Octoploid genome decoded

MPIPZ research groups collaborate to produce a fully phased, chromosome-scale genome assembly of Cardamine chenopodiifolia

January 17, 2025

The genome of C. chenopodiifolia is octoploid. Compared to the 10 chromosomes in diploid cells of Arabidopsis, this small weed has a whopping 64 chromosomes in each cell. In a recent study published in Gigabyte, Dr Angela Hay and colleagues – from the Max Planck Institute for Plant Breeding Research in Cologne, Germany – assembled every chromosome of the four sub-genomes that comprise the octoploid C. chenopodiifolia genome.

Polyploidy – or whole-genome duplication – is a common feature of plant genomes, including many of the plants we eat, such as wheat and potato. A diploid species (such as humans) inherits one copy of every chromosome from both mom and dad. On the other hand, an octoploid species inherits four copies of every chromosome from each parent.

Multiple copies of each chromosome make it challenging to assemble the genome and also to work out which set of chromosomes belong together as separate sub-genomes. Mohamed Awad tackled the first problem using GALA – a Gap-free long-read assembly tool – developed in the Gan research group. This resulted in an almost complete chromosome-level genome of 597 Mb. The second challenge of separating each chromosome copy into its correct sub-genome was accomplished using a gene tree approach by Nikita Tikhomirov from the Novikova research group.

It became clear from structural differences between chromosome copies that C. chenopodiifolia is likely to be allopolyploid, meaning that it arose from the hybridization of different species. This introduces a lot of genetic diversity into the genome and is one reason why polyploidy is often associated with the evolution of novel traits.

One such trait in C. chenopodiifolia is amphicarpy. This means the plant bears two types of fruit, one above and another buried below ground. This rare trait provides each plant with two very different means of seed dispersal: aerial seedpods are explosive, firing many seeds out across a large area, while underground fruit are non-explosive and produce fewer, larger seeds that are buried below ground. Aurélia Emonet, in the Hay research group, is keen to understand more about this striking trait and this motivated her to establish C. chenopodiifolia as an experimental system.

With the genome assembly of C. chenopodiifolia in hand, scientists can now study amphicarpy more easily and ask how this novel trait evolved in the context of allopolyploidy and also ask more general questions about trait evolution via polyploidy.

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