What is a Pangenome? A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. Unless you have an identical twin, no other person has a genome that is identical to yours. The same is true for other animal, plant, and microbial species that reproduce sexually: the genomes of individuals are unique. Less well known, but equally true, is that individual members of a species do not always share even the exact same genes. Nevertheless, scientists mostly use a single reference genome to represent an entire species: one human genome, one…
People of Japanese descent just moved a little closer toward the promise of precision medicine thanks to a population-specific reference genome based on the de novo genome assembly of three Japanese individuals. A new preprint describing the work shows that SMRT Sequencing was instrumental in the achievement. Scientists from Tohoku University, led by Jun Takayama (@jntkym), Kengo Kinoshita (@kk824), Masayuki Yamamoto, and Gen Tamiya, aimed to create an improved reference genome resource that would better represent the genetic background of a Japanese population than the current human reference genome. “Some ethnic ancestries are under-represented in the international human reference genome (e.g.,…
The modern world might benefit from a return to our ancient roots by expanding the cultivation of one of the first domesticated crops, broomcorn millet. Foodies will appreciate that the crop, a staple in many semi-arid regions of Asia and Europe, is gluten-free and extremely nutritious, with higher levels of protein, several minerals, and antioxidants than most other cereals. Farmers will appreciate that the drought-resistant plant has the highest water-use efficiency among all cereal crops, (i.e. the highest amount of grains produced with the same amount of water), a short life cycle (60–90 days), and a high harvest index. And…
Its reliable return to the same spot year after year has made the barn swallow a beloved symbol of Spring and safe passage, for mariners and landlubbers alike. But our changing climate is altering the birds’ migratory behavior, and Italian ecologists are turning to genetics to figure out how. As reported previously in this blog, scientists at the University of Milan joined forces with researchers from the University of Pavia and California State Polytechnic University to create the first high-quality reference genome for the European barn swallow (Hirundo rustica rustica), using SMRT Sequencing and newly available Bionano Genomics optical mapping…
A recent cover story in New Zealand Geographic vividly details the efforts to sequence not just the kākāpō genome, but the genomes of every single living kākāpō. If you missed our earlier blog about this bird, the kākāpō is a member of the parrot family known for its unique attributes: it’s heavy, flightless, and mostly active at night. As author Rebekah White reports in “Decoding Kākāpō,” the remaining members of this species — about 125 of them — live on islands near New Zealand. White recounts how scientist Jason Howard, a member of Erich Jarvis’s lab at Duke, first became…
When Doreen Ware and her team’s latest genome project is complete, the plant science community will have a critical new tool that once seemed virtually impossible: a robust reference assembly for the maize genome. This resource will support breeding of hardier, higher-yielding lines of maize, the number one crop plant in both the U.S. and China. Ware, a computational biologist with the USDA at Cold Spring Harbor Laboratory, says climate change and protecting the environment are major challenges facing agriculture. “We know that we must increase yield in order to meet the expected 9 billion people in less than 25…