A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome.

Robert Vanburen,Kevin Childs,Ivan Liachko,Ching Man Wai,Shawn Sullivan,David Chagné,Todd C Mockler,Chad E Finn,Michael Dossett,Nahla V Bassil,Jie Wang,Rubina Jibran,Kelly J Vining,Jill M Bushakra,Patrick P Edger,Marivi Colle

doi:10.1093/gigascience/giy094

Abstract

BackgroundThe fragmented nature of most draft plant genomes has hindered downstream gene discovery, trait mapping for breeding, and other functional genomics applications. There is a pressing need to improve or finish draft plant genome assemblies.FindingsHere, we present a chromosome-scale assembly of the black raspberry genome using single-molecule real-time Pacific Biosciences sequencing and high-throughput chromatin conformation capture (Hi-C) genome scaffolding. The updated V3 assembly has a contig N50 of 5.1 Mb, representing an ∼200-fold improvement over the previous Illumina-based version. Each of the 235 contigs was anchored and oriented into seven chromosomes, correcting several major misassemblies. Black raspberry V3 contains 47 Mb of new sequences including large pericentromeric regions and thousands of previously unannotated protein-coding genes. Among the new genes are hundreds of expanded tandem gene arrays that were collapsed in the Illumina-based assembly. Detailed comparative genomics with the high-quality V4 woodland strawberry genome (Fragaria vesca) revealed near-perfect 1:1 synteny with dramatic divergence in tandem gene array composition. Lineage-specific tandem gene arrays in black raspberry are related to agronomic traits such as disease resistance and secondary metabolite biosynthesis.ConclusionsThe improved resolution of tandem gene arrays highlights the need to reassemble these highly complex and biologically important regions in draft plant genomes. The updated, high-quality black raspberry reference genome will be useful for comparative genomics across the horticulturally important Rosaceae family and enable the development of marker assisted breeding in Rubus.

Highlights

1) For Pilon correction, what was the rationale for 2 rounds of correction? It may be be useful to run more rounds until it reaches a plateau
2) I was curious if other parameters for Canu or other assemblers, such as Falcon, were attempted in efforts to assemble the PacBio data
4) It is stated that there were several misassemblies in the V1 genome compared to V3

Summary

Introduction

1) For Pilon correction, what was the rationale for 2 rounds of correction? It may be be useful to run more rounds until it reaches a plateau. 2) I was curious if other parameters for Canu or other assemblers, such as Falcon, were attempted in efforts to assemble the PacBio data. It can be good to run several assemblies with the corrected reads to find the optimal one. If you have this data it would be nice to include it. 3) What was the average size and range of sizes of gaps in the assembly?

Results

Conclusion