A recent research partnership with KeyGene, a Dutch plant genomics and crop improvement company, has resulted in an integrated whole-genome assembly and transcriptome of Gossypium hirsutum, or tetraploid cotton. This is the first known complete assembly for a polyploid crop with a genome larger than 2 Gb. KeyGene has a long established reputation for generating high-quality data even for very complex genomes. For this project, the cotton genome was sequenced with 38x coverage using Single-Molecule, Real-Time (SMRT®) Sequencing. Assembly of PacBio® long reads reduced the number of contigs from more than 1 million in an existing short-read assembly to fewer…
A recent publication from senior author Laura Landweber at Princeton University offers a remarkable and unexpected look at sweeping genomic rearrangements in a unicellular organism. “The Architecture of a Scrambled Genome Reveals Massive Levels of Genomic Rearrangement during Development,” published in Cell, comes from lead authors Xiao Chen and John Bracht as well as other collaborators from Princeton, the Icahn School of Medicine at Mount Sinai, Benaroya Research Institute, and other institutions. The project focused on Oxytricha trifallax, a single-celled eukaryote that lives in ponds. Despite its unicellular simplicity, the organism has an extensive ability to scramble and rearrange its…
The Genomics Resource Center (GRC) at the Institute for Genome Sciences (IGS) has a scientific pedigree and a sample-to-interpretation service commitment that place it in a league of its own. The team operates under a simple mantra: ‘If it can be sequenced, we can do it.’ Both GRC and IGS were founded in 2007 when a high-powered team of investigators formerly at The Institute for Genomic Research (TIGR), led by Claire Fraser, joined the University of Maryland School of Medicine. “The group of faculty and senior staff that came here to start the institute was heavily focused on infectious disease…
As PacBio customers are upgrading to the new PacBio® RS II System, some of our core lab users have already begun blogging about the improved results. At the University of Maryland’s Institute for Genome Sciences (IGS), for example, one blogger posted data comparing read length, read count, and throughput for the PacBio RS and PacBio RS II. The post reports a comparison of an 8 Kb Mycobacterium project run on the PacBio RS and again on the PacBio RS II, finding that with the upgrade, “we see an almost 3x increase in total yield [per SMRT Cell], while read lengths…
It has been really gratifying to see that interest in Single Molecule, Real-Time (SMRT®) Sequencing has been steadily increasing — there seems to be lots of pent-up demand to run samples on the PacBio® sequencer and check out the long-read sequence data and methylation information! To help improve access to sequencers that are already in the field, some of our customers at service vendors and core facilities have volunteered to be part of our Sequencing Provider Program. These customers have PacBio RS instruments and can be contacted by anyone interested in generating SMRT Sequencing data for their own samples. Our…