The annotated, chromosome-scale Salicornia depressa (American pickleweed) genome

Salicornia depressa (American pickleweed) is the most widespread member of its salt-loving genus in North America. Pickleweeds typically colonize high marsh areas that tides make highly saline. Most other salt marsh plants cannot withstand the same salt pressure, so these bare patches are free from competitive pressures. Understanding the genetic origin of American Pickleweed’s high salinity adaptations has potential application to salt-tolerant agriculture and salt marsh conservation but requires genome resources to study. S. depressa is a tetraploid species, which presents unique challenges to traditional genome assembly pipelines. We present a high-quality, chromosome-scale reference genome of S. depressa and the pipeline we used to assemble it. Our reference is phased to each of the tetraploid’s ancestral subgenomes with a scaffold N50 of 69.3 Mb, BUSCO completeness of 96.4%, and k-mer completeness of 98.4%. The subassemblies are evenly split, with subassembly A containing 56.7% and subassembly B containing 59.1% of genomic k-mers. Our gene annotation identifies 80,883 genes and our methylome annotation contains 2.5 million methylated cytosines. We find that gene and methylation density are negatively correlated across the genome. We also assembled and annotated a chloroplast assembly which includes all expected photosystem, tRNA, and rRNA genes. We provide a guide to our successful assembly pipeline involving >30 programs. Our reference and annotation join resources for three other Salicornia species, allowing global scale ecological-evolutionary studies.