The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units
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 mem...
Đã lưu trong:
| Những tác giả chính: | , , , , , |
|---|---|
| Định dạng: | Journal article |
| Ngôn ngữ: | English |
| Được phát hành: |
2022
|
| Những chủ đề: | |
| Truy cập trực tuyến: | http://scholar.dlu.edu.vn/handle/123456789/1032 |
| Các nhãn: |
Thêm thẻ
Không có thẻ, Là người đầu tiên thẻ bản ghi này!
|
| Thư viện lưu trữ: | Thư viện Trường Đại học Đà Lạt |
|---|
| id |
oai:scholar.dlu.edu.vn:123456789-1032 |
|---|---|
| record_format |
dspace |
| institution |
Thư viện Trường Đại học Đà Lạt |
| collection |
Thư viện số |
| language |
English |
| topic |
Pistia stratiotes, FISH, gene organization, molecular evolution, 35S rDNA, 5S rDNA |
| spellingShingle |
Pistia stratiotes, FISH, gene organization, molecular evolution, 35S rDNA, 5S rDNA Anton Stepanenko Guimin Chen Phuong T. N. Hoang Jörg Fuchs Ingo Schubert Nikolai Borisjuk The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| description |
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. |
| format |
Journal article |
| author |
Anton Stepanenko Guimin Chen Phuong T. N. Hoang Jörg Fuchs Ingo Schubert Nikolai Borisjuk |
| author_facet |
Anton Stepanenko Guimin Chen Phuong T. N. Hoang Jörg Fuchs Ingo Schubert Nikolai Borisjuk |
| author_sort |
Anton Stepanenko |
| title |
The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| title_short |
The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| title_full |
The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| title_fullStr |
The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| title_full_unstemmed |
The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units |
| title_sort |
ribosomal dna loci of the ancient monocot pistia stratiotes l. (araceae) contain different variants of the 35s and 5s ribosomal rna gene units |
| publishDate |
2022 |
| url |
http://scholar.dlu.edu.vn/handle/123456789/1032 |
| _version_ |
1768305922429419520 |
| spelling |
oai:scholar.dlu.edu.vn:123456789-10322022-09-16T06:40:35Z The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units Anton Stepanenko Guimin Chen Phuong T. N. Hoang Jörg Fuchs Ingo Schubert Nikolai Borisjuk Pistia stratiotes, FISH, gene organization, molecular evolution, 35S rDNA, 5S rDNA 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. 13 819750 2022-09-15T11:58:00Z 2022-09-15T11:58:00Z 2022 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter http://scholar.dlu.edu.vn/handle/123456789/1032 10.3389/fpls.2022.819750 en Frontiers in Plant Science Delcasso-Tremousaygue, D., Grellet, F., Panabieres, F., Ananiev, E. D., and Delseny, M. (1988). Structural and transcriptional characterization of the external spacer of a ribosomal RNA nuclear gene from a higher plant. Eur. J. Biochem. 172, 767–776. doi: 10.1111/j.1432-1033.1988.tb13956.x Do, H. D. K., Kim, C., Chase, M. W., and Kim, J.-H. (2020). Implications of plastome evolution in the true lilies (monocot order Liliales). Mol. Phylogenet. Evol. 148:106818. doi: 10.1016/j.ympev.2020.106818 Dolezel, J., Bartos, J., Voglmayr, H., and Greilhuber, J. (2003). Nuclear DNA content and genome size of trout and human. Cytometry A 51, 127–128. author reply 129, doi: 10.1002/cyto.a.10013 French, J. C., Chung, M. G., and Hur, Y. K. (1995). Chloroplast DNA phylogeny of the Ariflorae. Monocotyledons: Syst. Evol. 1, 255–275. Friis, E. M., Pedersen, K. R., and Crane, P. R. (2004). Araceae from the Early Cretaceous of Portugal: evidence on the emergence of monocotyledons. Proc. Natl. Acad. Sci. U.S.A. 101, 16565–16570. doi: 10.1073/pnas.0407174101 Galián, J. A., Rosato, M., and Rosselló, J. A. (2014a). Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions. Syst. Biol. 63, 219–230. doi: 10.1093/sysbio/syt101 Galián, J. A., Rosato, M., and Rosselló, J. A. (2014b). Incomplete sequence homogenization in 45S rDNA multigene families: intermixed IGS heterogeneity within the single NOR locus of the polyploid species Medicago arborea (Fabaceae). Ann. Bot. 114, 243–251. doi: 10.1093/aob/mcu115 Gao, Y., Yin, S., Yang, H., Wu, L., and Yan, Y. (2018). Genetic diversity and phylogenetic relationships of seven Amorphophallus species in southwestern China revealed by chloroplast DNA sequences. Mitochondrial DNA A DNA Mapp. Seq. Anal. 29, 679–686. doi: 10.1080/24701394.2017.1350855 Garcia, S., Kovaˇrík, A., Leitch, A. R., and Garnatje, T. (2017). Cytogenetic features of rRNA genes across land plants: analysis of the plant rDNA database. Plant J. 89, 1020–1030. doi: 10.1111/tpj.13442 Geber, G. (1989). Zur Karyosystematik der Lemnaceae. Ph.D. dissertation. Vienna: UniversitätWien. Gottlob-McHugh, S. G., Lévesque, M., MacKenzie, K., Olson, M., Yarosh, O., and Johnson, D. A. (1990). Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants. Genome 33, 486–494. doi: 10.1139/g90-072 Havlová, K., and Fajkus, J. (2020). G4 Structures in control of replication and transcription of rRNA Genes. Front. Plant Sci. 11:593692. doi: 10.3389/fpls. 2020.593692 Hemleben, V., Grierson, D., Borisjuk, N., Volkov, R. A., and Kovarik, A. (2021). Personal perspectives on plant ribosomal RNA genes research – from precursorrRNA to molecular evolution. Front. Plant Sci. 12:797348. doi: 10.3389/fpls. 2021.797348 Hemleben, V., and Werts, D. (1988). Sequence organization and putative regulatory elements in the 5S rRNA genes of two higher plants (Vigna radiata and Matthiola incana). Gene 62, 165–169. doi: 10.1016/0378-1119(88)90591-4 Hemleben, V., and Zentgraf, U. (1994). “Structural organization and regulation of transcription by RNA Polymerase I of plant nuclear ribosomal RNA genes,” in Plant Promoters and Transcription Factors, ed. L. Nover (Berlin: Springer), 3–24. doi: 10.1007/978-3-540-48037-2_1 Henriquez, C. L., Arias, T., Pires, J. C., Croat, T. B., and Schaal, B. A. (2014). Phylogenomics of the plant family Araceae. Mol. Phylogenet. Evol. 75, 91–102. doi: 10.1016/j.ympev.2014.02.017 Hoang, P. T. N., Fiebig, A., Novák, P., Macas, J., Cao, H. X., Stepanenko, A., et al. (2020). Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries. Sci. Rep. 10:19230. doi: 10.1038/s41598-020-75728-9 Hoang, P. T. N., and Schubert, I. (2017). Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia. Chromosoma 126, 729–739. doi: 10.1007/s00412- 017-0636-7 Hoang, P. T. N., Schubert, V., Meister, A., Fuchs, J., and Schubert, I. (2019). Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Sci. Rep. 9:3234. doi: 10.1038/s41598-019-39 332-w Huang, Y., Yu, F., Li, X., Luo, L., Wu, J., Yang, Y., et al. (2017). Comparative genetic analysis of the 45S rDNA intergenic spacers from three Saccharum species. PLoS One 12:e0183447. doi: 10.1371/journal.pone.0183447 Keating, R. (2004). Vegetative anatomical data and its relationship to a revised classification of the genera of Araceae. Ann. Missouri Botanical Garden 91, 485–494. King, K., Torres, R. A., Zentgraf, U., and Hemleben, V. (1993). Molecular evolution of the intergenic spacer in the nuclear ribosomal RNA genes of cucurbitaceae. J. Mol. Evol. 36, 144–152. doi: 10.1007/BF00166250 Kodituwakku, K. A. R. K., and Yatawara, M. (2020). Phytoremediation of industrial sewage sludge with Eichhornia crassipes, Salvinia molesta and Pistia stratiotes in batch fed free water flow constructed wetlands. Bull. Environ. Contam Toxicol. 104, 627–633. doi: 10.1007/s00128-020-02805-0 Krawczyk, K., Nobis, M., Nowak, A., Szczeci´nska, M., and Sawicki, J. (2017). Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae). Sci. Rep. 7:11506. doi: 10.1038/s41598-017-11804-x Krishnappa, D. G. (1971). Cytological studies in some aquatic angiosperms. Proc. Ind. Acad. Sci.-Sect. B 73, 179–185. doi: 10.1007/bf03045290 Labudová, D., Hon, J., and Lexa, M. (2020). pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics 36, 2584–2586. doi: 10.1093/bioinformatics/btz928 Lakshmanan, P. S., Van Laere, K., Eeckhaut, T., Van Huylenbroeck, J., Van Bockstaele, E., and Khrustaleva, L. (2015). Karyotype analysis and visualization of 45S rRNA genes using fluorescence in situ hybridization in aroids (Araceae). Comp. Cytogenet. 9, 145–160. doi: 10.3897/CompCytogen.v9i2.4366 Lefort, V., Desper, R., and Gascuel, O. (2015). FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program. Mol. Biol. Evol. 32, 2798–2800. doi: 10.1093/molbev/msv150 Leitch, I. J., Johnston, E., Pellicer, J., Hidalgo, O., and Bennett, M. D. (2019). Plant DNA C-Values Database (Release 7.1). Available online at: https://cvalues. science.kew.org/ (accessed December 1, 2021). Lemoine, F., Correia, D., Lefort, V., Doppelt-Azeroual, O., Mareuil, F., Cohen- Boulakia, S., et al. (2019). NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Res. 47, W260–W265. doi: 10.1093/ nar/gkz303 Letunic, I., and Bork, P. (2021). Interactive Tree of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296. doi: 10.1093/nar/gkab301 |