Introduction
Plant species inhabiting diverse environmental conditions often undergo a series of local adaptations, leading to adaptive phenotypic traits and genetic changes that can result in incipient speciation or population divergence. Genetic elements, including the nuclear genome, coevolve synergistically with organelles, resulting in coordinated adaptations (Roux et al., 2016). However, this dynamic can shift in secondary contact zones or adjacent distribution areas where hybridization frequently occurs. In these regions, genetic introgression-where foreign genetic material from one species is introduced into another-can significantly impact the evolutionary trajectory of the recipient species. Additionally, organelle capture where a species retains and gradually replaces its original organelles (e.g., chloroplasts and mitochondria) with those from another species can occur. On one hand, organelle capture may introduce cytonuclear incompatibility and potentially lead to cytonuclear conflicts in genetically admixed individuals (Case, Finseth, Barr, & Fishman, 2016; Ellison & Burton, 2010; Sloan et al., 2018). On the other hand, this process can also interactively influence the reorganization of nuclear genome from the parental species, selectively retaining coevolved adaptive genes in the nuclear genome, and ultimately altering the local adaptivity of the recipient species(H. Wang et al., 2024).
Polyploidization is a widespread phenomenon in nature, with multiple polyploidization events occurring in closely related species or even within the same species (Brysting, Fay, Leitch, & Aiken, 2004; Cordeiro & Felix, 2018; Figueiredo et al., 2014; Wagner et al., 2019). Polyploids are known for their advantageous adaptation to various environments, often outperforming their diploid counterparts in terms of tolerance to ambient stresses such as drought, high salinity, cold, heat and nutrient deficits (Del Pozo & Ramirez-Parra, 2015). Hybridization between different ploidy levels is also common in nature. Adaptive introgression, where adaptive loci are transferred from one species or population to another, has been observed in various plant species, including Arabidopsis (Baduel, Hunter, Yeola, & Bomblies, 2018). This process can introduce beneficial phenotypic traits from one population to another. However, whether these adaptive loci can function stably in hybrid populations remains unclear.
Phragmites are a group of aquatic plants that have been playing important roles in the wetland ecosystems. They are commonly seen in streams, lowland rivers, estuaries, and creeks, and have high adaptability to different salinity regimes (Srivastava, Kalra, & Naraian, 2014). Genetically, the common reed has diverged into eight phylogeographic lineages worldwide (C Lambertini et al., 2006; L. L. Liu et al., 2022; Saltonstall, 2002; C. Wang, Liu, Yin, Eller, Brix, Wang, Salojärvi, et al., 2021). Using non-coding chloroplast regions trnT-trnL and rbcL-psaI, researchers have identified up to 57 haplotypes that based on their phylogenetic relationships can be used to distinguish these phylogeographic lineages (Eller et al., 2017; Saltonstall, 2016). In China, two major haplotypes were discovered: haplotype O (denoted as CN) primarily distributed in northern China, and haplotype P (denoted as AU) found in Korea and middle to southern China (L. L. Liu et al., 2022; Saltonstall, 2002; Tanaka, Irbis, & Inamura, 2017). These two distinct haplotypes are distantly related with haplotype O associated with the Eurasian lineage, and haplotype P belonging to a lineage primarily distributed in East Asia and Australia. They also differ in ploidy levels: haplotype O is tetraploid while Haplotype P is octoploid (Carla Lambertini et al., 2020; L. L. Liu et al., 2022; C. Wang, Liu, Yin, Eller, Brix, Wang, Salojärvi, et al., 2021). Ploidy level, along with sexual (seed production) and asexual (rhizome growth) reproductive modes, are key traits contributing to the strong environmental tolerance of Phragmites species (Guan et al., 2023; Meyerson et al., 2016; Te Beest et al., 2012). Population with higher genetic diversity, which may correlate with higher ploidy levels, have been found to be more tolerant to high salinity (Sun et al., 2021). The distribution of ploidy levels appears geographically specific, and individuals with the same ploidy level may have formed from different polyploidization events (C. Wang, Liu, Yin, Eller, Brix, Wang, Salojarvi, et al., 2021).
Ambient heavy metal pollution is another significant source of stress for plants. Cadmium (Cd), a nonessential and hazardous element, often contaminates aquatic ecosystems due to its water-soluble compounds, which facilitate rapid spread in soil and water sediments (Wright & Welbourn, 1994).Cadmium exposure can severely disrupt plant growth and metabolism, leading to reduced root elongation and biomass, water and nutrient deficiencies, and decreased enzyme activity (Kahle, 1993). In response, plants activate detoxification processes, such as increased synthesis of chelating peptides to sequester cadmium ions and restricted ion transport to compartmentalize cadmium in root vacuoles (Zhu, Li, Duan, Liu, & Chen, 2021). Aquatic plant species can extend their resistance to heavy metal stress through reduced water flow and interactions with rhizosphere microorganisms involved in phytoremediation processes(Javed et al., 2019).
The bioaccumulation of heavy metal has been well studied in P. australis (Bonanno & Giudice, 2010; Březinová & Vymazal, 2022). Common reed demonstrates high tolerance and adaptation to heavy metals by increasing rhizosphere surface area when exposed to polluted sediments (Cicero-Fernández, Peña-Fernández, Expósito-Camargo, & Antizar-Ladislao, 2016). Given its wide distribution range, and significant intraspecific phylogeographic variation, the effect of genetic divergence should be considered when assessing bioaccumulation and stress tolerance. Indeed, different lineages of common reed may exhibit diversified plasticity in their functional and physiological traits, showcasing high adaptability to local environmental conditions. These variations in plasticity may result in distinct responses to environmental stresses, such as temperature fluctuations or changes in CO2 levels (Eller et al., 2017). Although high levels of cadmium can be lethal to plants, lower levels (e.g., 50 μM) may not significantly perturb gene expression in some species, such as rice (Oono et al., 2016). Therefore, including a gradient of cadmium levels in experiments can be helpful for testing stress tolerance, plant responses and phytoremediation potential.
Transcriptomics has proven to be an effective tool for constructing phylogenetic relationships among individuals and detecting local adaptations in diverging species (Pieri et al., 2024). In this study, we aim to use transcriptomic approaches to explore the stress tolerance of individuals resulting from hybridizations between octoploids and tetraploids in contact zones. We address the following questions: 1) Are octoploids more tolerant to abiotic stresses such as salinity than tetraploids? 2) Is there adaptive introgression between ploidy levels that enhances genetic tolerance in hybrids? 3) If adaptive introgression related to abiotic stress tolerance occurs, do the introgressed loci function stably within the hybrid population? To answer these questions, we first constructed a phylogenetic tree encompassing populations of different ecotypes and genetic lineages to determine their evolutionary relationships. We then conducted a genome scan to identify polymorphic loci between the AU and CN lineages that may be under natural selection. Finally, we examined the gene expression profiles of hybrid individuals with similar genetic backgrounds to assess whether stress tolerance remains stable in hybrid populations.