NGS Technologies: Where Will the Future Take Us?

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The development of DNA sequencing technologies has experienced multiple paradigm shifts within just a few decades. From the early efforts to sequence biopolymers to the invention of electrophoretic methods for automated DNA sequencing, the journey has been remarkable (Shendure et al., 2017). As a bioinformatics student fifteen years ago, I witnessed the nascent impact of second-generation sequencing technologies on the biological sciences. Back then, long-read sequencing was merely a promising concept, and technologies like Oxford Nanopore were still prototypes with uncertain potential. It’s amazing to see how quickly things have advanced since then!

Next-generation sequencing (NGS) has completely transformed genomics research by offering an incomparable ability to analyze DNA and RNA molecules rapidly and cost-effectively. Such revolutionary technologies have boosted genomics advancements across several domains, from personalized medicine and cancer research to crop improvement. NGS has made sequencing DNA fast, efficient, and affordable, opening the doors to a vast range of applications.

Reflecting on the past, it’s hard to predict the “future” of NGS given the rapid pace of technical breakthroughs today and the growing advancements in the use of artificial intelligence. Yet, I want to highlight some key aspects that I believe will continue to shape NGS advancements over the next five to ten years, particularly in plant biology.

The future of genomics seems to belong to the evolving third-generation sequencing methods and single-cell sequencing techniques. Emerging technologies like in situ sequencing and spatial multi-omics hold great promise. The latter, for example, preserves spatial information and allows for a better understanding of plant development by linking data to cellular context (Serrano et al., 2024; Yin et al., 2023; Yu et al., 2023). Just thinking about the applications and discoveries that this technique could uncover in the near future is mind-blowing.

Newer generations of sequencing instruments are making great progress in long-range, direct, and single-cell sequencing while introducing novel types of measurements. As these technologies advance, we can expect faster and more accurate sequencing methods that require less input DNA and reagents. The increased portability of sequencing devices will make them invaluable for diagnostic use in medical, agricultural, ecological, and other field-based applications. Advances in bioinformatics, robotics and artificial intelligence will further facilitate these developments. NGS’s growing accessibility and affordability are revolutionizing numerous life science disciplines worldwide. However, with rapid technological advancements come new challenges around data storage, quality control, regulatory guidelines, and ethical considerations. Addressing these issues will be critical as we move forward.

Looking ahead, the reduction of sequencing costs and the enhancement of precision and read lengths will continue. Companies like Illumina, PacBio, and Oxford Nanopore Technologies are expected to lead these innovations, but new ones may surprise us. We will likely see ultralong reads and high precision from third-generation sequencers, improving the assembly of complex genomes and the identification of structural variants. Spatial multi-omics technologies will continue to improve and facilitate mapping the spatial distribution of genes, proteins, and metabolites within plant tissues in a more accessible way. This will provide detailed insights into cellular organization and functionality, aiding studies on plant development, stress response, and disease.

In precision agriculture, NGS will routinely assist in identifying genes and markers associated with crucial agricultural traits, such as disease resistance, drought tolerance, and yield. Integrating these insights with genome editing technologies, like CRISPR, will accelerate the development of resilient and productive crop varieties. Moreover, the development of portable and affordable sequencing devices will allow real-time genomic analysis in the field. This will enable immediate data collection and facilitate swift decision-making in crop management. It is essential to promote inclusive initiatives that involve scientists and farmers from developing countries by providing training and access to advanced NGS and precision agriculture technologies. Different programs and grants to support the acquisition and use of these technologies in resource-limited regions will be vital to ensure these innovations reach every corner of the globe.

The future of NGS is indeed bright, holding the potential to revolutionize many aspects of our lives. As NGS becomes faster, cheaper, and more accurate, its applications will expand, profoundly impacting our understanding of biology and disease and leading to the development of better treatments. NGS technologies will drive plant biology towards greater precision, efficiency, and sustainability in agriculture. The integration of spatial omics and advanced equipment will add a critical dimension to the analysis, deepening our understanding of cellular organization and function within plant tissues. Addressing the technological gap in low-resource countries through global projects and international collaborations will ensure that everyone benefits from these advancements.

We are merely scratching the surface of NGS’s potential applications. As technology evolves, we can expect to see its use in ways we can’t yet imagine. The future holds exciting possibilities for NGS, and I am eager to witness how it will continue improving our lives.

 

References

Serrano K, Tedeschi F, Andersen SU, Scheller HV. Unraveling plant-microbe symbioses using single-cell and spatial transcriptomics. Trends Plant Sci. 2024 Jul 10:S1360-1385(24)00152-3. doi: 10.1016/j.tplants.2024.06.008.

Shendure J, Balasubramanian S, Church GM, Gilbert W, Rogers J, Schloss JA, Waterston RH. DNA sequencing at 40: past, present and future. Nature. 2017 Oct 19;550(7676):345-353. doi: 10.1038/nature24286. Erratum in: Nature. 2019 Apr;568(7752):E11. doi: 10.1038/s41586-019-1120-8.

Yin R, Xia K, Xu X. Spatial transcriptomics drives a new era in plant research. Plant J. 2023 Dec;116(6):1571-1581. doi: 10.1111/tpj.16437.

Yu X, Liu Z, Sun X. Single-cell and spatial multi-omics in the plant sciences: Technical advances, applications, and perspectives. Plant Commun. 2023 May 8;4(3):100508. doi: 10.1016/j.xplc.2022.100508.

 

 

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About the Author

Ileana Tossolini is an Argentinean research associate in the small RNA Biology Lab at the Agrobiotechnology Institute of Litoral (IAL, UNL-CONICET), and a 2024 Plantae Fellow. She is a bioinformatician focused on studying the effects of siRNAs on genome structure, integrity, and evolution, as well as the mechanisms regulating miRNA biogenesis in plants. You can find her on X/Twitter at @IleanaDrt.