November 21, 2017; 1:30 pm; Room 260 Loftsgard Hall
"Longer and Cheaper" that is the current goal of researchers as they assemble new genome sequences. As always, the goal is to provide a high quality reference genome to a reserach community that can be used to annotate the genes, small RNAs, and repeats in the genome. Until recently, that required that sequence data be collected from muliple libraries of varying insert sizes, and the development of a in-depth genetic map with many SNP markers. From the sequencing and assembly perspective, the strategy was to collect data for a set of libraries that enable the development of scaffolds that were as long as possible. Recently, new library construction and mapping tools are available, and the use of these tools are resulting in higher quality genome sequences and much lower cost. The specific library development methods are sold by 10X Genomics (Chromium Genome Solution) and Dovetail Genomics (Hi-C and Chicago libraries). The preferred optical mapping method from Bionano Genomics. Those approaches are featured in the journal articles for this CTIG session.
You will again work as a team. Here are the team members and the papers you will focus on during the class discussion. But everyone will be responsible for reading and understanding all of the papers. One paper is general in focus and provides good background information.
Group 1: Amanda and Nathan
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Group 2: Azita, Sapna, Sudeshi
A hybrid approach for de novo human genome sequencing assembly and phasing
A critical comparison of technologies for a plant genome sequencing project
Improved maize reference genome with single-molecule technologies
All
Coming of age: ten years of next generation sequencing technologies
Presentations
Each group will make a 45 minute presentation that focuses on their three papers. Amanda and Nathan will discuss in detail the Bionano Genomics techniques (Hi-C and Chicago libraries). Azita, Sapna, and Sudeshi will describe in detail the 10X Genomics (Chromium) system. These discussions should provide detail of the techniques as well as the technical steps involved. Each group should also discuss how Bionano optical mapping works and how it was applied in the papers you are assigned. Each group should also discuss how a genome sequence has been improved by these techniques. Finally, the presentation should describe new information obtained from the improved Medicago and cassava (Group 1), and maize (Group 2) genome sequences.