Polyploid genome assembly of Cardamine chenopodiifolia

Area of Science:

• Plant genomics
• Evolutionary biology
• Reproductive biology

Background:

• Cardamine chenopodiifolia exhibits amphicarpy, producing aerial and subterranean fruits.
• This rare trait is linked to octoploidy, but genomic data has been lacking.
• Understanding amphicarpy's development and evolution is hindered by this data gap.

Purpose of the Study:

• To generate a high-quality, chromosome-scale genome assembly for Cardamine chenopodiifolia.
• To investigate the genomic basis of amphicarpy and octoploidy in this species.
• To provide a foundational resource for future research on plant reproductive strategies.

Main Methods:

• High-fidelity long-read sequencing using the Pacific Biosciences platform.
• Chromosome-level genome assembly and organelle genome sequencing.
• Analysis of structural variation and phasing of homeologous chromosomes to infer allopolyploid origins.

Main Results:

• A chromosome-scale assembly of 597.2 Mb with 32 chromosomes and two organelle genomes was produced.
• Genome completeness was high, estimated at 99.8%.
• Structural variations indicated an allopolyploid origin, and the octoploid genome was phased into four sub-genomes.

Conclusions:

• The chromosome-level genome assembly is a significant resource for studying amphicarpy.
• The findings provide insights into the origin of trait novelties through allopolyploidy.
• This work facilitates further investigation into the genetic mechanisms underlying amphicarpy in Cardamine chenopodiifolia.