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.