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Tuesday, December 1, 2020

Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing

Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…

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Tuesday, December 1, 2020

ASHG PacBio Workshop: Identification and characterization of informative genetic structural variants for neurodegenerative diseases

Michael Lutz, from the Duke University Medical Center, discussed a recently published software tool that can now be used in a pipeline with SMRT Sequencing data to find structural variant biomarkers for neurodegenerative diseases with a focus on Alzheimer’s disease, ALS, and Lewy body dementia. His team is particularly interested in short sequence repeats and short tandem repeats, which have already been implicated in neurodegenerative disease.

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Tuesday, December 1, 2020

Podcast: Going beyond the $1,000 genome with Mark Gerstein

Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project. “I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of this Mendelspod interview. “The great excitement of next generation sequencing—which is deserved—has…

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Tuesday, December 1, 2020

AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples

At AGBT 2017, Mike Schatz from Johns Hopkins University and Cold Spring Harbor Laboratory presented data from sequencing, assembling, and analyzing personalized, phased diploid genomes with either Illumina, 10x Genomics, and PacBio SMRT Sequencing. Compared to the short-read-based methods, PacBio data assembled in large, complete contigs and contained the broadest range of structural variants with the best resolution. Plus: unexpected translocation findings with SMRT Sequencing, validated in follow-up studies.

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Tuesday, December 1, 2020

AGBT PacBio Workshop: High-throughput HLA class I whole gene and HLA class II long range typing on PacBio RSII and Sequel Platforms

In a talk at AGBT 2017, Histogenetics CEO Nezih Cereb reported on how SMRT Sequencing is allowing his team to produce full-length, phased sequences for HLA alleles, which are important for matching organ transplants to recipients. The company is typing thousands of samples per day on their PacBio RS II systems and their new Sequel System. Cereb noted that SMRT Sequencing is unique in its ability to reliably phase mutations in the HLA alleles without imputation. Cereb concluded with his plans to use this approach for other complex regions, such as KIR, and announced their continued increasing HLA typing capacity…

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Tuesday, April 21, 2020

Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions.

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…

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Tuesday, April 21, 2020

Evolution of a 72-kb cointegrant, conjugative multiresistance plasmid from early community-associated methicillin-resistant Staphylococcus aureus isolates.

Horizontal transfer of plasmids encoding antimicrobial-resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s the first CA-MRSA isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline and penicillin-resistance genes on plasmid pWBG753 (~30 kb). WA-5 and pWBG753 appeared only briefly in WA, however, fusidic-acid-resistance plasmids related to pWBG753 were also present in the first European CA-MRSA at the time. Here we characterized a 72-kb conjugative plasmid pWBG731 present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a…

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Tuesday, April 21, 2020

Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae.

Neisseria gonorrhoeae, the sole causative agent of gonorrhea, constitutively undergoes diversification of the Type IV pilus. Gene conversion occurs between one of the several donor silent copies located in distinct loci and the recipient pilE gene, encoding the major pilin subunit of the pilus. A guanine quadruplex (G4) DNA structure and a cis-acting sRNA (G4-sRNA) are located upstream of the pilE gene and both are required for pilin antigenic variation (Av). We show that the reduced sRNA transcription lowers pilin Av frequencies. Extended transcriptional elongation is not required for Av, since limiting the transcript to 32 nt allows for normal…

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Tuesday, April 21, 2020

RNA sequencing: the teenage years.

Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for transcriptome-wide analysis of differential gene expression and differential splicing of mRNAs. However, as next-generation sequencing technologies have developed, so too has RNA-seq. Now, RNA-seq methods are available for studying many different aspects of RNA biology, including single-cell gene expression, translation (the translatome) and RNA structure (the structurome). Exciting new applications are being explored, such as spatial transcriptomics (spatialomics). Together with new long-read and direct RNA-seq technologies and better computational tools for data analysis, innovations in RNA-seq are contributing to a fuller understanding of RNA biology, from questions…

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Tuesday, April 21, 2020

Emergence of plasmid-mediated high-level tigecycline resistance genes in animals and humans.

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.…

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Tuesday, April 21, 2020

Complete genome sequence provides insights into the quorum sensing-related spoilage potential of Shewanella baltica 128 isolated from spoiled shrimp.

Shewanella baltica 128 is a specific spoilage organism (SSO) isolated from the refrigerated shrimp that results in shrimp spoilage. This study reported the complete genome sequencing of this strain, with the primary annotations associated with amino acid transport and metabolism (8.66%), indicating that S. baltica 128 has good potential for degrading proteins. In vitro experiments revealed Shewanella baltica 128 could adapt to the stress conditions by regulating its growth and biofilm formation. Genes that related to the spoilage-related metabolic pathways, including trimethylamine metabolism (torT), sulfur metabolism (cysM), putrescine metabolism (speC), biofilm formation (rpoS) and serine protease production (degS), were identified.…

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Tuesday, April 21, 2020

Insect genomes: progress and challenges.

In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a…

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Tuesday, April 21, 2020

The use of Online Tools for Antimicrobial Resistance Prediction by Whole Genome Sequencing in MRSA and VRE.

The antimicrobial resistance (AMR) crisis represents a serious threat to public health and has resulted in concentrated efforts to accelerate development of rapid molecular diagnostics for AMR. In combination with publicly-available web-based AMR databases, whole genome sequencing (WGS) offers the capacity for rapid detection of antibiotic resistance genes. Here we studied the concordance between WGS-based resistance prediction and phenotypic susceptibility testing results for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin resistant Enterococcus (VRE) clinical isolates using publicly-available tools and databases.Clinical isolates prospectively collected at the University of Pittsburgh Medical Center between December 2016 and December 2017 underwent WGS. Antibiotic resistance gene…

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Tuesday, April 21, 2020

Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses.

Pepper is an important vegetable with great economic value and unique biological features. In the past few years, significant development has been made towards understanding the huge complex pepper genome; however, pepper functional genomics has not been well studied. To better understand the pepper gene structure and pepper gene regulation, we conducted full-length mRNA sequencing by PacBio sequencing and obtained 57862 high-quality full-length mRNA sequences derived from 18362 previously annotated and 5769 newly detected genes. New gene models were built that combined the full-length mRNA sequences and corrected approximately 500 fragmented gene models from previous annotations. Based on the full-length…

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