Complete genome sequence assembly elucidates evolution and regulation of 5S rDNA loci in the greater duckweed Spirodela polyrhiza

Abstract

We resolved the molecular architecture of the 5S rDNA loci in an aquatic monocot Spirodela polyrhiza. Measurements of fluorescence in situ hybridization signals revealed two loci with 5S rDNA clusters. A combination of the extra-long DNA reads and conventional sequencing of 5S rDNA repeats allowed the assembling of complete loci sequences located on ChrSp6 and ChrSp13. The homologous chromosomes of the ChrSp6 locus contain clusters of 40 and >60 copies of 5S rDNA repeat units with intergenic spacer (IGS) of 400 bp. The ChrSp13 locus is represented by 5S rDNA clusters of rRNA genes spaced by IGSs of 1,056 or 1,069 bp arranged in two sub-clusters, suggesting a different rate of repeat homogenization between loci. The G/C-rich 5S rDNA arrays in both loci are embedded in A/T-enriched chromosome regions with possible regulatory functions. The TATA-like boxes of the 5S rDNA repeat on ChrSp6 and ChrSp13 exhibit different affinities for the TATA-binding protein in 3D modeling of protein/DNA interactions, suggesting a locus-specific regulation of rRNA transcription. Our findings shed light on the molecular architecture of the 5S rDNA loci, which could foster an innovative era for the principles of evolution and regulation of rRNA genes in plants.