Assembly of complex genome (Macadamia) using single molecule sequencing

Macadamia jansenii — Photo by Prof. Bruce Topp

Aims

To compare different long read sequencing approaches for assembly of a complex plant genome.

Brief project outline

Three long read sequencing technologies were applied to the de novo assembly of a plant genome, Macadamia jansenii.

Genomics-based innovative aspect

Several assemblers were benchmarked in the assembly of PacBio and Nanopore reads. The assemblies were compared for contiguity, accuracy and completeness as well as sequencing costs and DNA material requirements.

Broad applicability of the technique

Sequencing technologies have advanced to the point where it is possible to generate high accuracy, haplotype resolved, chromosome scale assemblies. Several long read sequencing technologies are available on the market and a growing number of algorithms have been developed over the last years to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology as well as the most appropriate software for assembly and polishing. For this reason, it is important to benchmark different approaches applied to the same sample. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION) and BGI (single-tube Long Fragment Read) technologies for the same plant sample.

Developments arising from this project

GIH Development: High Molecular Weight Nuclear DNA Extraction from difficult plant species for Long read sequencing (Oxford Nanopore Sequencing)

Publications arising from this project

Comparison of long-read methods for sequencing and assembly of a plant genome

Valentine Murigneux, Subash Kumar Rai, Agnelo Furtado, Timothy J C Bruxner, Wei Tian, Ivon Harliwong, Hanmin Wei, Bicheng Yang, Qianyu Ye, Ellis Anderson, Qing Mao, Radoje Drmanac, Ou Wang, Brock A Peters, Mengyang Xu, Pei Wu, Bruce Topp, Lachlan J M Coin, Robert J Henry

GigaScience, Volume 9, Issue 12, December 2020, giaa146, https://doi.org/10.1093/gigascience/giaa146

Improvements in the Sequencing and Assembly of Plant Genomes

Priyanka Sharma, Othman Aldossary, Bader Alsubaie, Ibrahim Al-Mssallem, Onkar Nath, Neena Mitter, Gabriel Margarido, Bruce Topp, Valentine Murigneux, Ardy Masouleh, Agnelo Furtado, Robert J Henry.

bioRxiv 2021.01.22.427724; doi: https://doi.org/10.1101/2021.01.22.427724