Discovery of Desiccation-Induced Long Non-Coding RNAs in the Resurrection Plant Craterostigma plantagineum: A Transcriptome-Wide Computational Analysis

Abstract Background . Resurrection plants survive near-complete vegetative desiccation and recover full physiological function upon rehydration, making them valuable models for extreme abiotic stress tolerance. Although protein-coding mechanisms underlying desiccation tolerance have been extensively studied, the potential regulatory roles of long non-coding RNAs (lncRNAs) in resurrection plants remain poorly characterized. Methods . We performed a transcriptome-wide computational reanalysis of publicly available RNA-seq data (GEO: GSE157098) from Craterostigma plantagineum across hydrated (n = 2), desiccated (n = 5), and rehydrated (n = 3) states. After standard read processing, alignment to the V2 transcriptome assembly, and transcript quantification, candidate lncRNAs were identified using length and coding-potential filters, with structural RNA exclusion. Differential expression, co-expression networks (Pearson r > = 0.90), and functional enrichment of co-expressed partners were conducted. Results . A substantial number of non-coding transcript candidates were identified among the assembled transcripts. Under nominal significance thresholds, 661 candidates showed elevated expression during desiccation relative to the hydrated state. Fourteen high-priority candidates exhibited minimal or undetectable expression in hydrated tissue and strong accumulation (590 to 1,957 TPM) under desiccation, with several remaining elevated during rehydration. These candidates were tightly co-expressed with known desiccation protectors, including LEA protein 6 (r = 0.991) and HSP70 (r = 0.986). Co-expressed partners were significantly enriched for chloroplast- and photosynthesis-related functions (3.7-fold enrichment, FDR = 6e-14), consistent with a potential association with chloroplast protection during extreme dehydration. Conclusions . This reanalysis highlights desiccation-associated lncRNA candidates in C. plantagineum and prioritizes a small set linked to chloroplast maintenance and canonical stress-response pathways. The findings provide an initial resource and candidate list for future functional studies of lncRNA contributions to vegetative desiccation tolerance. Analysis scripts are available on GitHub, and additional analysis outputs generated during this study will be made publicly available upon deposit.