Many scientists are using PacBio Single Molecule, Real-Time (SMRT) Sequencing to explore the genomes and transcriptomes of a wide variety of marine species and ecosystems. These studies are already adding to our understanding of how marine species adapt and evolve, contributing to conservation efforts, and informing how we can optimize food production through efficient aquaculture.
Penelope Bonnen, an assistant professor at Baylor College of Medicine, discusses her use of PacBio SMRT sequencing to look at whole mitochondrial genomes as she reviews her AGBT 2012 poster. Dr. Bonnen is studying a Micronesian population with unusually high rates of obesity, diabetes, and cardiovascular disease to figure out how mitochondrial genetics contributes to adult-onset metabolic syndrome. She describes two approaches in a pilot project for full-length mitochondrial sequencing: one using a 500-base pair insert library and another directly sequencing the single 17 kb amplicon.
Robert VanBuren of the Danforth Plant Science Center and winner of the 2014 SMRT Grant Program presents a de novo assembly of the Oro grass genome (Oropetium thomaeum). The reference genome will aid scientist studying drought tolerance in common crop species, especially cereals, though comparative genomics to understand potential key genetic underpinnings for this “resurrection” trait. Initial comparative results to Brachypodium and maize are presented, as well as secondary analysis to identify key metabolic traits.
Winston Timp from Johns Hopkins University studies the metabolism of hummingbirds, which sustain the highest metabolic rates among all vertebrates. Notably, hummingbirds can switch rapidly between a fuel of lipids to newly ingested sugars. This remarkable metabolism is supported by enzymes which operate at the extreme limit of catalytic efficiency. Understanding the molecular basis of enzymatic action will provide a foundation enabling rational engineering of metabolic circuits in other systems. To do this, Dr. Timp and his team generated a de novo transcriptome of the hummingbird liver using the Iso-Seq method. Characterization of the resulting protein coding sequences provides clues…
At AGBT 2017, Margaret Roy from Calico Life Sciences discussed a de novo genome sequencing effort for the naked mole rat. This animal has a remarkably long life span and resistance to cancer, both of which make it interesting for studies of life extension. The team is using SMRT Sequencing for a more complete, contiguous assembly than the two existing short-read-based assemblies. Included: data from the Sequel System.
In this AGBT 2017 poster, the University of Helsinki’s Petri Auevinen reports on efforts to understand bacteria that grow on, and subsequently spoil, food. This analysis monitored DNA modifications and transcriptomic changes in three species of lactic acid bacteria. Scientists discovered that the organisms’ metabolic profiles change substantially when grown together compared to those cultured individually, and are now studying how Cas protein activity changes under these conditions too.
In this PacBio User Group Meeting presentation, PacBio scientist Meredith Ashby shared several examples of analysis — from full-length 16S sequencing to shotgun sequencing — showing how SMRT Sequencing enables accurate representation for metagenomics and microbiome characterization, in some cases even without fully assembling genomes. New updates will provide users with a dedicated microbial assembly pipeline, optimized for all classes of bacteria, as well as increased multiplexing on the Sequel II System, now with 48 validated barcoded adapters. That throughput could reduce the cost of microbial analysis substantially.
In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.
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…
In this webinar, Kristin Mars, Sequencing Specialist, PacBio, presents an introduction to PacBio’s technology and its applications followed by a panel discussion among sequencing experts. The panel discussion addresses such things as what long reads are and how are they useful, what differentiates PacBio long-read sequencing from other technologies, and the applications PacBio offers and how they can benefit scientific research.
China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism,…
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 Ganoderma genus represents clear biotechnological potential, due to the large quantity of molecules with biological activity that could be explored. However, available information regarding the biotechnological importance of species within Ganoderma, other than G. lucidum, is quite limited. Genomic studies of little-known species can contribute to the knowledge thereof, as well as the search for metabolic pathways and the identification of genes which code for proteins that may be of biotechnological relevance. Therefore, the objective of the present study was to obtain the G. australe genome, through the use of new sequencing technologies. Genomic DNA from G. australe was…
A major barrier to both metabolic engineering and fundamental biological studies is the lack of genetic tools in most microorganisms. One example is Clostridium thermocellum ATCC 27405T, where genetic tools are not available to help validate decades of hypotheses. A significant barrier to DNA transformation is restriction-modification systems, which defend against foreign DNA methylated differently than the host. To determine the active restriction-modification systems in this strain, we performed complete methylome analysis via single-molecule, real-time sequencing to detect 6-methyladenine and 4-methylcytosine and the rarely used whole-genome bisulfite sequencing to detect 5-methylcytosine. Multiple active systems were identified, and corresponding DNA methyltransferases…
Paracoccus sp. Arc7-R13, a silver nanoparticles (AgNPs) synthesizing bacterium, was isolated from Arctic Ocean sediment. Here we describe the complete genome of Paracoccus sp. Arc7-R13. The complete genome contains 4,040,012?bp with 66.66?mol%?G?+?C content, including one circular chromosome of 3,231,929?bp (67.45?mol%?G?+?C content), and eight plasmids with length ranging from 24,536?bp to 199,685?bp. The genome contains 3835 protein-coding genes (CDSs), 49 tRNA genes, as well as 3 rRNA operons as 16S-23S-5S rRNA. Based on the gene annotation and Swiss-Prot analysis, a total of 15 genes belonging to 11 kinds, including silver exporting P-type ATPase (SilP), alkaline phosphatase, nitroreductase, thioredoxin reductase, NADPH dehydrogenase…