Drought and salinity recruit largely distinct lncRNAs in sunflower, converging on a compact dual-responsive core
Abstract
Abstract Background — Drought and salinity increasingly co-occur where sunflower ( Helianthus annuus L.) is grown, yet which responses the two stresses share and which they keep stress-specific is unknown. Part of that decision is made in the long non-coding RNA (lncRNA) layer, where transcripts carrying microRNA (miRNA)-complementary sites can act as competing endogenous RNAs (ceRNAs) and couple several genes into one module. Sunflower has no abiotic-stress lncRNA catalogue; its stress biology has been resolved only at the coding and small-RNA tiers. We asked whether drought and salinity recruit a shared, dual-responsive lncRNA module, and whether the messenger RNAs (mRNAs) predicted to partner it behave differently in cultivars of contrasting tolerance. Results — A three-tool, plant-aware coding-potential consensus with Rfam screening defined 5,046 structurally validated lncRNAs, of which 2,172 were reliably expressed. Testing each stress separately against its own control gave 289 differentially expressed lncRNAs: 196 salinity-specific, 33 drought-specific and only 60 dual-responsive; shared regulation is a compact exception, not a broad common programme. A predicted ceRNA network of 2,575 lncRNA-mRNA edges, built from microRNA target-site prediction and co-expression-module membership, had an mRNA layer over-represented for jasmonate signalling, a candidate stress-responsive axis, and for water-channel activity, a candidate shared osmotic core. Photosynthetic and…
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