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Tuesday, June 13, 2017

New Maize Reference Genome Will Support Crop Improvement Programs

[caption id="attachment_17369" align="alignright" width="300"] Photo by Carl Davies, CSIRO[/caption] A large group of scientists published a new reference genome assembly for maize. It was generated with SMRT Sequencing and other technologies, and represents a major leap forward in accurately portraying and annotating the genome of this important crop. “Improved maize reference genome with single-molecule technologies” comes from lead author Yinping Jiao, senior author Doreen Ware, and collaborators at Cold Spring Harbor Laboratory, the USDA ARS, and many other institutions. They embarked on the project because the existing reference for maize, based on Sanger technology and released in 2009, “is composed…

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Thursday, March 23, 2017

Metal-Devouring Plant Genomes Get SMRT Treatment with Sequel System: 2016 SMRT Grant Program Winner Results

Blog readers may recall that last year’s SMRT Grant winner was Renying Zhuo from the Chinese Academy of Forestry. We’re pleased to report that the project is now complete! Zhuo proposed sequencing the genomes of two strains of the Sedum alfredii plant from the same ecosystem — one that accumulates cadmium ions from polluted soil and one that doesn’t. The goal was to use high-quality assemblies for comparative genomic analysis to determine the genetic mechanisms responsible for this remediation effect. Plant DNA was sequenced on the Sequel System by RTL Genomics, and genome assembly was performed by Computomics. (We’re also grateful…

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Tuesday, March 7, 2017

High-Quality, Chromosome-Scale Quinoa Genome Valuable for Breeding Better Crops

A new genome assembly has remarkable promise to boost the global food supply. Scientists from King Abdullah University of Science and Technology and other institutions sequenced quinoa, a nutritious grain that can grow in marginal lands and other suboptimal environments. Their assembly offers new clues that could help improve breeding efforts to make the plant more accessible worldwide. “The genome of Chenopodium quinoa” was published recently in Nature by lead author David Jarvis, senior author Mark Tester, and a large group of collaborators. They focused on this plant, which is believed to have been domesticated more than 7,000 years ago in…

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Friday, August 26, 2016

Scientists Turn to SMRT Sequencing to Decode Chardonnay Genome

A case study produced by QRIScloud, an Australia-based cloud computing service, offers interesting insight into a recent project that is using SMRT Sequencing to generate a reference-quality de novo genome assembly for the grape used to make Chardonnay wine. The sequencing effort was conducted by collaborating scientists at the Australian Wine Research Institute (AWRI) and the BC Genome Sciences Centre in Canada. This new assembly, which is still undergoing polishing and in-depth analysis, adds to very sparse genome resources for wine grapes. Until recently, the only genome assemblies available were draft-quality ones for the Pinot Noir varietal. With PacBio long-read…

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Wednesday, November 11, 2015

Scientists Publish High-Quality, Near-Complete Genome of Resurrection Grass Oropetium

We’re excited about a new Nature paper from the winners of our 2014 “Most Interesting Genome in the World” SMRT Grant program. “Single-molecule sequencing of the desiccation tolerant grass Oropetium thomaeum” comes from lead authors Robert VanBuren and Doug Bryant along with senior author Todd Mockler at the Donald Danforth Plant Science Center, as well as a number of collaborators at other institutions. In it, the authors report a virtually complete genome of Oropetium thomaeum, a grass with an estimated genome size of 245 Mb and the handy ability to regrow even after extreme drought once water becomes available. The…

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