Maize genome complexity traversed with Oxford Nanopore technology

Thu, Nov 8, 2018 10:00 AM PST{LOCAL_TZ}

Maize genome complexity traversed with Oxford Nanopore technology

Thu, Nov 8, 2018 10:00 AM PST


Abstract:

Maize is one of the most economically important crops globally and much effort has been spent generating the high quality B73 reference genome. However, the 10 chromosome, 2.3 gigabase (Gb) B73 reference genome was a substantial challenge due to the fact it is comprised of 85% transposable elements, 75% of which are long terminal repeat (LTR) retrotransposons that share high sequence similarity and form nested repeat structures. Ultralong Oxford Nanopore Technology (ONT) holds the promise of traversing the complex repeat structures of maize and enabling rapid sequencing of new breeding lines. The key to sequencing any complex genome on ONT is starting with ultra-clean, high molecular weight (HMW) DNA.

We tested both standard CTAB DNA extraction and nuclear extractions and found relative trade-offs between read length and throughput. We generated 50x coverage (115 Gb) of the maize genome that we filtered for the longest 30x reads (70 Gb) for correction-less assembly using the minimap/miniasm/racon/pilon pipeline, which resulted in an assembly with high co-linearity to the B73v4 reference genome. In addition to the protein coding regions, the ONT assembly captured much of the repeat structure with 62,682 full length LTRs, which highlights its complexity compared to the number of full-length LTRs found in other ONT-based plant genome assemblies: Arabidopsis (500), rice (4,036), tomato (14,381), and sorghum (17,451). Now with the PromethION generating >100 Gb per flow cell, it is possible to rapidly sequence new breeding lines and generate high contiguity assemblies with modest resources.



Speaker:



Todd Michael, PhD - J. Craig Venter Institute

Dr. Todd Michael is Professor and Director of Informatics at the J. Craig Venter Institute (JCVI) in San Diego, CA USA. Dr. Michael has led commercial and academic genome centers, and currently directs the JCVI Sequencing Core. In addition, his research group is interested in leveraging sequencing technologies and informatics to understand how information is stored in genomes, such as genome architecture, gene and repeat content, and epigenomic state.

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