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. Salicornia is a halophytic flowering plants in the family Amaranthaceae. Here, the authors report chromosome-scale genome assemblies for six Salicornia species and reveal subgenome diversity, species boundaries and signatures of halophyte adaptation.
Yun-Chuan Wang, Laxman Adhikari, Lina María Cáceres Leal et al.· Nature Communications· 0 citations
ABSTRACT Earth's biodiversity is central to ecosystem health and resilience, providing essential functions and services. The Red Sea is a recognised marine biodiversity hotspot with high endemism and unique environmental conditions that support extensive but poorly resolved biodiversity. Here, we applied metagenomic analyses to sediment samples collected from coastal to deep‐sea environments during the Red Sea Decade Expedition 2022 to characterise biodiversity across the web of life. From a single shotgun assay per sample, this approach simultaneously characterised the sediment microbiome, which amplicon‐based surveys recover only through parallel, targeted assays, and extended detection to higher eukaryotes. Using high‐throughput sequencing, we generated 12.8 billion sequences, revealing taxa covering all domains of life. Although eukaryotic sequences represented only 0.7% of the taxonomically annotated dataset, we managed to identify 679 eukaryotic families. Prokaryotic diversity was high, as expected in a basin‐scale sampling coupled with high sequencing depth, with groups covering a wide functional array. Community structure analyses revealed depth‐driven stratification of open‐ocean benthic microbial communities and latitudinal structuring of coastal benthic eukaryotes. Overall, this dataset provides an empirical reliability–coverage trade‐off with direct consequences for the design of eDNA monitoring programmes targeting conservation‐priority taxa, and clear priorities for taxa specific reference‐database expansion.
Elisa Laiolo, Christopher A. Hempel, Balegh A. Abukabbos et al.· Environmental Microbiology· 0 citations
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