The 8th International Conference on Water Resource and Environment (WRE 2022)

Abstract: Because of their function to produce the RNA components required for assembling ribosomes, the riboprotein structures responsible for protein synthesis, ribosomal DNA (rDNA) plays a pivotal in all eukaryotic cells. Plants typically have two types of rDNA loci: 35S rDNA loci containing clusters of tandemly repeated units composed of conserved sequences encoding three linked rRNA genes (18S-5.8S-25S) separated by more diverse intergenic spacers (IGSs), and 5S rDNA loci containing tandem copies of 5S rRNA genes separated by non-transcribed spacers (NTS). Due to its high copy number, conserved coding sequence, and more rapidly evolving spacer sequences, the rDNA has become a favorite subject for studies related to plant systematics, evolution, and biodiversity. Our research on rDNA in aquatic duckweed plants (Lemnaceae) and water lettuce, Pistia stratiotes (Araceae), showed a number of specific features. Genome surveys of two ancient duckweed species, Spirodela polyrhiza [1] and Spirodela intermedia [2] revealed a very low representation of 35S and 5S rRNA genes, at around 100 copies per genome, compared to the thousands of copies usually present in land plants. Molecular cloning and nucleotide sequencing of 35S rDNA of all three species displayed molecular architecture typical for other plants with high conservation of the sequences coding for 18S, 5.8S, and 25S rRNAs and significant divergence of large intergenic spacer (IGS) region. Comparative analysis of the IGS in two duckweed species demonstrated relatively low intra- and inter-genomic heterogeneity, high GC content, and an unorthodox molecular structure of usually conserved rRNA transcription initiation site (TIS). The latter finding is intriguing considering that the TIS in other characterized duckweed species representing two younger genera (Lemna and Wolffia), as well as in Pistia stratiotes [3] has a canonic TATAGGGG signature typical for the majority of land species. Characterization of 5S rDNA revealed two major length variants of the gene repeat units in genomes of S. polyrhiza, S. intermedia, and Pistia stratiotes. Analyses of 5S rDNA in twenty S. polyrhiza ecotypes from five continents showed that European ecotypes contain a predominant NTS type of about 1060 bp, whereas the Asian and American ecotypes predominantly have a 400-bp NTS. The two NTS length variants differ in their cis element repertoire, which may influence transcription of the linked 5S rRNA genes. Comprehensive analysis of 5S rDNA units in Pistia stratiotes demonstrated an unusual, mosaic arrangement of genes with different types of NTS within the locus, further challenging the postulated homogenization of rDNA repeats within the rDNA loci. In summary, our findings put duckweeds in the spotlight for research on the molecular evolution of the rDNA, promising new insights into basic principles of organization and regulation of rRNA genes in plants.

1. Michael T, Bryant D, Gutierrez R, Borisjuk N et al. Comprehensive definitions of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies. The Plant Journal, 2017, 89: 617-637.
2. Hoang PTN, Fiebig A, Novák P, Macas J, Cao HX, Stepanenko A, Chen G, Borisjuk N, Scholz U, Schubert I. Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Scientific Reports, 2020, 10: 19230.
3. Stepanenko A, Chen G, Hoang PTN, Fuchs J, Schubert I, Borisjuk N. The ribosomal DNA loci of the ancient monocot Pistia stratiotes L. (Araceae) contain different variants of the 35S and 5S ribosomal RNA gene units. Front. Plant Sci. 2022, 13:819750.