The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units

Abstract

The freshwater plant water lettuce (Pistia stratiotes L.) grows in warm climatic zones and is used for phytoremediation and biomass production. P. stratiotes belongs to the Araceae, an ecologically and structurally diverse early monocot family, but the phylogenetic relationships among Araceae members are poorly understood. Ribosomal DNAs (rDNAs), including the 35S and 5S rDNA, encode the RNA components of ribosomes and are widely used in phylogenetic and evolutionary studies of various plant taxa. Here, we comprehensively characterized the chromosomal locations and molecular organization of 35S and 5S rDNA genes in water lettuce using karyological and molecular methods. Fluorescence in situ hybridization revealed a single location for the 35S and 5S rDNA loci, each on a different pair of the species’ 28 chromosomes. Molecular cloning and nucleotide sequencing of 35S rDNA of P. stratiotes, the first representative Araceae sensu stricto in which such a study was performed, displayed typical structural characteristics. The full-length repeat showed high sequence conservation of the regions producing the 18S, 5.8S, and 25S rRNAs and divergence of the internal transcribed spacers ITS1 and ITS2 as well as the large intergenic spacer (IGS). Alignments of the deduced sequence of 18S rDNA with the sequences available for other Araceae and representatives of other clades were used for phylogenetic analysis. Examination of 11 IGS sequences revealed significant intra-genomic length variability due to variation in subrepeat number, with four types of units detected within the 35S rDNA locus of the P. stratiotes genome (estimated size 407 Mb/1C). Similarly, the 5S rDNA locus harbors gene units comprising a conserved 119-bp sequence encoding 5S rRNA and two types of non-transcribed spacer (NTS) sequences. Type I was classified into four subtypes, which apparently originated via progressive loss of subrepeats within the duplicated NTS region containing the 3’ part of the 5S rRNA gene. The minor Type II NTS is shorter than Type I and differs in nucleotide composition. Some DNA clones containing two or three consecutive 5S rDNA repeats harbored 5S rDNA genes with different types of NTSs, confirming the mosaic composition of the 5S rDNA locus.

Contrasting patterns of 5S rDNA repeats in European and Asian ecotypes of greater duckweed, Spirodela polyrhiza (Lemnaceae)

“…However, the 2-D secondary structure model built for the S. polyrhiza , following a stem–loop architecture that is typical for plants, showed a characteristic difference in the β domain ( Figure 3 ). This difference in the β domain was previously observed in Landoltia and Pistia ( Chen et al., 2021 ; Stepanenko et al., 2022 ) and in species from the Asteraceae family ( Garcia et al., 2010 ). In particular, in addition to a smaller loop C compared to the majority of plants, these species have an additional minor loop between loops B and C.…”

“…The ribosomal DNA (rDNA) has become a favorite molecular target in studies related to plant systematics, evolution, and biodiversity and is used as a genome-specific marker in allopolyploids and hybrids ( Borisjuk et al., 1988 ; Stadler et al., 1995 ; Mahelka et al., 2017 ; Volkov et al., 2017 ; Stepanenko et al., 2022 ). The 35S and 5S rDNA loci are organized in clusters of tandemly repeated units composed of conserved sequences that are transcribed to produce rRNAs; these are separated by diverse intergenic spacers (NTSs), which are not transcribed ( Volkov et al., 2003 ; Hemleben et al., 2021 ).…”

Biodiversity of Duckweed (Lemnaceae) in Water Reservoirs of Ukraine and China Assessed by Chloroplast DNA Barcoding

“…Phylogenetic analysis of our 69 duckweed specimens using ATP and PSB sequences separately showed no conclusive results. Therefore, we performed a combined ATP and PSB analysis of 70 taxa, including Pistia stratiotes [ 42 ] as an outgroup species. The combined data matrix included 1197 characters divided in two partitions: 1–560 for ATP and 561–1197 for PSB , of which 751 were constant, 103 were parsimony uninformative, and 343 were parsimony informative.…”

Karyotype Description and Comparative Chromosomal Mapping of 5S rDNA in 21 species

“…After comparing the 5S rDNA in previous studies and in ours, both perfectly reflect the extensive diversity in P. nepalensis , which can distinguish all 18 chromosomes according to the signal position, signal intensity, and signal number. Nevertheless, 5S rDNA was quite conserved and dormant in numerous species, such as C. campanulatus , C. sativa , H. rhamnoides , J. regia , M. atropurpureum , P. stratiotes , P. trichocarpa , and Sanguisorba L. (Mishima et al 2002, Luo and Chen 2019, 2020, Xin et al 2020, Alexandrov et al 2022, Luo et al 2022a, Stepanenko et al 2022, de Barros et al 2023). Why is there such a big difference in 5S rDNA among the above species?…”

“…However, the 5S rDNA as a FISH probe lacked discrimination (only stable two chromosomes with signal) in Pistia stratiotes L. of Araceae (Stepanenko et al 2022); in Chimonanthus campanulatus R.H. Chang & C.S. Ding of Calycanthaceae (Luo and Chen 2019); in four Citrullus Schrad.…”