The Targeted Locus Amplification (TLA) Technology from Cergentis enables the targeted, hypothesis-neutral, amplification of any genomic locus of interest over 50 kb using just one primer pair complementary to a short locus-specific sequence. TLA is a strategy to selectively amplify complete loci on the basis of crosslinking physically proximal sequences. Unlike other targeted sequencing methods, TLA works without prior detailed locus information, as one primer pair is sufficient to amplify tens to hundreds of kilobases of DNA surrounding that locus. In a separate application of TLA, the unamplified template can be used for genome-wide phasing and assembly. TLA enables targeted…
At the University of California, Davis, Dario Cantu is applying long-read PacBio sequencing to the heterozygous genome of the Cabernet Sauvignon grape. Now, his team has access to whole genome data that could help guard against the effects of climate change and disease.
The utility of new highly accurate long reads, or HiFi reads, was first demonstrated for calling all variant types in human genomes. It has since been shown that HiFi reads can be used to generate contiguous, complete, and accurate human genomes, even in repeat structures such as centromeres and telomeres. In this virtual workshop scientists from PacBio as well as Tina Graves-Lindsay from the McDonnell Genome Institute at Washington University share the many improvements we’ve made to HiFi sequencing in the past year, tools that take advantage of HiFi data for variant detection and assembly, and examples in numerous genomics…
Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. Testing included the recharacterization of 137 genomic DNAs that were genotyped in previous Genetic Testing Reference Material Coordination…
Chlorella vulgaris is a fast-growing fresh-water microalga cultivated at the industrial scale for applications ranging from food to biofuel production. To advance our understanding of its biology and to establish genetics tools for biotechnological manipulation, we sequenced the nuclear and organelle genomes of Chlorella vulgaris 211/11P by combining next generation sequencing and optical mapping of isolated DNA molecules. This hybrid approach allowed to assemble the nuclear genome in 14 pseudo-molecules with an N50 of 2.8 Mb and 98.9% of scaffolded genome. The integration of RNA-seq data obtained at two different irradiances of growth (high light-HL versus low light -LL) enabled…
The domestic pig (Sus scrofa) is important both as a food source and as a biomedical model with high anatomical and immunological similarity to humans. The draft reference genome (Sscrofa10.2) represented a purebred female pig from a commercial pork production breed (Duroc), and was established using older clone-based sequencing methods. The Sscrofa10.2 assembly was incomplete and unresolved redundancies, short range order and orientation errors and associated misassembled genes limited its utility. We present two highly contiguous chromosome-level genome assemblies created with more recent long read technologies and a whole genome shotgun strategy, one for the same Duroc female (Sscrofa11.1) and…
Tigecycline is a last-resort antibiotic that is used to treat severe infections caused by extensively drug-resistant bacteria. tet(X) has been shown to encode a flavin-dependent monooxygenase that modifies tigecycline1,2. Here, we report two unique mobile tigecycline-resistance genes, tet(X3) and tet(X4), in numerous Enterobacteriaceae and Acinetobacter that were isolated from animals, meat for consumption and humans. Tet(X3) and Tet(X4) inactivate all tetracyclines, including tigecycline and the newly FDA-approved eravacycline and omadacycline. Both tet(X3) and tet(X4) increase (by 64-128-fold) the tigecycline minimal inhibitory concentration values for Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii. In addition, both Tet(X3) (A. baumannii) and Tet(X4) (E.…
Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) of the digestive tract in humans. There is evidence that Parabacteroides distasonis could contribute to IBD. Here, we present the complete genome sequence of a strain designated CavFT-hAR46, which was isolated from a gut intramural cavernous fistulous tract (CavFT) microlesion in a CD patient.Copyright © 2019 Yang et al.
Bacillus anthracis, the etiologic agent of anthrax, is susceptible to beta-lactam antibiotics, but few cases of naturally occurring penicillin-resistant strains have been reported. We report the genome sequence of penicillin-resistant strain Bacillus anthracis PCr, isolated from imported bone powder in 1978 in Japan.Copyright © 2019 Okutani et al.
Dehalococcoides mccartyi strain FL2 couples growth to hydrogen oxidation and reductive dechlorination of trichloroethene and cis- and trans-1,2-dichloroethenes. Strain FL2 has a 1.42-Mb genome with a G+C content of 47.0% and carries 1,465 protein-coding sequences, including 24 reductive dehalogenase genes.Copyright © 2019 Yan et al.
Here, we report the complete genome sequence and full methylome analysis of a newly isolated, aerobic, thermophilic, Gram-positive actinomycete, a strain of Thermoactinomyces vulgaris designated strain 2H.Copyright © 2019 Mankai et al.
Azospirillum sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate N2O from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan. Here, we present the genome sequences of these two strains.Copyright © 2019 Gao et al.
Seven Salmonella enterica subsp. enterica isolates were identified as carrying the mcr-1 gene, by using a real-time fluorescence quantitative PCR method, from a total of 2,558 isolates which were cultured from various food origins in China between 2011 and 2016. Few complete genomes of Salmonella strains harboring the mcr-1 gene have been reported to date, so we report here the complete genome and plasmid sequences of all of these isolates to provide useful references for understanding the prevalence of foodborne Salmonella enterica subsp. enterica isolates carrying mcr-1.Copyright © 2019 Hu et al.
In this announcement, we present the complete annotated genome sequence of an Escherichia coli MC4100 mutant strain, BE104. This strain has several methionine sulfoxide reductase gene deletions, making it ideal for studying enzymes that alter the redox state of methionine.Copyright © 2019 Anton et al.
The bacteriophage exclusion (BREX) system is a novel prokaryotic defense system against bacteriophages. To our knowledge, no study has systematically characterized the function of the BREX system in lactic acid bacteria. Lactobacillus casei Zhang is a probiotic bacterium originating from koumiss. By using single-molecule real-time sequencing, we previously identified N6-methyladenine (m6A) signatures in the genome of L. casei Zhang and a putative methyltransferase (MTase), namely, pglX This work further analyzed the genomic locus near the pglX gene and identified it as a component of the BREX system. To decipher the biological role of pglX, an L. casei Zhang pglX mutant…