Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia.

Yunchuan Wang, Laxman Adhikari, Lina María Cáceres Leal, Nataliya Kovalchuk, Jana Čížková, Denisa Beránková, Noha Saber, Gabriele Fiene, Turki A Al-Turki, Luis F Rivera, Francisco Molina-Freaner, Corina Hayano-Kanashiro, Dongryung Lee, Angelina Jordine, Joost T van Dongen, Davide De Battisti, Huirong Duan, Xiaofei Zeng, Salim Bougouffa, Xin Gao, Yveline Pailles, Jesse Poland, Eva Hřibová, Mark Tester, Vanessa J Melino

Journal: Nature communications 2026;17(1):

PMID: 42728248

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Abstract

Amid escalating water scarcity and groundwater depletion, halophytes such as Salicornia (Amaranthaceae) represent valuable models for extreme salt tolerance and hold promise for saltwater-based agriculture. Here, we show chromosome-scale genome assemblies for six Salicornia species, revealing four distinct subgenomes, reconciling our assemblies with two existing reference genomes (S. ramosissima UK and S. europaea China), correcting chromosome numbering and orientation. Comparative analyses across ploidy levels demonstrate genome expansion in North American lineages driven by Gypsy retrotransposons, and lineage-specific expansions of two gene families implicated in stress metabolism. Phylogenetic and population-structure analyses of a global resequencing panel of 318 accessions resolve interspecific relationships and establish curated germplasm collections for future crop breeding. Genetic analyses uncover a contrasting population-genetic signal on chromosome 6A between two species, highlighting an OSCA calcium-permeable channel gene as a candidate locus for osmotic adaptation. Together, these resources establish a genomic framework for Salicornia that supports evolutionary studies of halophyte adaptation and crop development.

Address: Plant Science Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.; Plant Science Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.; Australian Plant Phenomics Network, Adelaide University, Waite Campus, Glen Osmond, SA, Australia.; Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics, Olomouc, Czech Republic.; Consultant National Afforestation Program, National Center for Vegetation Cover Development & Combating Desertification, Riyadh, Saudi Arabia.; Plant Science Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.; King Abdullah University of Science and Technology (KAUST), KAUST Solar Research Centre, Thuwal, Saudi Arabia.; Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), Hermosillo, Mexico.; Departamento de Investigaciones Científicas y Tecnológicas de la Universidad de Sonora, Hermosillo-Sonora, Mexico.; Plant Science Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.; Department of Plant Bioscience, Pusan National University, Miryang, Republic of Korea.; Molecular Ecology of the Rhizosphere, Institute of Biology I, RWTH Aachen University, Aachen, Germany.; Plant Molecular Systems Biology, Institute of Biology III, RWTH Aachen University, Aachen, Germany.; Molecular Ecology of the Rhizosphere, Institute of Biology I, RWTH Aachen University, Aachen, Germany.; Chioggia Hydrobiological Station 'Umberto D'Ancona', Department of Biology, University of Padova, Chioggia, Italy.; Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.; State Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.; The Bioinformatics Platform, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.; Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia.; Plant Science Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia. [email protected].; Centre for Plant Science, School of Science, University of Newcastle, Callaghan, NSW, Australia. [email protected].

DOI: 10.1038/s41467-026-77346-x

MeSH Terms: Chenopodiaceae, Genome, Plant, Salt-Tolerant Plants, Phylogeny, Chromosomes, Plant, Genetic Variation, Salt Tolerance, Adaptation, Physiological