The corrected nucleotide sequences of 5 S RNAs from six angiosperms

Vandenberghe, Antoon; Chen, Min-Wei; Dams, Erna; Baere, Raymond De; Roeck, Els De; Huysmans, Erik; Wächter, Rupert De

doi:10.1016/0014-5793(84)80452-4

Cited by 24 publications

(8 citation statements)

References 29 publications

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“…One can speculate that in the case of lupin seed one of these genes [ 181 represents a pseudogene as has assistance. The nucleotide sequence data for tobacco and maize 5 S rRNAs presented here ( fig.1) together with previous results [8,15] strongly support the hypothesis of the conservation of the 5 S rRNA nucleotide sequence of plants belonging to the same species.…”

Section: Discussionsupporting

confidence: 89%

“…The question was whether 5 S rRNA follows a phylogenic relationship in plants. So far, 213 5 S rRNA sequences have been established [8,15], 10 being of higher plant origin (table 1). In the case of the Gramineae and Papilionaceae, the sequences_ of two 5 S rRNAs are known in each case, whereas in the other species only one sequence had been resolved.…”

Section: Discussionmentioning

confidence: 99%

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The primary structure of maize and tobacco 5 S rRNA

Barciszewska

Mashkova²,

Kisselev³

et al. 1985

FEBS Letters

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Section: Discussionsupporting

confidence: 89%

Section: Discussionmentioning

confidence: 99%

The primary structure of maize and tobacco 5 S rRNA

Barciszewska

Mashkova²,

Kisselev³

et al. 1985

FEBS Letters

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“…Phylogenic Tree of 5S rRNA from Green Plants (Chlorophyta). We have determined the sequences of cytoplasmic 5S rRNAs from two green algae (7,14) and from six land plants [four Bryophyta species (15) and two Pteridophyta species (16) (7,(14)(15)(16)(17)(18)(19)(20)(21)(22)(23) (Fig. 2), we have constructed a phylogenic tree of green plants (Fig.…”

Section: Resultsmentioning

confidence: 99%

Evolution of green plants as deduced from 5S rRNA sequences

Hori

Lim

Osawa

1985

Proc. Natl. Acad. Sci. U.S.A.

123

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We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni-and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other.In 1979, we published a phylogenic tree of fifty-four 5S rRNAs (1). Since then, we as well as others have reported 5S rRNA sequences of nearly 200 species of organisms with frequent constructions of 5S rRNA phylogenic trees for certain groups of organisms, such as eubacteria (2), the metabacteria (3-5), fungi (6), the Protozoa (7), and the Meso-and Metazoa (8). However, the 5S rRNA tree of green plants has been wanting. We have thus constructed a phylogenic tree of representative green plants using twenty-eight 5S rRNA sequences, and we report it here.MATERIALS AND METHODS Cytoplasmic 5S rRNAs were isolated from 400-800 g of whole organisms by the phenol method and purified by polyacrylamide gel electrophoresis as described (2, 7). The sequences were determined by both chemical and enzymatic methods (2, 9, 10). Certain parts of the sequences were confirmed by electrophoresis on a hot plate at 70°C (11). The sequence alignment was done as described (1, 5) with minor manual corrections.The evolutionary distance, Knuc, and the standard error of the Knuc, 0ok, between two sequences being compared were calculated by the equations described by Kimura (12): Fig. 2) versus one nucleotide was counted as equal to one transversion-type substitution. Using the Knuc values, we constructed a phylogenic tree by using the weighted pair-group method using arithmetic averages (WPGMA) or the unweighted pair-group method using arithmetic averages (UPGMA) (13). RESULTS AND DISCUSSIONPhylogeny of Various Groups of Organisms and Emergence of Green Plants. First, using the two hundred forty-nine 5S rRNA sequences available to date, including those described below and shown in Fig. 2, we have constructed a phylogenic tree by the WPGMA to see the phylogenic relationships of representative groups of organisms...

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“…The duckweed 5S rDNA locus was among the first plant loci whose sequence was determined in the 1980s ( Vandenberghe et al, 1984 ). However, rDNA loci of duckweeds did not attract substantial attention until recently.…”

Section: Discussionmentioning

confidence: 99%

“…In addition to these applications, the genetic diversity seen in duckweeds has stimulated a recent burst of studies examining duckweed genomics, molecular evolution, ecology, and biodiversity ( Appenroth et al, 2015 ; Laird and Barks, 2018 ; Ho et al, 2019 ). Despite the fact that the duckweed 5S rDNA was one of the first sequenced genes in plants ( Vandenberghe et al, 1984 ), the rDNA remains relatively poorly studied in duckweeds and in the Araceae. Our current knowledge of the molecular organization of the rDNA in the duckweed relates to the partial sequencing of 35S rDNA repeats from representative duckweed species in a study aiming to investigate the phylogenetic relationships and evolutionary history of Lemnaceae by Tippery et al (2015) and to whole genome sequences of Spirodela polyrhiza ( Michael et al, 2017 ) and Spirodela intermedia ( Hoang et al, 2020 ), which revealed important characteristics of the 35S and 5S rDNA loci.…”

Section: Introductionmentioning

confidence: 99%

Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae)

2021

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Duckweeds are a group of monocotyledonous aquatic plants in the Araceae superfamily, represented by 37 species divided into five genera. Duckweeds are the fastest growing flowering plants and are distributed around the globe; moreover, these plants have multiple applications, including biomass production, wastewater remediation, and making pharmaceutical proteins. Dotted duckweed (Landoltia punctata), the sole species in genus Landoltia, is one of the most resilient duckweed species. The ribosomal DNA (rDNA) encodes the RNA components of ribosomes and represents a significant part of plant genomes but has not been comprehensively studied in duckweeds. Here, we characterized the 5S rDNA genes in L. punctata by cloning and sequencing 25 PCR fragments containing the 5S rDNA repeats. No length variation was detected in the 5S rDNA gene sequence, whereas the nontranscribed spacer (NTS) varied from 151 to 524 bp. The NTS variants were grouped into two major classes, which differed both in nucleotide sequence and the type and arrangement of the spacer subrepeats. The dominant class I NTS, with a characteristic 12-bp TC-rich sequence present in 3–18 copies, was classified into four subclasses, whereas the minor class II NTS, with shorter, 9-bp nucleotide repeats, was represented by two identical sequences. In addition to these diverse subrepeats, class I and class II NTSs differed in their representation of cis-elements and the patterns of predicted G-quadruplex structures, which may influence the transcription of the 5S rDNA. Similar to related duckweed species in the genus Spirodela, L. punctata has a relatively low rDNA copy number, but in contrast to Spirodela and the majority of other plants, the arrangement of the 5S rDNA units demonstrated an unusual, heterogeneous pattern in L. punctata, as revealed by analyzing clones containing double 5S rDNA neighboring units. Our findings may further stimulate the research on the evolution of the plant rDNA and discussion of the molecular forces driving homogenization of rDNA repeats in concerted evolution.

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The corrected nucleotide sequences of 5 S RNAs from six angiosperms

Cited by 24 publications

References 29 publications

The primary structure of maize and tobacco 5 S rRNA

The primary structure of maize and tobacco 5 S rRNA

Evolution of green plants as deduced from 5S rRNA sequences

Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae)

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