Advances In De Novo Sequencing Of Complex Eukaryotic Genomes

A major goal of the U.S. Department of Energy Joint Genome Institute (JGI) is to facilitate DOE-relevant biological science by creating and curating genomic reference sequences and resources.  These projects fall into broad scientific categories including: de novo genome sequencing and improvement, diversity and population analysis, transcript profiling with RNA-seq, and mapping and recombination analysis of populations. As DOE science spans many fields of biological science we have experience producing genomic reference sequences across a wide variety and type of organisms including fungi, algae, protists vertebrates and plants.  These organisms include outbred diploids and difficult to sequence plant genomes. As we move away from established procedures for whole-genome shotgun with Sanger based sequencing and toward short read, Illumina-based genomic sequences, we are striving to continue to produce high quality, high completeness, and informative reference genomes.

We will share the latest developments for eukaryotic genome sequencing, assembly, and analysis developed at the JGI, including: characterization of genomic content using Illumina data, experimental advances for mate pair construction, assembling genomes with our modified Arachne pipeline, development of Meraculous (a short read assembler), and advanced genetic mapping techniques based on genotyping by sequencing that can be applied to complex tetraploid plant genomes.