Chromosome-scale scaffolding of the black raspberry (Rubus occidentalis L.) genome based on chromatin interaction data

Abstract

Plant genomics: Improved genome for the black raspberry Assembly of a high-quality reference genome for the black raspberry plant will inform future crop improvements. Sequencing the genomes of widely-grown, profitable fruit crops can help researchers identify the DNA markers linked to desirable traits, potentially improving crop health and yields. David Chagné at the New Zealand Institute for Plant and Food Research Limited and co-workers combined new techniques to significantly improve on an existing genome for the black raspberry (Rubus occidentalis L.). The researchers used Hi-C analysis to create a map identifying the interactions between chromatin fragments – macromolecules made from DNA, proteins and RNA – and the three-dimensional structure of chromosomes inside the cell nucleus. Then, they used a bioinformatics assembly method to construct the genome from this data. The new genome showed high accuracy when compared to another genome from the same family.