Chromosome-scale genomes and population resequencing resolve subgenome diversity and halophyte adaptation in Salicornia
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.
Authors
- Salim Bougouffa (ORCID: https://orcid.org/0000-0001-9218-6452)
- Denisa Beránková (ORCID: https://orcid.org/0000-0002-1066-0577)
- Joost T. van Dongen (ORCID: https://orcid.org/0000-0001-7944-9289)
- Eva Hřibová (ORCID: https://orcid.org/0000-0002-6868-4344)
- Dongryung Lee (ORCID: https://orcid.org/0000-0002-0783-5911)
- Mark Tester (ORCID: https://orcid.org/0000-0002-5085-8801)
- Yunchuan Wang (ORCID: https://orcid.org/0000-0003-0432-868X)
- Luis F. Rivera (ORCID: https://orcid.org/0000-0003-3978-7640)
- Francisco Molina‐Freaner (ORCID: https://orcid.org/0000-0003-1099-5841)
- Angelina Jordine (ORCID: https://orcid.org/0009-0001-2121-2454)
- Vanessa Melino (ORCID: https://orcid.org/0000-0003-2742-5079)
- Xiaofei Zeng (ORCID: https://orcid.org/0000-0001-8127-3825)
- Davide De Battisti (ORCID: https://orcid.org/0000-0001-7847-0414)
- Yveline Pailles (ORCID: https://orcid.org/0000-0003-2283-2759)
- Jesse Poland (ORCID: https://orcid.org/0000-0002-7856-1399)
- Corina Hayano‐Kanashiro (ORCID: https://orcid.org/0000-0001-7846-6124)
- Laxman Adhikari (ORCID: https://orcid.org/0000-0001-9507-5117)
- Jana Čížková (ORCID: https://orcid.org/0000-0001-7787-1849)
- Xin Gao (ORCID: https://orcid.org/0000-0002-7108-3574)
- Lina María Cáceres Leal (ORCID: https://orcid.org/0009-0003-6408-2260)
- Nataliya Kovalchuk (ORCID: https://orcid.org/0000-0003-0285-2859)
- Huirong Duan
- Gabriele Fiene
- Noha Saber
- Turki A. Al-Turki
Institutions
- Australian Centre for Plant Functional Genomics (AU)
- Universidad de Sonora (MX)
- Agricultural Genomics Institute at Shenzhen (CN)
- Saudi Heart Association (SA)
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Czech Academy of Sciences, Institute of Experimental Botany (CZ)
- Ospedali Riuniti Umberto I (IT)
- Pusan National University (KR)
- King Abdullah University of Science and Technology (SA)
- University of Newcastle Australia (AU)
- RWTH Aachen University (DE)
- Universidad Nacional Autónoma de México (MX)
Publication Details
- Journal
- Nature Communications
- Published
- 2026-09-11
- DOI
- https://doi.org/10.1038/s41467-026-77346-x
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 0.00