require high degrees of precision. Long reads generated by third-generation sequencing technologies are particularly suitable to address the challenges associated with T...
April 30, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29700142/complete-genome-sequence-of-multiple-antibiotic-resistant-streptococcus-parauberis-strain-spof3k-isolated-from-diseased-olive-flounder-paralichthys-olivaceus
#18
Yoonhang Lee, Thanh Luan Nguyen, Ahran Kim, Nameun Kim, Heyong Jin Roh, Hyun-Ja Han, Sung-Hee Jung, Mi-Young Cho, Ho Young Kang, Do-Hyung Kim
Here, we report the complete genome sequence of multiple-antibiotic-resistant Streptococcus parauberis strain SPOF3K, isolated from the kidney of a diseased olive flounder in South Korea in 2013. Sequencing using a PacBio platform yielded a circular chromosome of 2,128,740 bp and a plasmid of 23,538 bp, harboring 2,123 and 24 protein-coding genes, respectively.
April 26, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29696375/genomic-characterization-of-nitrospirillum-amazonense-strain-cbamc-a-nitrogen-fixing-bacterium-isolated-from-surface-sterilized-sugarcane-stems
#19
Stefan Schwab, Leonardo Araujo Terra, José Ivo Baldani
Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp...
April 25, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29688220/the-effects-of-sequencing-platforms-on-phylogenetic-resolution-in-16-s-rrna-gene-profiling-of-human-feces
#20
Tae Woong Whon, Won-Hyong Chung, Mi Young Lim, Eun-Ji Song, Pil Soo Kim, Dong-Wook Hyun, Na-Ri Shin, Jin-Woo Bae, Young-Do Nam
High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1-4), Illumina MiSeq (V1-3, V3-4 and V4), and PacBio (V1-9) systems. Comparative analyses revealed that the PacBio data showed the weakest relationship with the reference whole-metagenome shotgun datasets...
April 24, 2018: Scientific Data
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