Ultra-long nanopore sequencing for assembly and scaffolding of sex chromosomes

Matthew Brian Couger

Matthew Brian Couger, Brigham and Women's Hospital, USA


Recent advances in long-read sequencing have improved genome assembly and allowed researchers to achieve “reference” type assemblies in a fraction of time and cost as original. While these advances have greatly propelled assembly of non-model organisms, many challenging areas still exist in genomes which prevent the goal of single contig per chromosome assemblies. One area that is understudied and has presented challenges to assembly due to repetitive structure is mammalian sex chromosome systems. Here we apply ultra-long-read nanopore sequencing to finish an assembly for a highly atypical sex mammalian chromosome system. We demonstrate these reads bridge problematic assembly areas and provide an increase in contig continuity that allows researchers to fully investigate working hypotheses involving sex chromosomes and other repetitive genomic areas. This work highlights that generating ultra-long nanopore reads for genome assembly can be employed rapidly and their unique utility in assembling recalcitrant genome areas.  


Matthew Brian Couger has worked on many sequencing and big data projects. These include the first use of long-read sequencing for assembly in a non-model organism to produce the first genome assembly for anaerobic fungi, co-authoring the popular annotation program Trinotate, and recently publishing a highly atypical mammalian sex chromosome system in Science Magazine. This has resulted in over 50 publications in a variety of genomic and cellular systems. Current research includes working with long-read sequencing and single-cell transcriptomics to understand cancer biology, using long-read sequencing to assemble atypical mammalian genomes, and generating ultra-large metagenomics assemblies.