Long-read sequencing technologies together with proximity ligation-based techniques have fundamentally shifted genome sequencing from contig-scale to chromosome-scale. Here, I will discuss the strengths and weaknesses of PacBio SMRT, ONT Nanopore and Hi-C data for achieving chromosome-scale assemblies of challenging genomes. I will show how all three datatypes in synergy can drive discoveries in genome biology. Using highly repetitive, dikaryotic plant pathogen genomes as examples, I will show how I have utilized Hi-C data to find incorrectly assembled chimeric contigs, to phase haplotypes in dikaryons and to identify centromeric regions. In addition, Nanopore sequencing data can uncover epigenetics such as methylated genomic regions. Finally, I will highlight the challenges that remain in achieving phased, accurate and complete chromosome-scale genome assemblies and how the field is moving forward.
ARC DECRA Research Fellow, The Australian National University
Jana is an ARC DECRA fellow at the Australian National University in Canberra, Australia. She is a bioinformatician who uses computational techniques to drive knowledge discovery in plant sciences. Jana completed an MSc in Computer Science with a focus on Bioinformatics at the University of Freiburg, Germany. In 2008, she commenced a PhD at the University of Western Australia (Crawley, WA, Australia) in which she developed novel methods for the computational prediction of noncoding RNA structure. In 2012, she joined the Commonwealth Scientific and Industrial Research Organization (CSIRO) as a Postdoctoral Fellow to work on plant–pathogen interactions and genomics. In 2018, she joined the Australian National University as an ARC DECRA fellow to uncover how rust fungi cause devastating plant diseases. Jana is an accredited Software Carpentry instructor and is passionate about collaborative, reproducible and inclusive science.