Interview: Single platform telomere-to-telomere assemblies: examples from the tomato and maize genomes

Alexander Wittenberg is a Genomics Scientist at KeyGene, where he is currently responsible for scouting new genomics technologies and is involved in the development of innovative sequence-based technologies within KeyGene’s Genome Insights crop innovation platform. He also works closely with R&D and business development departments within KeyGene to translate these technologies to the market for KeyGene’s partners.

We caught up with Alexander to discuss his research interests, what led him to focus on plant breeding and crop innovation, and how nanopore sequencing is changing our understanding of plant genomics. You can also hear more about Alexander’s work in the Knowledge Exchange ‘Making telomere-to-telomere genomic assemblies accessible: examples from human and plant genomes’.

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What are your current research interests?

My main interest lies in utilising the latest sequencing technologies to sequence plant genomes, in order to uncover and comprehend variation that can be leveraged to induce desirable changes, ultimately leading to enhanced breeding efficiency.

Genome sequencing has revolutionised plant breeding research, enabling us to accurately determine the complete genetic composition of individual plant varieties at the nucleotide level. In the past, generating high-quality genome assemblies required the use of multiple sequencing platforms and strategies. However, recent advancements in read accuracy and length have made it possible to generate the first telomere-to-telomere (T2T) crop genome assemblies using a single sequencing platform.

Previous sequencing and assembly technologies were limited to resolving diploid, homozygous genomes. However, recent advancements in read accuracy, length, and analysis tools have made it possible to resolve the distinct haplotypes of heterozygous and polyploid genomes at a chromosome scale. These haplotype-phased genomes offer exciting new opportunities for more effective crop breeding strategies. To explore this further, we recently initiated a banana pan-genome initiative aimed at generating a large number of (near) complete, fully phased reference genomes. Moreover, we anticipate we can achieve this goal in a cost-effective way by combining Oxford Nanopore duplex sequencing with Pore-C. The first results are promising, and there is no doubt that we will move away from single reference genomes towards a haplotype-phased pan-genome context that will be more informative for plant breeding in the coming years.

What first ignited your interest in genomics and what led you to focus on plant breeding and crop innovation?

I am fascinated by the immense variation in nature that has the potential to be harnessed for optimising crops. Plant breeding utilises this genetic variation through the selection of desired traits, such as increased yield, resistance to biotic and abiotic stresses, and longer shelf life to minimise food waste. The rapid development of genomic technologies presents exciting opportunities to study processes from phenotypes down to the single-cell level. However, the pressing challenge is to ensure that crop breeding can keep pace with the growing demand for food production while also reducing resource consumption in a sustainable manner.

How is nanopore sequencing changing our understanding of plant genomics? How has it benefitted your work?

Advanced genomic tools, such as nanopore sequencing, are providing us with comprehensive insights into the crops we work with. Plant genomes can be complex, repetitive, and difficult to analyse, but long-read sequencing can help elucidate these complex regions. This has resulted in the development of de novo reference genomes that are more contiguous, accurate, and valuable. For instance, we have successfully closed a complex region in a flower genome that we had previously fine-mapped for a resistance trait using long reads. In contrast, short-read sequencing technologies often fail to provide a realistic view of genome organisation.

In another recent example, we used adaptive sequencing to uncover variations in quantitative trait loci (QTL) regions associated with fungal resistance in banana varieties. The insights gained from this research can be utilised in our breeding program, which aims to develop and introduce new, resistant varieties to the market.

What impact could a single-instrument solution for complete genome assembly have for researchers?

Until recently, only specialised genome centers and consortia could generate high-quality reference genomes. However, Oxford Nanopore Technologies has made this accessible to a wider research community by offering a single-platform approach to data generation. Coupled with user-friendly assembly pipelines, such as Verkko and Hifiasm that can be initiated with ‘the press of a button’, researchers can now generate their own T2T reference genomes in-house, democratising access to high-quality genome information. These advances have opened up new research possibilities, including the study of less-known species that were previously limited by the lack of available genomic information.

What have been the main challenges in your work and how have you approached them?

With the generation of data no longer a bottleneck, the main challenges now lie in scaling up the ultra-high molecular weight DNA isolation and sample preparations, as well as accelerating the entire genome analysis process in a cost-effective manner.

What’s next for your research?

Our team is dedicated to developing innovative methods for more efficient extraction of longer DNA, while also investing in scaling up DNA extractions and reducing the cost of sample preparation. In addition, we are developing a computational toolset that enables real-time genome assembly from long reads, as well as whole-genome alignment and pan-genome reconstruction at a population scale. Our goal is to accelerate crop innovation and provide plant breeders with insights into the potential of natural alleles, ultimately reducing the time to market for new varieties.