Efficient de novo assembly of phased, telomere-to-centromere human genomes
Dr. Benedict Paten is an assistant professor in the department of Biomolecular Engineering at the University of California Santa Cruz (UCSC) and an associate director of the UCSC Genomics Institute. He directs the Computational Genomics Lab at UCSC, which is broadly focused on computational genomics, creating algorithms, software and services addressing biomolecular challenges. He has a PhD from the University of Cambridge and the European Molecular Biology Laboratory in computational biology.
Long-read sequencing of human tissues to study allelic effects on transcriptome structure
Dr. Dafni Glinos is a Postdoctoral Researcher in the Lappalainen lab in the New York Genome Center and Columbia University. She is interested in the contribution of coding and non-coding variants on the molecular mechanisms which define human traits, with a focus on diseases. She is leveraging allelic data from the human transcriptome to quantify variation within individuals. Dafni obtained her PhD at the Wellcome Sanger Institute and University of Cambridge, under the supervision of Gosia Trynka. Her research focused on the human gene regulatory landscape of T cells, studying the impact of non-coding variants on immune processes.
Oxford Nanopore Technologies Ltd
Dan Turner is Vice President, Applications at Oxford Nanopore Technologies. He provides leadership for multi-disciplinary teams in Oxford, New York and San Francisco. The Applications group aims to bring together sample prep technologies, genomics applications and bioinformatics, to expand the utility of Oxford Nanopore Technologies devices and illustrate the benefits of these technologies to the wider world. The team is also responsible for providing Field Applications Support. Before joining Oxford Nanopore Technologies, Dan was Head of Sequencing Technology Development at the Wellcome Trust Sanger Institute, and prior to this he held postdoctoral positions at the Sanger Institute and Cornell University Medical College in Manhattan.
Return to Vatnajokull Expedition
Alongside his PhD studies at Imperial College, Glen spent his spare time self-organising an expedition to retrace a 1932 route across Europe’s largest icecap, the Vatnajökull in Iceland, with a team of 3 friends in 2019. Inspired by the pioneering scientific programme of the young 1932 team, he wanted to push the bounds of expedition science. Packing an entire lab into the back of his sledge, Glen and the team performed the first example of entirely off-grid sequencing in a polar environment, running only on human and solar power. Their work here aimed to create a blueprint for expedition science for any team to sequencing anything, anywhere, untethered from research stations.
Bridging the gap: long reads enable more contiguous assembly of repeat-rich plant genomes
Due to its large genome size (4Gb) and highly repetitive nature, previous short read assemblies of cultivated lentil (Lens culinaris) were highly collapsed and fragmented. Only 2.7Gb could be assembled (scaffold N50 54Kb), and 1.1Gb anchored, despite using a combination of long mate pair data, chromosome flow sorting, consensus genetic map, and an optical map. Long read technology has resulted in dramatic improvements, with 3.7Gb (contig N50 1.4Mb) now assembled from 50-fold coverage of the genome. The updated genome assembly uncovers an additional 25% of the lentil genome with 121x increase in sequence contiguity. A HiC contact map provided final anchoring and orientation for 92% of the long-read contigs. Using the same process, we have also assembled de novo several wild relatives of interest to the lentil breeding program. Higher assembly contiguity allows us to fully characterize structural rearrangements previously seen only in interspecific genetic maps as well as identify novel structural variation relative to cultivated species. Improved assembly of highly repetitive regions and intact TE elements also allows for a closer look at genomic expansion within the genus Lens.
Larissa Ramsay is the lead bioinformatician in the Bett lab at the University of Saskatchewan’s Department of Plant Sciences. She has been pivotal in the assembly of multiple, highly repetitive, lentil species genomes and is currently immersed in an analysis of their abundant structural rearrangements. She has also contributed to work in other species of agricultural interest from chickpeas to canola. Before moving to the University of Saskatchewan, she was employed as a bioinformatician at the National Research Council of Canada.
Sequencing and assembling highly heterozygous and/or repeat-rich plant genomes using Oxford Nanopore technology
Prof. Victor A. Albert is currently Empire Innovation Professor of Biological Sciences at the University at Buffalo, USA, and Visiting Professor in the School of Biological Sciences, Nanyang Technological University, Singapore. Prof. Albert’s research currently employs genomic approaches to understanding problems in plant evolutionary biology - his current research interests include genome sequencing and biodiversity "omics" analysis of the flora of Bukit Timah Nature Reserve in Singapore, which contains almost 1,200 plant species representing most of the flowering plant clades on Earth, as well as understanding the genetic basis for convergent evolution and “adaptive” radiations of plant forms, such as carnivorous plants. This work requires complete genome sequencing of carnivores from different plant families as well as looking at the role of mechanistic co-option in the evolution of carnivorous plant physiology, for example, by repurposing of pathogenesis-related gene functions. He is also interested in population genomic approaches to the study of interspecies admixture, local environmental adaptation, and the evolution of agriculturally important traits.