KeyGene evaluates Roche AXELIOS 1 platform

SBX-D for High-Accuracy Resequencing

For agricultural genomics, one of the applications for the AXELIOS 1 is SBX-Duplex high-accuracy resequencing. High accuracy matters, because breeders and trait discovery teams increasingly need to screen large germplasm collections, characterize diversity panels, gene edits and resequence breeding material at scale, while minimizing false positive rates. Such screens are difficult to support with current sequencing platforms, due to slower workflows or lower-confidence output data.

The duplex run on several WGS samples generated 20.4 Billion reads with a mean read length of 295 bp and 2.07 Tb (~71%) concordant duplex bases. In the run we included tomato, cultivar Heinz 1706, and lettuce, cultivar Salinas for which high-quality public reference genomes are available. At 30× down sampled concordant duplex coverage, Heinz 1706 aligned to SL4.0 and Salinas to Lsat_Salinas_v15 with 99.99% mapped reads and read accuracies of 39.4 and 39.6, respectively.

SBX-S for Single-Nucleus RNA-Sequencing

In a second pilot using the SBX‑S workflow on Roche’s AXELIOS 1, scientists looked at how tomato roots form suberin, a protective layer that appears in response to drought or a drought‑mimicking stress-hormone (ABA) treatment. By isolating and sequencing the nuclei from ABA-treated and untreated roots, the team generated an enormous amount of data—around 3.3 billion reads per sample—and captured thousands of individual nuclei, each with thousands of genes detected. UMAP visualization (Figure 1) separated cell types and confirmed exodermal expression of suberin biosynthesis genes (as recently published by Canto‑Pastor et al., 2024). With the much higher read counts from AXELIOS, KeyGene was able to annotate low expression clusters—such as the xylem—and refine the root meristematic cluster into the meristem and Quiescent Center/root cap/ columella. Since these cell types exhibit low global transcription levels, the team demonstrated that deeper sequencing improves identification and resolution of rare or weakly expressed plant cell populations.

These data support the claim that a single AXELIOS run can deliver 30× duplex coverage for ≥75 tomato genomes in 4 hours, or 27 lettuce genomes in the same time window. In practice, this can translate into faster iteration for line selection, denser sampling across segregating populations, and more economical screening of genetically complex materials. The value proposition is especially strong for crops with large genomes, where resequencing costs and cycle times can limit experimental ambition.

KeyGene’s genomics scientist, Alexander Wittenberg, is impressed by the data and summarizes:

“The SBX‑D duplex workflow on AXELIOS 1 produced 30× concordant duplex coverage for ~75 tomato genomes in a single 4‑hour run, enabling rapid, cost‑effective resequencing of crops such as tomato and lettuce.” 

This opens the ability for researchers to run bigger, richer experiments—more cells, with more conditions, and more timepoints—without having to choose between depth and scale, speeding up studies of development, stress responses, and lead gene discovery involved in important agricultural traits.

KeyGene’s single-cell transcriptomics specialist, Petra van Bergeijk, is enthusiastic about using this new technology in crop research.

“Using the SBX‑S workflow on AXELIOS 1, we were able to resolve thousands of individual nuclei with unprecedented detail—confirming drought response through exodermal suberin gene expression and enabling deeper, broader plant single‑nucleus studies” 

More information

• Roche Overview of sequencing by expansion (SBX) technology
• Roche Next-generation sequencing platform
• KeyGene to deploy Chromium X for single-nuclei transcriptomics