Genomic evolution of extreme abiotic stress tolerance in plants: Vegetative desiccation tolerance in Xerophyta resurrection plants and nickel hyperaccumulation in Senecio coronatus

Kabamba, Eugene Kabwe Ntuntu

Genomic evolution of extreme abiotic stress tolerance in plants: Vegetative desiccation tolerance in Xerophyta resurrection plants and nickel hyperaccumulation in Senecio coronatus

Thesis / Dissertation

2026

Publisher

University of Cape Town

Department

Department of Molecular and Cell Biology

Faculty

Faculty of Science

Abstract

The evolution of extreme stress tolerance phenotypes in plants is associated with changes in the genome. Performing comparative genomics analyses enables the identification of genomic changes that are associated with the extreme phenotype. This project focused on two rare and extreme phenotypes, namely vegetative desiccation tolerance (VDT) and nickel (Ni) hyperaccumulation. VDT is defined as the ability of a plant to survive extreme dehydration (<5% relative water content) and subsequently revitalize after the re-addition of water, and plants that display this trait are known collectively as resurrection plants. The monocot genus Xerophyta (Velloziaceae) comprises ~45 species, all of which are resurrection plants. The first part of this project aimed to identify expanded gene families in the Velloziaceae and evaluate their potential role in VDT. The genomes of X. elegans and X. humilis were assembled in this study using PacBio HiFi sequencing. The assembly process resulted in a 379 Mbp draft haploid assembly of the diploid X. elegans genome, and a 1.8 Gbp draft tetraploid assembly of the tetraploid X. humilis genome. A syntenic depth analysis showed that the Xerophyta genus likely experienced a recent whole genome triplication (WGT) event prior to species diversification, after which diploidization occurred. A comparative genomics analysis of four Velloziaceae resurrection plants, X. elegans, X. humilis, Xerophyta schlechteri, and Acanthochlamys bracteata, with 26 other angiosperms revealed twelve gene families that were expanded in the Velloziaceae. A combination of functional annotations and the conserved gene expression patterns across the three Xerophyta species revealed that five of the expanded gene families were possibly involved in VDT, including the EARLY LIGHT-INDUCED PROTEIN (ELIP) and STAYGREEN (SGR) genes which encode proteins involved in chlorophyll metabolism, and the FCS-LIKE ZINC FINGER PROTEIN 3 (FLZ3), ZINC FINGER PROTEIN (ZAT), and HEAT STRESS TRANSCRIPTION FACTOR C (HSF-C) genes which encode proteins involved in the abscisic acid (ABA)-mediated stress response. While the expansion of ELIP genes in resurrection plants has been reported before, this study is the first to report on SGR genes possibly involved in VDT. Members of both gene families were significantly upregulated during dehydration across the three Xerophyta species, suggesting a possible role in preventing photo-oxidative damage during desiccation. Members of the FLZ3 genes, which encode proteins that inhibit SnRK1, a central regulator of energy metabolism, were significantly downregulated during dehydration, while some of the ZAT and HSF-C genes, both of which encode stress-responsive transcription factors (TFs), were upregulated. The expansion of all these gene families was due to tandem duplications, some of which likely occurred prior to the WGT event. The second part of the project focused on Ni hyperaccumulation, which is defined as the ability of a plant to accumulate Ni in shoot tissues to concentrations exceeding 0.1% on a dry weight basis, without succumbing to the toxic effects. The eudicot Senecio coronatus (Asteraceae) is a geophyte that has evolved the capacity to hyperaccumulate Ni from the Ni-rich serpentine soils. However, this is not a species-wide trait as not all S. coronatus populations on these ultramafic outcrops are able to hyperaccumulate Ni. Previous soil-swap studies have shown that these differences in the ability to accumulate Ni were not a result of Ni availability in the soil and instead have a genetic basis. The aim of the study was therefore to perform a comparative genomics analysis of an S. coronatus hyperaccumulator and non-accumulator plant from the Kaapsehoop (KP) and Galaxy Mine (GAL) populations respectively, to identify genomic changes in the KP genome that are associated the hyperaccumulation phenotype. Draft haploid genome assemblies of the two plants were assembled using PacBio HiFi reads, resulting in 2.5 Gbp genomes for both plants. Differential gene expression (DGE) analysis comparing the gene expression pattern between two hyperaccumulator and two non-accumulator plants identified 704 and 781 significantly upregulated genes in the shoot and root tissues of the hyperaccumulators respectively. Single nucleotide polymorphisms (SNPs) were identified in TF-binding motifs of some upregulated genes, suggesting potential changes to TF binding affinity. The DGE analysis identified the upregulation of the HISTIDINOL DEHYDROGENASE (HISN8) gene, caused by a tandem duplication in the KP genome, which encodes the last enzyme of the histidine biosynthetic pathway, an amino acid that prevents Ni sequestration in the roots of Brassicaceae hyperaccumulators. The DGE analysis also identified metal transporter genes, including IRON-REGULATED/FERROPORTIN (IREG) and ZRT/IRT-LIKE PROTEIN 10 (ZIP10), that were significantly upregulated in both tissues, consistent with a previous transcriptomics study. However, the comparative genomics analysis revealed that the elevated expression of these genes was at least in part due to tandem duplications that occurred in the KP hyperaccumulator genome, with IREG and ZIP10 gene ratios of 11:1 and 6:1 (KP:GAL), respectively. Gene coverage analysis using DNBSEQ reads generated from the KP, GAL and an additional hyperaccumulator Agnes Mine (AM) population revealed a higher read coverage from the KP and AM reads compared to GAL reads, confirming the gene expansions in the hyperaccumulators. Furthermore, the gene expression of the ZIP10 paralogs in the KP genome revealed an apparent organ-specific expression pattern, whereby only one paralog was highly upregulated in the shoots, while the other five paralogs were expressed in the roots. The comparison of promoter sequences revealed that the five root-upregulated paralogs shared more predicted TF-binding motifs (≥92) with each other compared to the overlap with the shoot-upregulated paralog which had less (32), suggesting a potential case of neofunctionalization. In conclusion, this project has identified key expanded gene families that have possibly contributed to the acquisition of the two extreme phenotypes, which adds to the understanding of the molecular mechanisms involved in VDT and Ni hyperaccumulation in angiosperms. This project also provides a foundation for future research, including functional genetics studies to determine the roles of these expanded gene families in these extreme tolerance phenotypes.

Keywords

Xerophyta

genomic evolution

Reference:

Collections

PhD / Doctoral

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