The Complete External Transcribed Spacer of 18S-26S rDNA: Amplification and Phylogenetic Utility at Low Taxonomic Levels in Asteraceae and Closely Allied Families

The apparent recency of diversification of Californian Lessingia (Compositae, Astereae) makes the genus a particularly interesting group for evolutionary investigation. Here we focus on the major evolutionary lineages within Lessingia (sensu Lane 1992) and the higher-level relationships of the genus and presumed close relatives using sequence data from the 18S–26S nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) region and the 3’ end (561–563 bp) of the external transcribed spacer (ETS). We present new 3‘ETS primers that are useful across Astereae and examine the phylogenetic utility of the 3‘ETS in Lessingia and close relatives. In Lessingia, the 3‘ETS region appears to have evolved up to 1.4 times more rapidly by nucleotide substitution than has the ITS region. Our results show that data from the ETS greatly augments data from the ITS region; the combined data set yields the best resolved and best supported molecular trees for Lessingia. These topologies lead us to five conclusio...

https://bioone.org/journals/systematic-botany/volume-26/issue-1/0363-6445-26.1.168/Higher-Level-Relationships-and-Major-Lineages-of-Lessingia-Compositae-Astereae/10.1043/0363-6445-26.1.168.pdf

Higher-Level Relationships and Major Lineages of Lessingia (Compositae, Astereae) Based on Nuclear rDNA Internal and External Transcribed Spacer (ITS and ETS) Sequences

The ribosomal RNA gene region of Nosema apis (Microspora) : DNA sequence for small and large subunit rRNA genes and evidence of a large tandem repeat unit size

Ribosomal RNA genes (rDNA) represent a useful tool to study reticulate evolution. In allopolyploid plant species biparental or uniparental inheritance of 35S rDNA was demonstrated. Uniparental inheritance; as a result of differential elimination of one of the parental rDNA, can be accompanied by structural rearrangements of rDNA ofthe other parent and by formation of new rDNA variants. Particularly, homo‐genization of rDNA in allopolyploids appears to be an example of fast concerted evolution of repeated sequences. At the functional level, interaction between parental 35S rDNA loci in hybrids/allopolyploids leads to differential transcription/silencing, known as nucleolar dominance (ND). Depending on the combination of parental species, ND may be strong and stable, or weak, unstable and even reversible. Differential transcription of parental rDNA is regulated via cytosine methylation of DNA, histone modifications, and chromatin remodelling factors, but mechanisms providing discrimination of paren...

Ribosomal DNA in plant hybrids: Inheritance, rearrangement, expression

rDNA intergenic region from Arabidopsis thaliana structural analysis, intraspecific variation and functional implications

Restriction enzyme analysis and cloning of the 18S, 5.8S, and 25S ribosomal RNA genes (rDNA) of the mung bean (Vigna radiata = Phaseolus aureus) reveal length heterogeneity in the repeating units (10-11 kbp) localized within two different regions in the ribosomal spacer. The 1.5-2.0 kbp region flanking the 3' end of the 25S rRNA contains various numbers (8-10) of tandemly arranged 180 bp subrepeats. After DNA sequencing a complex organized length heterogeneous 5' external spacer built up of different numbers of 340 bp subrepeats, each flanked by 52 bp direct repeats, is detected and described for the first time for plant ribosomal DNA repeating units. Sequences occurring in front of and within this repeated structure (elements II-IV) can be combined with the motifs P1, P2, and P3. These exhibit a strong similarity to transcription initiation sites specific for RNA polymerase I described for other plant and animal rDNA investigated to date. Transcription products complementary to the complex repeated structures are detected by hybridization to total nuclear RNA. The 9 bp element V located in fron of the first 340 bp region appears in duplicated form as a direct repeat with sequence similarity to SV40 (or RNA polymerase II) enhancer sequences.

G. Von Waldburg

Papers

Complex organization of the length heterogeneous 5′ external spacer of mung bean (Vigna radiata) ribosomal DNA