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25S–18S rDNA IGS of Capsicum: molecular structure and comparison

Abstract

The primary and secondary structures of the intergenic spacer (IGS) between the 3′-end of 25S ribosomal RNA (rRNA) gene and the 5′-end of 18S rRNA gene are described for the cultivated chili pepper Capsicum pubescens. The recognized functional IGS is 2,078 bp in length. According to nucleotide base composition, regulatory elements, and conserved and repeated sequences the IGS can be divided into seven structural regions (SRI–VII). SRI comprises three copies of GAGGTTTTT-like motif, a probable transcription termination site in Solanaceae. At 3′-end, there are 21 bp matching the 18S rDNA. SRII is formed by 47 repeats of CACCATGG-like motif, the shortest repetitive region found in plant rDNA to date. SRIII is highly AT-rich, preceding SRIV, a highly conserved region in Solanaceae containing the transcription initiation site (TIS) TATATAAGGGGGG. The external transcribed spacer (ETS) is 966 bp in length. SRV-VII, downstream of the TIS, possesses eight inverted repeats, and three predicted stem-loops show pre-micro RNA (miRNA)-like structural features. Intragenomic variation is presented, and data are compared with characterized Solanaceae 25S–18S rDNA IGS.

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Acknowledgments

This study was supported by grant no. PICT 20196 of the Agencia Nacional de Promoción Científica y Tecnológica de Argentina (ANPCyT) and Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina (CONICET) as part of the doctoral thesis of M.G. Additional support came from doctoral and postdoctoral research fellowships of CONICET to H.J.D. and M.G., respectively, who contributed equally to this work. H.J.D. carried out the DNA methods with the aid of M.G. and both performed the bioinformatic and secondary structures analyses. M.G. generated the figures and wrote the manuscript, and H.J.D., D.A.D., and E.A.M. revised it. The authors thank Prof. Elba Villanueva for critical reading of the manuscript.

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Correspondence to Mauro Grabiele.

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Grabiele, M., Debat, H.J., Moscone, E.A. et al. 25S–18S rDNA IGS of Capsicum: molecular structure and comparison. Plant Syst Evol 298, 313–321 (2012). https://doi.org/10.1007/s00606-011-0546-8

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  • DOI: https://doi.org/10.1007/s00606-011-0546-8

Keywords

  • Solanaceae
  • Capsicum
  • rDNA IGS