The last few years have seen a revolution in DNA sequencing instrumentation and technology. In that short time period sequencing instrument capabilities have increased more than 1000 fold and are likely to continue to increase about 5-fold each year for the next several years. As such it is now affordable and efficient to sequence to high coverage large plant genomes that had previously been prohibitively too expensive and complex to attempt. However, analysis methods have not improved nearly as much during the same time period and a variety of technical limitations of these new DNA sequencing instruments make it even more difficult to carry out whole genome sequencing of novel genomes (de novo sequencing). These limitations also make it more difficult to use the new instruments to carry out older clone based strategies for de novo sequencing, such as BAC-by-BAC approaches. The purpose of this meeting to be held at Cold Spring Harbor Laboratory May 18-20, 2011 are to assess the current state of next generation sequencing in terms of de novo, whole genome plant sequencing, what can be expected to develop in the near future, and then determine which advances are needed to allow these exciting technologies to be used to carry out de novo sequencing of entire complex plant genomes. The meeting will bring together stakeholders with broad range of expertise in high-throughput sequencing and genomics, plant biology, bioinformatics and databases drawn from the academic, private and international sectors. Meeting outcomes will be captured in the form of a report to be developed by participants that will be submitted for publication to Genome Research.
The proposal was to host a meeting at Cold Spring Harbor Laboratory during May 18-20, 2011 to assess and discuss the state of the art of de novo whole genome sequencing and assembly for plant genomes. This meeting was needed because de novo genome assembly is a complex and rapidly changing topic, and requires deep biological, computational, and biotechnology expertise that few individuals possess, especially for plant genomes. We hosted the meeting as planned to bring together these diverse experts, and included two dozen scientists from academic and industrial labs around the US and around the world. All participants of the meeting were educated on the state of the art in genome assembly, sequencing technology, and other biotechnologies. The meeting focused primarily on PIs and other experts so that we could draw the most informed conclusions from the meeting. A major conclusion of the panel was that it was now affordable and efficient to sequence and assemble great numbers of interesting plant genomes into highly useful draft genome assemblies by applying the state of the art biotechnology and computer algorithms. The participants also stressed the need for improved training for PIs, postdocs, and students in genome assembly technology, and other computational issues, as these topics are becoming extremely important to the field and critical to the success of the downstream analyses. The meeting report was published in the journal Genome Biology in April and documents the major findings of the meeting with respect to sequencing technologies, assembly technologies, and analytics. The meeting report has immediately become one of the most highly accessed publications in the journal with more than 3500 views since publication (currently ranked #2 for the past 30 days for the entire journal). The meeting report is likely to become the de facto guide for sequencing plant and other genomes for the next several years. We hope that it will guide researchers to more successful genome analysis projects, and guide the funding agencies to make the most of their available funds. Co-PI Schatz also presented the conclusions of the meeting to an audience of ~300 people, including PIs, postdocs, and students, at the annual Plant and Animal Genome meeting in San Diego in January of 2012. The long-term contribution of our meeting, the meeting report, and the presentation will be to improve plant genome and other genome sciences. This has substantial potential to advance agriculture, medicine, and energy, to name a few.
