Hostname: page-component-78c5997874-v9fdk Total loading time: 0 Render date: 2024-11-03T03:43:44.747Z Has data issue: false hasContentIssue false
  • English
  • Français

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

Published online by Cambridge University Press:  01 September 2021

Zainab M. Almutairi Open the ORCID record for Zainab M. Almutairi [Opens in a new window]
Zainab M. Almutairi*
Affiliation:
Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, P.O. Box 83, Al-Kharj 11942, Saudi Arabia
*
Author for correspondence: Zainab M. Almutairi, E-mail: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

Keywords

5.8S rRNAITSsPennisetum glaucumphylogeneticssecondary structure
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 4 , August 2021 , pp. 339 - 346
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Al-Turki, TA, Al-Namazi, AA and Masrahi, YS (2019) Conservation of genetic resources for five traditional crops from Jazan, SW Saudi Arabia, at the KACST Gene-Bank. Saudi Journal of Biological Sciences 26(7): 1626–1632.CrossRefGoogle Scholar
Álvarez, I and Wendel, JF (2003) Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3): 417–434.CrossRefGoogle ScholarPubMed
Ankenbrand, MJ, Keller, A, Wolf, M, Schultz, J and Förster, F (2015) ITS2 database V: Twice as much. Molecular Biology and Evolution 32(11): 3030–3032.CrossRefGoogle ScholarPubMed
Bailey, TL and Elkan, C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings. International Conference on Intelligent Systems for Molecular Biology 2: 28–36.Google Scholar
Baldwin, BG, Sanderson, MJ, Porter, JM, Wojciechowski, MF, Campbell, CS and Donoghue, MJ (1995) The ITS Region of Nuclear Ribosomal DNA A Valuable Source of Evidence on Angiosperm Phylogeny. Annals of the Missouri Botanical Garden 82(2): 247–277.CrossRefGoogle Scholar
Bhattacharjee, R, Bramel, P, Hash, C, Kolesnikova-Allen, M and Khairwal, I (2002) Assessment of genetic diversity within and between pearl millet landraces. Theoretical and Applied Genetics 105(5): 666–673.CrossRefGoogle ScholarPubMed
Bidinger, FR and Hash, TC (2003) Pearl millet. In Nguyen, H T and Blum, A (Eds.), Physiology and Biotechnology Integration for Plant Breeding (pp. 225–270) New York: Marcel Dekker.Google Scholar
Buckler, ES, Ippolito, A and Holtsford, TP (1997) The evolution of ribosomal DNA: Divergent paralogues and phylogenetic implications. Genetics 145(3): 821–832.CrossRefGoogle ScholarPubMed
Coleman, A, Preparata, R, Mehrotra, B and Mai, J (1998) Derivation of the Secondary Structure of the ITS-1 Transcript in Volvocales and its Taxonomic Correlations. Protist 149: 135–146.CrossRefGoogle ScholarPubMed
Coleman, AW (2000) The Significance of a Coincidence between Evolutionary Landmarks Found in Mating Affinity and a DNA Sequence. Protist 151(1): 1–9.CrossRefGoogle Scholar
Coleman, AW (2009) Is there a molecular key to the level of “biological species” in eukaryotes? A DNA guide. Molecular Phylogenetics and Evolution 50(1): 197–203.CrossRefGoogle Scholar
Felsenstein, J (1985) Confidence Limits on Phylogenies: an Approach Using the Bootstrap. Evolution 39(4): 783–791.CrossRefGoogle ScholarPubMed
Felsenstein, J and Churchill, GA (1996) A hidden markov model approach evolution to variation among sites in rate of evolution, Molecular Biology and Evolution 13(1): 93–104.CrossRefGoogle ScholarPubMed
