APEX-05 — Arabidopsis spaceflight transcriptomics, root architecture & ML sample QC

A FAIR, reproducible data-and-code package comparing four Arabidopsis thaliana genotypes flown on the ISS against matched ground controls — paired shoot/root RNA-seq and RSML root-architecture morphometrics, with a machine-learning quality-control layer.

MIT licensedFAIR RNA-seq + RSMLg:Profiler enrichment scikit-learn QC
Read the Final manuscript → Figures CAX2 QC story Code & data (GitHub)

Headline: wild-type and rbohD mount a strong spaceflight response localised to the outer root (epidermis, cortex, gravity- sensing columella); cax2-2 abolishes the transcriptional response (CAX2 required) yet its roots still shorten — uncoupling expression from growth.

Abstract

Spaceflight imposes a unique combination of microgravity and space-radiation stress on plants, yet the signalling pathways that translate the orbital environment into altered growth remain incompletely mapped. The Advanced Plant Experiment-05 (APEX-05) flew four Arabidopsis thaliana genotypes — wild-type Col-0, a mutant in reactive-oxygen (ROS) production (rbohD), and two independent alleles of the calcium/H⁺ exchanger CAX2 (cax2-2 and cax2-3) — aboard the International Space Station, alongside matched ground controls, and profiled both the shoot and root transcriptome (RNA-seq) and root system architecture (RSML morphometrics). A QC concordance test between the two CAX2 alleles found cax2-3 strongly discordant with its sibling cax2-2 (DEG set ~10–17× inflated and no more similar to cax2-2 than to unrelated genotypes); cax2-3 was therefore excluded, leaving a primary set of three genotypes (Col-0, cax2-2, rbohD). Wild-type rosette leaf area was reduced under spaceflight [TO CONFIRM: exact means/CI from the leaf-area analysis; storyboard indicates ~4.0 cm² ground control vs ~2.7 cm² flight], and this response was altered in the ROS- and calcium-signalling mutants, implicating both pathways in the spaceflight growth response. Differential-expression analysis identified hundreds of flight-responsive genes in each genotype and tissue (e.g. Col-0 root: 799 DEGs, 268 flight-induced / 531 flight-repressed; see Table 1 and the direction note in §2), enriched for photosynthesis, stress-response, cell-wall and redox pathways (Fig. 9; results/tables/apex05_primary_enrichment_*). Beyond the biology, we release APEX-05 as a FAIR, reproducible data package and demonstrate a machine-learning quality-control workflow that (i) recovers tissue identity from expression with 100% leave-one-out accuracy and detects deliberately mislabelled samples at ~97% recall, and (ii) shows that day-4 primary-root morphology only weakly distinguishes these subtle mutants — the finding that motivated our provenance- based correction of a historical cax23 sample-labelling anomaly. Together the data and tooling provide a reusable resource for the plant space-biology community.

Highlights

4 genotypes × 2 tissues × 2 conditions

Col-0, cax2-2, cax2-3, rbohD; root & shoot; spaceflight vs ground control.

ML sample QC

100% leave-one-out tissue recovery; ~97% recall detecting injected label-swaps.

CAX2 allele concordance

cax2-3's flight-DEG set is 10–17× inflated and discordant with its sibling allele — excluded on QC grounds.

Functional signatures

Root core → photosynthesis; shoot core → cell wall + peroxidase; rbohD → redox/detox.

Selected figures

Fig 6a — cax2-3's flight-DEG set is 10–17× inflated vs its sibling allele cax2-2.
Fig 6a — cax2-3's flight-DEG set is 10–17× inflated vs its sibling allele cax2-2.
Fig 8 — Core enrichment: root = photosynthesis; shoot = cell wall + peroxidase.
Fig 8 — Core enrichment: root = photosynthesis; shoot = cell wall + peroxidase.
Fig 9 — Genotype-resolved flight-DEG enrichment (Col-0, cax2-2, rbohD).
Fig 9 — Genotype-resolved flight-DEG enrichment (Col-0, cax2-2, rbohD).

Data & code