Research Scientist King Abdullah University of Science and Technology Thuwal, Makkah, Saudi Arabia
The Arabian aquifer system of Saudi Arabia is challenged by groundwater depletion, very low recharge rates and salinization that has led to farm abandonment. Seawater based agriculture provides new opportunities to grow halophytes for food, fodder and fuels (Melino and Tester, 2023, Annual Review of Plant Biology). Edible halophytes such as Salicornia spp. can be rich in oil (15-45%) and protein (25-48%) with the oil suitable for human consumption and the meal for fish-feed composites. Neo-domestication of Salicornia requires genomic and genetic resources. We generated draft genomes of autotetraploid Salicornia bigelovii (2n = 4x = 18, origin USA) and diploid Salicornia europaea (2n= 2x = 9, origin Israel) and studied their transcriptomic and proteomic responses (Salazar et al. 2023, BioRxiv). We now present these genomes as high quality, chromosome-scale reference genomes. Integration of Hi-C reads lead to a total length of 2,043,548,619 bp (S. bigelovii) and 518,560,261 bp (S. europaea) with 99% of the genome anchored to scaffolds. The quality of the assembly was confirmed using chromosome painting and pools of short oligonucleotides covering three chromosomes were designed based on the diploid assembly, fluorescently labeled, and hybridized to mitotic metaphase chromosome spreads of both species. 99.5% of the single copy genes were complete (BUSCO 5.4.7, viridiplantae) yet gene duplication did not explain the enlarged genome size of S. bigelovii relative to the diploid species. The retrotransposon families TY3/Ogre and TY3/Tekay (RepeatExplorer) accounted for 36% of the genome size of S. bigelovii explaining, in part, the genome expansion. To support neo-domestication of this wild species, germplasm across ten countries was collected. Lines were inbred for one to two generations in field trials treating with saline water at 30 dSm-1. Preliminary field trials suggest that the Saudi Arabian species produces a large quantity of very small seeds resulting in the highest comparative yields.