Freire, MCM, Silva, MR da, Zhang, X, Almeida, ÁMR, Stacey, G and Oliveira, LO de (2012) Nucleotide polymorphism in the 5.8S nrDNA gene and internal transcribed spacers in Phakopsora pachyrhizi viewed from structural models. Fungal Genetics and Biology 49(2): 95–100.CrossRefGoogle ScholarPubMed
Gao, T, Yao, H, Song, J, Liu, C, Zhu, Y, Ma, X, Panga, X, Xu, H and Chen, S (2010) Identification of medicinal plants in the family Fabaceae using a potential DNA barcode ITS2. Journal of Ethnopharmacology 130(1): 116–121.CrossRefGoogle ScholarPubMed
Geerlings, TH, Vos, JANC and Raue, HA (2000) The final step in the formation of 25S rRNA in Saccharomyces cerevisiae is performed by 5′ → 3′ exonucleases. RNA 6(12): 1698–1703.CrossRefGoogle ScholarPubMed
Han, J, Zhu, Y, Chen, X, Liao, B, Yao, H, Song, J, Chen, S and Meng, F (2013) The short ITS2 sequence serves as an efficient taxonomic sequence tag in comparison with the full-length ITS. BioMed Research International 2013(741476): 1–7.Google Scholar
Harpke, D and Peterson, A (2008) 5.8S motifs for the identification of pseudogenic ITS regions. Botany 86: 300–305.CrossRefGoogle Scholar
Havilah, E. J (2011) Forages and Pastures | Annual Forage and Pasture Crops – Species and Varieties. In Fuquay, J. W. (Ed.), Encyclopedia of Dairy Sciences (2nd ed., pp. 552–562) San Diego: Academic Press.CrossRefGoogle Scholar
Hemleben, V (1993) Repetitive and highly repetitive DNA components as molecular markers for evolutionary studies and in plant breeding. Current Topics in Molecular Genetics (Life Science Advances) 1:173–85Google Scholar
Hershkovitz, MA and Zimmer, EA (1996) Conservation patterns in angiosperm rDNA ITS2 sequences. Nucleic Acids Research, 24(15): 2857–2867.CrossRefGoogle ScholarPubMed
Hodač, L, Scheben, AP, Hojsgaard, D, Paun, O and Hörand, E (2014) ITS polymorphisms shed light on hybrid evolution in apomictic plants: a case study on the Ranunculus auricomus complex. PLoS ONE 9(7): e103003.CrossRefGoogle ScholarPubMed
Hsiao, C, Chatterton, NJ, Asay, KH and Jensen, KB (1994) Phylogenetic relationships of 10 grass species: an assessment of phylogenetic utility of the internal transcribed spacer region in nuclear ribosomal DNA in monocots. Genome 37(1): 112–120.CrossRefGoogle ScholarPubMed
ICRISAT (1996) Improving the unimprovable — succeeding with pearl millet. Food from thought. No. 3 Patancheru, India: ICRISAT.Google Scholar
Jauhar, PP and Hanna, WW (1998) Cytogenetics and Genetics of Pearl Millet. In Sparks, D L (Ed.), Advances in Agronomy (Vol. 64, pp. 1–26) Academic Press. New YorkGoogle Scholar
Jobes, DV and Thien, LB (1997) A Conserved Motif in the 5.8S Ribosomal RNA (rRNA) Gene is a Useful Diagnostic Marker for Plant Internal Transcribed Spacer (ITS) Sequences. Plant Molecular Biology Reporter 15(4): 326–334.CrossRefGoogle Scholar
Kibbe, WA (2007) OligoCalc: An online oligonucleotide properties calculator. Nucleic Acids Research 35(Suppl_2): W43-W46.CrossRefGoogle ScholarPubMed
Kress, WJ, Wurdack, KJ, Zimmer, EA, Weigt, LA and Janzen, D H (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the United States of America 102(23): 8369–8374.CrossRefGoogle ScholarPubMed
Kumar, S, Stecher, G, Li, M, Knyaz, C and Tamura, K (2018) MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution 35(6): 1547–1549.CrossRefGoogle ScholarPubMed
