How did the amphibious <i>Eleocharis vivipara</i> acquire its C₃–C₄ photosynthetic plasticity?

The recently published study by Liu et al. (2024) on a high-quality, chromosome-level genome of Eleocharis vivipara provides new insight into the multiple evolution of C4 photosynthesis in Cyperaceae and in particular in Eleocharis. The species studied has the rare feature of alternately using C3 photosynthesis underwater and C4 photosynthesis on land (Ueno et al., 1988), making it an exciting model to better understand the genetic control and evolution of the C4 trait and, in particular, the evolutionary challenge to switch from C3 to C4 photosynthesis from the aquatic to the terrestrial environment. This may imply both the control of genes involved in the C4 pathway and deep cellular anatomical changes. Alternately using C3 or C4 photosynthesis may also lead to evolutionary trade-offs (e.g., optimization of photosynthetic enzymes in contrasting C3 and C4 biochemical contexts). Maintaining C3 and C4 genes may therefore be necessary; hybridization (e.g., allopolyploidization) between non-C4 and C4 taxa could have been involved to favor the emergence of such facultative photosynthetic strategy. Wide variation in photosynthetic type has been previously reported within Eleocharis (Murphy et al., 2007). Phylogenetics of this genus have supported the idea that C4 photosynthesis has been derived at least three times, with several cases of possible reversion to C3-like or intermediate pathways and several additional origins of C3–C4 intermediate photosynthetic pathways (Roalson et al., 2010). Inferring such transitions based solely on species phylogenies, however, can be tricky (Christin et al., 2010), requiring consideration of other evidence. In another study, genes encoding C4 PEPCs were investigated in two phylogenetically distant C4 species, Eleocharis baldwinii and E. vivipara (Besnard et al., 2009). Unexpectedly, C4 PEPC genes have recently diverged between the two Eleocharis species, supporting the idea that one of them has borrowed this core C4 gene from the other lineage by hybridization or by a horizontal transfer event, as widely reported in grasses (Bianconi et al., 2020). As E. vivipara belongs to a monotypic C4 lineage, the C4 PEPC genes were probably obtained from the more diverse E. baldwinii clade (Roalson et al., 2010; Larridon et al., 2021). In their study, Liu et al. (2024) used genomic and transcriptomic data to document karyotype evolution within the Cyperaceae family and the origin of C4 genes in E. vivipara, and then to achieve new insight into the genetic control of C3 and C4 photosynthesis in this amphibious species. This group first demonstrated that holocentromeric chromosomes in Eleocharis should favor genomic reorganizations and, in turn, hybrid speciation. This could have promoted gene exchange between distantly related lineages. They also demonstrated that, although E. vivipara is tetraploid, C4 genes were evenly distributed in the two subgenomes A and B, strongly suggesting that C4 photosynthesis had predated the polyploidization event in its ancestor. Liu et al. then dated a whole genome duplication (WGD) at 3.5 Mya based on the divergence between the two subgenomes. However, allopolyploidy between two C4 taxa should be at the origin of the currently sequenced accession, meaning that the WGD could have been a more recent event than this estimate suggested. Finally, they demonstrated that epigenetic control allowed integrated responses to water deprivation during the C3 to C4 switch involving various biological processes related to photosynthesis and anatomy. This also confirmed that the transition from aquatic to terrestrial environment involved a huge reprogramming of gene expression. While Liu et al. (2024) have brought very important insight into the understanding of the (epi)genetic determinants governing photosynthetic transition and chromosomal organizations favoring hybrid stability, some questions remain open, in particular on when and how did the ancestor(s) of E. vivipara acquire C4 photosynthetic traits. This is important to better understand the multiple evolution of the C4 trait within Eleocharis. Was the diploid ancestor of E. vivipara already a facultative C3 versus C4 species? When did the exchange of C4 genes between distantly related extent C4 Eleocharis lineages, as suggested by previous phylogenetic works, occur? How extensive were the genomic reorganizations following the WGD event detected by Liu et al., notably with regard to gene retention from each ancestral Eleocharis genome (especially for C4 genes)? Liu et al. provide new genomic and transcriptomic resources that will be extremely useful to address such questions with a phylogenomic approach (e.g., Dunning et al., 2019). By reconstructing gene phylogenies and comparing the genome location and the synteny of DNA fragments carrying C4 genes between different Eleocharis species, especially between E. vivipara and close relatives of E. baldwinii, it would now be possible to retrace the evolutionary history of core C4 genes within the genus, as well as to study the genomic reorganizations that are particularly frequent in this clade (Roalson, 2008; Liu et al., 2024). The work of Liu et al. thus represents an important step toward a better understanding of C3–C4 photosynthetic plasticity in an amphibious lineage. Such knowledge could have major application in the improvement of crops growing under various hydric conditions (e.g., rice), although consideration of the ecological consequences of such manipulations should still be measured. G.B. is supported by LabEx TULIP (ANR-10-LABX-0041) and CEBA (ANR-10-LABX-25-01) both managed by the French Agence nationale de la recherche. The authors declare no conflict of interest.