Episodic and Ongoing Mechanisms Drive Plastid-Derived Nuclear DNA Evolution in Angiosperms

Area of Science:

• Genomics
• Molecular Evolution
• Plant Biology

Background:

• Nuclear-plastid DNA transfers (NUPTs) are DNA sequences from plastids found in plant nuclear genomes.
• Previous assumptions about NUPT formation and turnover (continuous formation, constant removal rate) were based on limited species data.
• The age and size distributions of NUPTs were expected to follow exponential decay and negative correlation, respectively.

Purpose of the Study:

• To investigate the mechanisms driving the origin and evolution of NUPTs.
• To test the assumptions of continuous formation and constant turnover rate for NUPTs.
• To analyze NUPT distribution, association with genomic features, and evolutionary drivers across major angiosperm lineages.

Main Methods:

• Surveyed nuclear and plastid genomes of 30 angiosperm species.
• Modeled NUPT age and size distributions.
• Examined NUPT linear arrangement within the plastid genome.
• Statistically assessed spatial biases of NUPTs relative to other genomic features, including RNA genes and transposons.

Main Results:

• NUPTs originate from both continuous and episodic formation mechanisms.
• NUPT distribution is uneven across the plastid genome.
• NUPTs show consistent association with rRNA, tRNA, and regulatory RNA genes.
• NUPTs are differentially involved in structural genes and exhibit species-specific proximity to transposon superfamilies.

Conclusions:

• NUPT origin and evolution are more complex than previously assumed, involving episodic events.
• NUPTs are a significant source for noncoding RNA genes and other genomic features.
• The study provides a comprehensive view of evolutionary drivers shaping NUPT dynamics at the genome level.