LB 20-215 - Genome profiling of Salicornia depressa: a potential tool for phytoremediation and marsh restoration

Background/Question/Methods:

Salicornia depressa is a marsh pioneer plant species adapted to high salinity environments. This tolerance is in part due to nonspecific antiporters that pump positively charged metal ions into storage vacuoles within the plant’s vascular tissue. Because these antiporters are nonspecific, S. depressa could be used as a tool in the remediation of heavy metals, including lead, arsenic, and nickel, during the process of salt marsh ecological restoration. To support our study of the genetic basis of phytoremediation-related traits in S. depressa and their application to marsh restoration, we are planning to assemble a reference genome. To inform our assembly we started with one lane of whole genome Illumina sequencing and used Smudgeplot and GenomeScope2.0 to estimate ploidy, length, and heterozygosity of the S. depressa genome. We also performed root tip chromosome squashes and fluorescence microscopy to resolve discrepancies between our results and the published literature.

Results/Conclusions:

Our sequence profiling results demonstrate strong evidence that S. depressa is a diploid, with a genome length of approximately 1.13 Gbp and 6.87% heterozygosity. This observation conflicts with previously published data that the species is tetraploid based on root tip chromosome squashes from Atlantic coast populations in the 1980s, including two in Maine and two in Massachusetts. Our own root tip chromosome squashes support our sequencing results: it appears that at least one Boston-area population of S. depressa is diploid with n = 9 chromosomes. These results will inform the sequencing and assembly of the diploid S. depressa genome to support our population and ecological genomic work with this species. Development of S. depressa as a resource for ecological restoration projects will also help offset contamination and degradation of Atlantic coastal salt marshes. Further population sampling is needed to determine if Atlantic coast populations of S. depressa contain cryptic polyploidy or if the previous estimates were incorrect, ascribed to a species with similar morphology, or sampled individuals have evolved since the 1980s.