Polyploid genome assembly ofCardamine chenopodiifolia
Abstract
Background
Cardamine chenopodiifoliais an amphicarpic plant that develops two fruit morphs, one above and the other below ground. Above-ground fruit disperse their seeds by explosive coiling of the fruit valves, while below-ground fruit are non-explosive. Amphicarpy is a rare trait that is associated with polyploidy inC. chenopodiifolia. Studies into the development and evolution of this trait are currently limited by the absence of genomic data forC. chenopodiifolia.
Results
We produced a chromosome-scale assembly of the octoploidC. chenopodiifoliagenome using high-fidelity long read sequencing with the Pacific Biosciences platform. We successfully assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mbp and an N50 of 18.8 kbp (estimated genome size from flow cytometry: 626 Mbp). We assessed the quality of this assembly using genome-wide chromosome conformation capture (Omni-C) and BUSCO analysis (97.1% genome completeness). Additionally, we conducted synteny analysis to infer thatC. chenopodiifolialikely originated via allo-rather than auto-polyploidy and phased one of the four sub-genomes.
Conclusions
This study provides a draft genome assembly forC. chenopodiifolia, which is a polyploid, amphicarpic species within the Brassicaceae family. This genome offers a valuable resource to investigate the under-studied trait of amphicarpy and the origin of new traits by allopolyploidy.
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