Assembly of complex genome (Macadamia) using single molecule sequencing
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 Al-dossary, Bader Alsubaie, Ibrahim Al-mssallem, Onkar Nath, Neena Mitter, Gabriel Rodrigues Alves Margarido, Bruce Topp, Valentine Murigneux, Ardashir Kharabian Masouleh, Agnelo Furtado, Robert J. Henry, Improvements in the sequencing and assembly of plant genomes, Gigabyte, 1, 2021 https://doi.org/10.46471/gigabyte.24
The genome of the endangered Macadamia jansenii displays little diversity but represents an important genetic resource for plant breeding.
Sharma, P., Murigneux, V., Haimovitz, J., Nock, C. J., Tian, W., Kharabian Masouleh, A., Topp, B., Alam, M., Furtado, A., & Henry, R. J. (2021). Plant Direct, 5( 12), e364. https://doi.org/10.1002/pld3.364
News and media releases
Our sister GigaByte Journal has published its first Update article, GigaScience Journal, Facebook, 11 June 2021.
Endangered Plant Species Becomes Model for Genome Sequencing, International Service for the Acquisition of Agri-biotech Applications (ISAAA) Crop Biotech Update, March 10 2021
Critically endangered macadamia species becomes a plant supermodel. Physics.org, 8 March 2021
Critically endangered macadamia species becomes a plant supermodel. The SeqComplete Daily&Nightly, 4 March 2021
Endangered CQ macadamia becomes genetic supermodel, Courier Mail/The Observer/The Chronicle, 28 February 2021
Researchers at the University of Queensland studying the endangered Macadamia Jansenii say it could be the supermodel for global plant genomics, Gladstone Observer (Australia), 27 February, 2021
Critically endangered macadamia species becomes a plant supermodel, QAAFI Innovation in Agriculture, February 2021
Critically endangered macadamia species becomes a plant supermodel, QAAFI news, 25 February 2021
Cracking a tough nut for macadamia growers, UQ news, 24 January 2021
Improvements in the sequencing and assembly of plant genomes, Oxford Nanopore Technologies, Resource Centre, 22 January 2021
Genome Innovation Hub Facilitates a Novel Plant Sequencing Project, UQ Research Bulletin, 31 July 2020
Webinar: Comparison of long read methods for sequencing and assembly of a plant genome, Australian BioCommons, 2 July 2020
MGI Webinar: Comparison of long read methods for sequencing and assembly of a plant genome, MGI Tech, 13 April 2020