Liu, JS and Schardl, CL (1994) A conserved sequence in internal transcribed spacer 1 of plant nuclear rRNA genes. Plant Molecular Biology 26(2): 775–778.CrossRefGoogle ScholarPubMed
Mai, JC and Coleman, AW (1997) The internal transcribed spacer 2 exhibits a common secondary structure in green algae and flowering plants. Journal of Molecular Evolution 44(3): 258–271.CrossRefGoogle ScholarPubMed
Martel, E, Poncet, V, Lamy, F, Siljak-Yakovlev, S, Lejeune, B and Sarr, A (2004) Chromosome evolution of Pennisetum species (Poaceae): Implications of ITS phylogeny. Plant Systematics and Evolution 249(3–4): 139–149.CrossRefGoogle Scholar
McBenedict, B, Chimwamurombe, P, Kwembeya, E and Maggs-Kölling, G (2016) Genetic diversity of Namibian Pennisetum glaucum (L) R. BR (Pearl Millet) landraces analyzed by SSR and morphological markers. Scientific World Journal 1439739: 1–11.CrossRefGoogle Scholar
Rampersad, SN (2014) ITS1, 5.8S and ITS2 secondary structure modelling for intra-specific differentiation among species of the Colletotrichum gloeosporioides sensu lato species complex. SpringerPlus 3(1): 1–10.CrossRefGoogle ScholarPubMed
Rozas, J, Ferrer-Mata, A, Sanchez-DelBarrio, JC, Guirao-Rico, S, Librado, P, Ramos-Onsins, SE and Sanchez-Gracia, A (2017) DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution 34(12): 3299–3302.CrossRefGoogle ScholarPubMed
Sanger, F, Nicklen, S and Coulson, AR (1977) DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74(12): 5463–5467.CrossRefGoogle ScholarPubMed
Sayers, EW, Agarwala, R, Bolton, EE, Brister, JR, Canese, K, Clark, K, Connor, R, Fiorini, N, Funk, K, Hefferon, T, Holmes, JB, Kim, S, Kimchi, A, Kitts, PA, Lathrop, S, Lu, Z, Madden, TL, Marchler-Bauer, A, Phan, L, Schneider, VA, Schoch, CL, Pruitt, KD and Ostell, J (2019) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 47(D1): D23–D28.CrossRefGoogle ScholarPubMed
Schultz, J, Maisel, S, Gerlach, D, Müller, T and Wolf, M (2005) A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 2: 361–364.CrossRefGoogle Scholar
Van Nues, RW, Rientjes, JMJ, Van Der Sande, CAFM, Zerp, SF, Sluiter, C, Venema, J, Planta, RJ and Raué, HA (1994) Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA Nucleic Acids Research 22(6): 912–919.CrossRefGoogle ScholarPubMed
Veldkamp, JF (2014) A revision of Cenchrus incl. Pennisetum (Gramineae) in Malesia with some general nomenclatural notes. Blumea: Journal of Plant Taxonomy and Plant Geography 59(1): 59–75.CrossRefGoogle Scholar
Veldman, GM, Klootwijk, J, van Heerikhuizen, H and Planta, RJ (1981) The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript. Nucleic Acids Research 9(19): 4847–4862.CrossRefGoogle ScholarPubMed
Venkateswarlu, K and Nazar, R (1991) A conserved core structure in the 18-25S rRNA intergenic region from tobacco, Nicotiana rustica. Plant Molecular Biology 17(2): 189–194.CrossRefGoogle Scholar
Will, S, Joshi, T, Hofacker, IL, Stadler, PF and Backofen, R (2012) LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA 18(5): 900–914.CrossRefGoogle ScholarPubMed
Wolf, M, Schultz, J, Dandekar, T and Achtziger, M (2005) Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA, 11(11): 1616–1623.CrossRefGoogle ScholarPubMed
Zuker, M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31(13): 3406–3415.CrossRefGoogle ScholarPubMed
Supplementary material: File

Almutairi supplementary material

Tables S1-S2 and Figures S1-S2

Download Almutairi supplementary material(File)
File 654.3 KB