Soil salinity is a growing concern for global crop production and the sustainable development of humanity. Therefore, it is crucial to comprehend salt tolerance mechanisms and identify salt-tolerance genes to enhance crop tolerance to salt stress. Suaeda glauca, a halophyte species well adapted to the seawater environment, possesses a unique ability to absorb and retain high salt concentrations within its cells, particularly in its leaves, suggesting the presence of a distinct mechanism for salt tolerance. In this study, we performed de novo sequencing of the S. glauca genome. The genome has a size of 1.02 Gb (consisting of two sets of haplotypes) and contains 54 761 annotated genes, including alleles and repeats. Comparative genomic analysis revealed a strong synteny between the genomes of S. glauca and Beta vulgaris. Of the S. glauca genome, 70.56% comprises repeat sequences, with retroelements being the most abundant. Leveraging the allele-aware assembly of the S. glauca genome, we investigated genome-wide allele-specific expression in the analyzed samples. The results indicated that the diversity in promoter sequences might contribute to consistent allele-specific expression. Moreover, a systematic analysis of the ABCE gene families shed light on the formation of S. glauca’s flower morphology, suggesting that dysfunction of A-class genes is responsible for the absence of petals in S. glauca. Gene family expansion analysis demonstrated significant enrichment of Gene Ontology (GO) terms associated with DNA repair, chromosome stability, DNA demethylation, cation binding, and red/far-red light signaling pathways in the co-expanded gene families of S. glauca and S. aralocaspica, in comparison with glycophytic species within the chenopodium family. Time-course transcriptome analysis under salt treatments revealed detailed responses of S. glauca to salt tolerance, and the enrichment of the transition-upregulated genes in the leaves associated with DNA repair and chromosome stability, lipid biosynthetic process, and isoprenoid metabolic process. Additionally, genome-wide analysis of transcription factors indicated a significant expansion of FAR1 gene family. However, further investigation is needed to determine the exact role of the FAR1 gene family in salt tolerance in S. glauca.

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 in 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 geness 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 (CQAs), a medicinal component found in IPC.

As an important mangrove species, Kandelia obovata plays an irreplaceable role in the coastal ecosystem. However, due to a lack of genetic technology, there is limited research on its functional genes. As such, establishing an efficient and rapid functional verification system is particularly important. In this study,tobacco rattle virus (TRV) and the phytoene desaturase gene KoPDS were used as the vector and target gene, respectively, to establish a virus-induced gene silencing system (VIGS) in K. obovata. Besides, the system was also used to verify the role of a Chlorophyll a/b binding protein (Cab) gene KoCAB in leaf carbon sequestration of K. obovata.RNA-Seq and qRT-PCR showed that the highest gene-silencing efficiency could reach 90% after 10 days of inoculation and maintain above 80% after 15 days, which was achieved with resuspension buffer at pH 5.8 and Agrobacterium culture at OD₆₀₀ of 0.4-0.6. Taken together, the TRV-mediated VIGS system established herein is the first genetic analysis tool for mangroves, which may greatly impel functional genomics studies in mangrove plants.

Heavy metal pollution is becoming increasingly severe, and cadmium (Cd) is one of the most threatening pollutants. The PCR (Plant cadmium resistance) gene encodes a class of small transmembrane proteins containing the PLAC8 motif, which confer cadmium tolerance to plants through multiple mechanisms such as efflux, compartmentalization, chelation, and antioxidant activity, and regulate fruit size and ion homeostasis. This study systematically integrated the PLAC8/PCR gene families from mosses, monocots, and dicots, revealing their structural and functional relationships, evolutionary trajectories, and functional diversification patterns through phylogenetic and motif analyses, providing a theoretical basis for cadmium-resistant breeding and environmental remediation. Future research should further integrate multi-omics and gene editing technologies to deeply elucidate the transport mechanism of the PCR protein pentamer and the functional differences of key motifs (CCXXXXCPC, CCXXCAL, and CCXXG), and conduct field trials to assess their ecological safety and crop application potential.