Unveiling the genomic blueprint of salt stress: insights from <i>Ipomoea pes-caprae</i> L.

Adverse environmental conditions often present challenges for organisms; however, they can also serve as selective pressures that propel adaptive evolution. In this study, we present the first chromosome-scale genome of Ipomoea pes-caprae L (IPC), an exceptionally salt-tolerant plant species of considerable significance due to its medicinal, ecological, and biological attributes. The haplotype IPC genome comprises 15 chromosomes spanning 1.05 GB and includes 34,077 protein-coding genes, exhibiting an impressive completeness of 97.4%. Comparative genomic analysis with non-salt-tolerant Ipomoea species has highlighted the prevalence of highly duplicated sequences and genes within the IPC genome. Analysis of gene ortholog expansion, when compared those Ipomoea species, reveals that expanded TRD (transposed duplication) and DSD (dispersed duplication) genes are predominantly associated with functions related to salt tolerance. Furthermore, our findings suggest strong correlations between DSD and TRD gene duplication and transposable element (TE) events, implying that TE-induced expansion of repeat genes is a driving force behind gene diversification. Moreover, a time-course RNA-seq analysis unveils the salt response of IPC roots and leaves, showing the involvement of several key salt-tolerance genes exhibiting copy number expansion. These include genes responsible for ion uptake, transportation, and sequestration into vacuoles, as well as genes responsible for the maintenance of DNA and chromosome stability. Given the significant induction of TE events by salt stress in plant genomes, we propose a putative mechanism for the rapid evolution of salt tolerance in IPC. Additionally, this study delves into the metabolic pathway and regulatory mechanisms of Caffeoylquinic acids (CQA), a medicinal component found in IPC.