Genomic and Transcriptomic Analysis of Nine Resurrection Plant Species: Conserved Regulation Versus Structural Paralog Capacity in Desiccation Tolerance

Background/Objectives: Vegetative desiccation tolerance (VDT) has arisen independently in numerous angiosperm lineages, yet it remains unclear which of its molecular features are genuinely conserved beyond individual lineages. Methods: We compiled and compared available genome assemblies and de novo transcriptomes for the nine DT species and three desiccation-sensitive (DS) sister species. Conservatively regulated orthogroups were mapped onto eleven literature-established canonical desiccation-tolerance gene families, and species-level paralog representation was examined by principal component analysis and hierarchical clustering. An exact, one-sided Mann–Whitney test compared the number of trend-conforming paralogs per species between DT and DS groups across 32 canonical orthogroups. Results: Copy-number variation aligned more closely with taxonomic affiliation than with tolerance status itself. For instance, the expansion of the ELIP orthogroup (OG0000271) was particular to the Poaceae family instead of DT status. Of the 32 canonical orthogroups, three (dehydrin, a NAC-domain transcription factor, and a LEA hydroxyproline-rich glycoprotein) exhibited a nominally greater count of trend-conforming paralogs in DT compared to DS species using a genuinely exact one-sided Mann–Whitney test (uncorrected p < 0.05). None passed multiple-testing correction, a finding with a clear mathematical rationale: given the exact test’s combinatorial floor and a DS sample comprising only three species. Conclusions: The current analysis provides no statistically robust evidence that conserved desiccation-associated transcriptional responses are accompanied by systematic paralog enrichment in desiccation-tolerant species. We present an integrated transcriptomic-genomic analysis of paralog (“structural”) capacity, reflecting gene copies that follow each orthogroup’s dominant regulatory trend, whether identified from genome or de novo transcriptome data, in conservatively regulated gene families relevant to desiccation tolerance, together with a concrete, functionally diverse set of candidate genes for future targeted validation.