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Molecular characterization of ribosomal DNA intergenic spacer (IGS) region in pomegranate (Punica granatum L.)

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Abstract

The large intergenic spacer (IGS) region of rDNA is a valuable DNA sequence because it contains the signals for transcription and processing of rRNAs. In this study, we sequenced and analyzed the complete nucleotide of rDNA IGS region of pomegranate for the first time. This IGS sequence was 3,712 bp in length with GC content of 67.8 %. The sequence analysis indicated that the spacer could be divided into three main regions: a central repetitive region and two flanking unique domains on on both sides of the central area. Central region is composed of two repeat families (A and B), and the third region contained two short direct repeats (C1 and C2). By comparisons with the IGS sequence of other plant species and computer-aided searches, we determined the putative transcription initiation and termination sites, and the large number of methylable sites. The presence of some conserved motifs in this region may play an important role in regulation of rRNA transcription. Taken together, the pomegranate IGS revealed the complex structure. However, its organization and structure are similar to most other rDNA spacers studied.

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Abbreviations

rDNA:

Ribosomal DNA

IGS:

Intergenic spacer

ETS:

External transcribed spacer

ITS:

Internal transcribed spacer

NOR:

Nucleolus organizer region

NTS:

Non-transcribed spacer

TIS:

Transcription initiation site

TTS:

Transcription termination site

PCR:

Polymerase chain reaction

CTAB:

Cetyltrimethylammonium bromide

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Acknowledgments

This work was supported by Isfahan University of Technology, Iran. We thank the Agricultural Research Center of Isfahan, Iran, and the USDA-ARS, National Clonal Germplasm Repository, Davis, California, USA, for providing the plant materials.

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  1. Department of Biotechnology, College of Agriculture, Isfahan University of Technology, 84156-83111, Isfahan, Iran

    Maryam Parvaresh, Majid Talebi & Badraldin-Ebrahim Sayed-Tabatabaei

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  1. Maryam Parvaresh
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  2. Majid Talebi
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Correspondence to Majid Talebi.

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Parvaresh, M., Talebi, M. & Sayed-Tabatabaei, BE. Molecular characterization of ribosomal DNA intergenic spacer (IGS) region in pomegranate (Punica granatum L.). Plant Syst Evol 300, 899–908 (2014). https://doi.org/10.1007/s00606-013-0928-1

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