‘A Quiet Revolution’: SMRT Sequencing Powers Increasing Genome Assembly Quality
A news article in Science magazine nicely captures the improvements in the quality of genome assemblies made possible by long-read sequencing and other methods. “New technologies boost genome quality” was written by Elizabeth Pennisi and includes interviews with a number of leading scientists.
One of those is Erich Jarvis, the neuroscientist at Rockefeller University who is best known in the genomics community for his work on vocal learning with songbirds and has been instrumental in both the G10K and B10K programs. As he told Pennisi, “The genome quality makes a huge difference in the type of science we can do.” For sequencing through repetitive or other challenging regions, he added, “the long read is always more accurate.”
“He and many other genomics experts are launching a quiet revolution aimed at building better genomes, one made possible by newer sequencing technologies, novel methods for locating sequences on chromosomes, and improved software for piecing DNA together,” Pennisi reports. “In the past 6 months, these approaches have led to a flood of high-quality animal and plant genomes in preprints and published papers.”
The USDA’s Tim Smith is also included, with a look at the impressive goat genome assembly he and his team recently produced. For that effort, he used SMRT Sequencing and complementary approaches, such as Hi-C and optical mapping, for optimal quality and contiguity. The finished assembly, Pennisi notes, “consists of chromosome-length pieces of DNA and only has 492 gaps, a 500-fold improvement over the first goat genome, done in late 2012.”
The article features a chart showing improvements in assembly metrics for three recently published genomes: hummingbird, goat, and maize. We have followed each of those assemblies closely, but there’s something about seeing all the data in one quick chart to really underscore how significant these advances have been — and in such a short period of time. If you have a moment, it’s definitely worth a look.