Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance

Area of Science:

• Plant genomics
• Evolutionary biology
• Chromatin structure

Background:

• The Melanthiaceae family exhibits significant variation in genome size.
• Understanding genome size evolution requires detailed genomic analysis of key species.

Purpose of the Study:

• To characterize genome size evolution in Melanthiaceae.
• To assemble and analyze the giant genome of Paris polyphylla var. yunnanensis.
• To investigate the structural basis of giant chromosome formation.

Main Methods:

• Whole-genome sequencing of Paris polyphylla and Veratrum dahuricum.
• Hierarchical bottom-up chromosome assembly strategy.
• Hi-C interaction analysis to infer chromatin structure.
• Gene family expansion analysis.

Main Results:

• Successfully assembled the giant genome of P. polyphylla (54.58 Gb) and V. dahuricum (3.93 Gb).
• Identified a higher-order helical chromatin structure in P. polyphylla with ~250 Mb per turn.
• P. polyphylla lacks recent whole-genome duplications since divergence from V. dahuricum.
• Significantly expanded gene families in P. polyphylla are enriched in DNA repair pathways.

Conclusions:

• Giant chromosome evolution in P. polyphylla is attributed to chromatin organization rather than recent whole-genome duplication.
• The expanded DNA repair gene families may play a role in maintaining the integrity of the giant genome.
• This study provides a high-quality genome resource and insights into the mechanisms of giant chromosome retention.