On DNA Day Honoring Discoveries – Y chromosome, Reference Grade De Novo Assemblies & Methylation
Monday, April 25, 2016
Happy DNA Day, everyone! This scientific celebration has us reflecting on the many advancements the community has made in the past year. For a molecule that is sequenced thousands of times a day all over the world, there is still much to learn. Today we’d like to honor some of the remarkable science enabled by SMRT Sequencing since last year’s DNA Day.
Scientists have continued to make progress exploring regions of the genome that have long been considered intractable. Two of our favorite stories this year came from the always-challenging Y chromosome. Researchers studying the mosquitoes that carry malaria — Anopheles gambiae — delivered the first detailed analysis of their Y chromosome, which is essentially a giant string of repeat sequences. The information may prove essential for efforts to shift the sex ratio of mosquito populations toward males, which do not transmit disease. In a separate study, scientists analyzed the Y chromosome in Drosophila and found evidence of an ancient gene duplication from an autosome; the gene had since acquired a new function on the Y chromosome. The gene had never been discovered before because of its location in a highly repetitive, complex genomic region that was inaccessible to other sequencers.
We’ve also seen a number of great examples of reference-grade de novo genome assemblies in the past year. A large team of scientists produced what they called “the most contiguous clone-free human genome assembly to date” using SMRT Sequencing along with single-molecule genome maps from BioNano Genomics. A similar strategy was used to generate “a gapless telomere-to-telomere genome assembly” of the filamentous fungus Verticillium dahliae, according to the publication in mBio. Just recently researchers published a new assembly for the gorilla genome, representing better than 150-fold improvement over the previous assembly. We loved the story of Oropetium thomaeum, a resurrection grass that was sequenced for one of our SMRT Grant winners and resulted in a virtually complete assembly.
DNA methylation has been another area of interesting developments as scientists delve into this poorly understood genetic mechanism. A recent Joint Genome Institute project involved a sweeping analysis of 230 prokaryotes that revealed more methylation, and more complex patterns, than ever suspected. A separate study detected methylation for the first time in C. elegans, proving that even well-characterized organisms still have secrets to reveal. Scientists also made progress in understanding the role of epigenetics in virulence and antibiotic resistance; this study found an epigenetic switch in non-typeable Haemophilus influenza that alters the organism’s pathogenicity and drug resistance.
The past year has also been an exciting time for the PacBio team. In October, we launched our new Sequel System, a sequencer one-third the size and half the cost of the PacBio RS II with nearly seven-fold higher throughput. And right now we’re gathering votes for our first-ever community poll to award a new SMRT Grant. If you haven’t voted yet, now’s the time!