Multilevel genomic constraints shape nuclear tRNA gene organization in plants

Area of Science:

• Genomics
• Molecular Biology
• Evolutionary Biology

Background:

• Transfer RNAs (tRNAs) are crucial for protein synthesis, with their abundance and diversity impacting translation efficiency and accuracy.
• tRNA gene (tDNA) copy number and genomic organization influence tRNA abundance, but nuclear tDNA organization principles are not well understood.
• Understanding tDNA organization is key to deciphering the regulation of the translational system.

Purpose of the Study:

• To analyze nuclear tDNA repertoires and organization across diverse photosynthetic eukaryotes.
• To identify conserved and lineage-specific principles governing nuclear tDNA organization.
• To develop a web application for standardized, genome-scale analysis of tDNA organization.

Main Methods:

• Comparative genomic analyses at sequence, chromosomal, and genome-wide scales.
• Analysis of nuclear tDNA repertoires in 53 photosynthetic eukaryotes and 7 non-plant outgroups.
• Development of the ShinytRNA web application for interactive tDNA organization exploration.

Main Results:

• Nuclear tDNA copy numbers vary over two orders of magnitude, but relative tRNA family representation is conserved, showing evolutionary constraints on tDNA dosage.
• Angiosperm tDNAs show coordinated enrichment of cis-regulatory elements for RNA polymerase III transcription.
• Chromosomal tDNA distribution is generally dispersed with homogeneous spacing, exclusion from centromeres, and occasional clustering, scaling with genome size.

Conclusions:

• Conserved evolutionary constraints shape tDNA dosage across lineages.
• Nuclear tDNA organization in plants involves both conserved principles and lineage-specific adaptations.
• Genomic constraints significantly influence the evolution of nuclear tDNA repertoires.