Abstract
Atriplex hortensis (2n = 2x = 18, 1C genome size ∼1.1 gigabases), also known as garden orach and mountain-spinach, is a highly nutritious, broadleaf annual of the Amaranthaceae-Chenopodiaceae alliance (Chenopodiaceae sensu stricto, subfam. Chenopodioideae) that has spread in cultivation from its native primary domestication area in Eurasia to other temperate and subtropical regions worldwide. Atriplex L. is a highly complex but, as understood now, a monophyletic group of mainly halophytic and/or xerophytic plants, of which A. hortensis has been a vegetable of minor importance in some areas of Eurasia (from Central Asia to the Mediterranean) at least since antiquity. Nonetheless, it is a crop with tremendous nutritional potential due primarily to its exceptional leaf and seed protein quantities (approaching 30%) and quality (high levels of lysine). Although there is some literature describing the taxonomy and production of A. hortensis, there is a general lack of genetic and genomic data that would otherwise help elucidate the genetic variation, phylogenetic positioning, and future potential of the species. Here, we report the assembly of the first high-quality, chromosome-scale reference genome for A. hortensis cv. “Golden.” Long-read data from Oxford Nanopore’s MinION DNA sequencer was assembled with the program Canu and polished with Illumina short reads. Contigs were scaffolded to chromosome scale using chromatin-proximity maps (Hi-C) yielding a final assembly containing 1,325 scaffolds with a N50 of 98.9 Mb – with 94.7% of the assembly represented in the nine largest, chromosome-scale scaffolds. Sixty-six percent of the genome was classified as highly repetitive DNA, with the most common repetitive elements being Gypsy-(32%) and Copia-like (11%) long-terminal repeats. The annotation was completed using MAKER which identified 37,083 gene models and 2,555 tRNA genes. Completeness of the genome, assessed using the Benchmarking Universal Single Copy Orthologs (BUSCO) metric, identified 97.5% of the conserved orthologs as complete, with only 2.2% being duplicated, reflecting the diploid nature of A. hortensis. A resequencing panel of 21 wild, unimproved and cultivated A. hortensis accessions revealed three distinct populations with little variation within subpopulations. These resources provide vital information to better understand A. hortensis and facilitate future study.
Highlights
Introduction(2n = 9x = 18), known as garden orach or mountain-spinach, is a highly nutritious, leafy annual plant
Atriplex hortensis L. (2n = 9x = 18), known as garden orach or mountain-spinach, is a highly nutritious, leafy annual plant
We annotated the genome with a deeply sequenced transcriptome from various A. hortensis plant tissues, and we demonstrate the quality of the chromosomelevel genome assembly and annotation using Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simão et al, 2015) to assess the completeness of the assembled genome
Summary
(2n = 9x = 18), known as garden orach or mountain-spinach, is a highly nutritious, leafy annual plant It is a moderately xero-halophytic species that is resistant to salinity, a wide range of temperatures, and drought. Originating in Eurasia, A. hortensis has been a minor vegetable food source in multiple areas of the Trans-Himalayan region and has since become naturalized throughout the Americas. It exhibits incredible variation in pigmentation as a result of its variable content of betalains, as well as substantial differences in height and seed production (Tanaka et al, 2008; Simcox and Stonescu, 2014). Despite its affinity for low to moderate saline areas where it has little competition from non-halophytes, A. hortensis can grow where total soluble salts are low, making it well suited to a multitude of different environments (Welsh and Crompton, 1995)
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