We present a genome assembly of Aponogeton distachyos (Cape pondweed; Streptophyta; Magnoliopsida; Alismatales; Aponogetonaceae). The assembly consists of two haplotypes with total lengths of 4,442.33 megabases and 4,498.62 megabases. Haplotypes 1 and 2 each contain 18 chromosomal pseudomolecules; these account for 96.45% and 96.42% of their respective sequences. The mitochondrial sequence has a length of 231.09 kilobases and the plastid genome assembly has a length of 153.52 kilobases. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.
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