Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta

Yellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed, and while native to North America, it is distributed across Europe, Asia, and Africa. To date, only 2 other genomes from the Oxalidaceae family have been published, star fruit (Averrhoa carambola L.) and Oxalis articulata Savigny. Here, we present a chromosome-scale assembly for O. stricta, revealing its allotetraploid nature and synteny within its 2 subgenomes as well as synteny with A. carambola and O. articulata. Using Oxford Nanopore Technologies long-read sequences coupled with chromatin capture sequencing, we generated a 436 Mb chromosome-scale assembly of O. stricta with a scaffold N50 length of 36.2 Mb that is anchored to 12 chromosomes across the 2 subgenomes. Assessment of the final genome assembly using the Long Terminal Repeat Assembly Index yielded a score of 13.12, and assessment of Benchmarking Universal Single Copy Orthologs revealed 99.6% complete orthologs; both metrics are suggestive of a high-quality reference genome. Total repetitive sequence content in the O. stricta genome was 39.7% with retroelements being the largest class of transposable elements. Annotation of protein-coding genes yielded 61,550 high-confidence genes encoding 115,089 gene models. Synteny between the 2 O. stricta subgenomes was present in 93 syntenic blocks containing 40,750 genes, of which, 76.47% were present in 1:1 syntenic relationships between the 2 subgenomes. The availability of an annotated chromosome-scale high-quality genome assembly for O. stricta will provide a launching point to understand the high fecundity of this weed and provide further foundation for comparative genomics within the Oxalidaceae.