A T2T gap-free genome provides insights into tetraploid Salicornia europaea evolution and aquaporin function in stress tolerance

Abstract The model halophyte Salicornia europaea (2n = 4x = 36) lacks high-quality genomic information, hindering in-depth analysis of its salt resistance mechanisms. In this study, we report a complete telomere-to-telomere (T2T) gap-free genome of tetraploid S. europaea using deep coverage ultralong Oxford Nanopore Technology (ONT), PacBio HiFi reads, and High-Throughput Chromatin Conformation Capture (Hi-C) scaffolding technologies. The S. europaea genome is 984.58 Mb, containing 41,963 annotated protein-coding genes. Repeat sequences make up 70.11% of the S. europaea genome, with transposable elements (TEs) being the most abundant. We identified structural variations (SVs) in diploid and tetraploid species and found 65% of subgenome A-associated SVs are localized to intergenic regions, while 79% of subgenome B-associated SVs are in intronic regions. Analysis of gene family expansion and contraction revealed that 7 gene families are commonly expanded in diploid and tetraploid species, suggesting their potential functional significance during evolution. Moreover, we identified aquaporins in the diploid and tetraploid genomes, and they exhibit high synteny. Heterologous expression of SeTIP2;1, SeTIP2;2, and SeTIP2;4 conferred salt and drought tolerance in Arabidopsis (Arabidopsis thaliana), accompanied by increased water status. SeTIP2;1 and SeTIP2;2 OE lines also showed improved K+/Na+ ratios in leaves, reduced malondialdehyde content, greater osmolyte accumulation (proline and soluble sugars), and increased chlorophyll content under both salt and drought stresses. Our findings provide deeper insights into polyploidization and evolution in the S. europaea genome and contribute important genetic resources for studying salt resistance mechanisms in S. europaea.