Allen Van Deynze from UC Davis presents the genome sequencing and assembly project for spinach, an organism of 980 Mb. Results indicate a high-accuracy assembly with significantly higher N50 contig length than a previous short-read assembly. The PacBio assembly has allowed for filling gaps in the prior assembly.
From USDA’s Agricultural Research Service, molecular biologist Sean Gordon discusses the need for long-read sequencing to map an organism’s transcriptome. His team analyzed the wood-decaying fungus Plicaturopsis crispa first with short reads and found that they were missing exons and other important information. They switched to SMRT Sequencing so they could observe, rather than infer, full-length transcripts.
Tim Smith of the USDA presents his work to establish a high-quality reference genome of the San Clemente goat. After generating 70-fold PacBio sequence data, the PacBio assembly proved to be far more complete than the existing draft reference genome, with contigs extending 100 times longer on average.
Shane Brubaker from renewable oil manufacturer Solazyme reports using the PacBio system to sequence the genome of a GC-rich strain of algae that couldn’t be fully assembled with short-read sequence data. He notes that CCS reads exceed Sanger quality at significantly lower cost.
Robert VanBuren of the Danforth Plant Science Center and winner of the 2014 SMRT Grant Program presents a de novo assembly of the Oro grass genome (Oropetium thomaeum). The reference genome will aid scientist studying drought tolerance in common crop species, especially cereals, though comparative genomics to understand potential key genetic underpinnings for this “resurrection” trait. Initial comparative results to Brachypodium and maize are presented, as well as secondary analysis to identify key metabolic traits.
Michiel van Eijk of KeyGene shared a de novo PacBio assembly of tetraploid cotton. The genome assembly was further enhanced and annotated using Iso-Seq data collected from cotton root, leaf, and stem tissues. The data, full-length cDNA transcripts, captured alternative splicing diversity across these tissue types, allowing for isoform differentiation.
Susan Strickler of the Boyce Thompson Institute presented strategies for assembling the genome of Arabica coffee, an allotetraploid with a genome size of approximately 1.3 Gb. A de novo PacBio assembly was constructed and presented. The new high-quality reference will be used to guide assemblies of the diploid ancestors of Arabica coffee and re-sequencing data for a set of C. arabica accessions to more fully characterize the genetic diversity of this crop species that is highly susceptible to climate change.
Alan Archibald compares two new de novo PacBio pig genome assemblies to a previously released draft genome, finding significant improvement that could be important for breeding programs. In one example, he shows chromosome 1, which was split into more than 9,000 contigs in the draft genome, is now represented in just 10 contigs.
PacBio’s Jenny Gu and Christina Tran from Experiment talk about the use of alternative funding sources to support SMRT Sequencing projects. The Genome Galaxy Initiative is a new program from PacBio that helps scientists launch their long-read sequencing projects on Experiment’s crowdfunding platform. Experiment has raised more than $5 million to fund hundreds of scientific projects since it kicked off in 2012.
Oliver Ryder speaks about efforts to rescue the Hawaiian crow, a bird that has been extinct in the wild since 2002, and reintroduce it to its native habitat. Critical to this work is a new SMRT Sequencing reference genome assembly, which Ryder says is already one of the best avian assemblies out there. The resource may help deal with challenges like inbreeding and disease susceptibility.
Ho Yung Shwen presented this talk about a new genome assembly of Chenopodium quinoa, the native South American plant known for its ability to grow in harsh environments. He used SMRT Sequencing and other tools to characterize the organism’s allotetraploid genome and to infer new information about the plant’s unknown diploid ancestors
Doreen Ware introduces her team’s new assembly of maize, built with PacBio long-read sequencing and genome maps from BioNano Genomics. With a contig N50 of nearly 10 Mb and more complete information than any previous assembly, Ware says, “This is just an amazing time to be a plant scientist.” Her presentation includes a number of highlights from the new assembly, which may help crop improvement efforts for maize.
Chongyuan Luo from the Salk Institute for Biological Studies describes sequencing three strains of Arabidopsis thaliana using PacBio technology. The goal: uncover structural variants that have been missed by short-read and other sequencers. Luo notes that PacBio sequencing provides highly accurate SNP detection and also extends the mappability of reads beyond what is possible with short-read data, producing better and more accurate assemblies.
Kim Worley from Baylor’s Human Genome Sequencing Center describes the improvement of the sooty mangabey primate genome. Sooty mangabey is a model organism for HIV research, since this particular primate can be infected with the immunodeficiency virus and never develop any symptoms. Worley and her team used PacBio long reads in conjunction with their own assembly tool, PBJelly, closing 64% and improving another 19% of the gaps.
Simon Chan, UC Davis on how PacBio long read sequencing revealed higher order repeats in centromeres of switchgrass which would have been hidden if you are restricted by the much shorter Sanger reads.