A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing

Frontiers in Plant Science
Spencer P HuntPeter J Maughan

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." Lo...Continue Reading

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Datasets Mentioned

BETA
SRR11123183
SRR11123172
SRR11123170
345962
SRR11123175
SRR11147367
SRR11147375
PRJNA607334
SRR11147376

Methods Mentioned

BETA
Whole Genome Sequencing
Hi-C
DNA Assay
proximity ligation sequencing
RNA-seq
Assay
PCR
our
flow cytometry

Software Mentioned

Albacore
Picard
HiRiSE TM
CoGe
StringTie
PCAngsd
Bowtie2
RepeatModeler
AUGUSTUS
MinKNOW

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