Journal of Plant Biology

, Volume 55, Issue 1, pp 15–25 | Cite as

Sequence Variation and Comparison of the 5S rRNA Sequences in Allium Species and their Chromosomal Distribution in Four Allium Species

  • Jae-Han Son
  • Kyong-Cheul Park
  • Sung-Il Lee
  • Eun-Jin Jeon
  • Hyun-Hee Kim
  • Nam-Soo KimEmail author
Original Research


The gene structure and sequence diversity of 5S rRNA genes were analyzed in 13 Allium species. While the lengths and sequences of the coding gene segments were conserved, the spacers were highly variable and could be characterized as either short (213–404 bp) or long (384–486 bp) spacers. The short spacers were further classified into five subtypes (SS-I to SS-V) and the long spacers into four subtypes (LS-I to LS-IV). The short spacers were more conserved than were the long spacers. There was a sequence duplication of 85 bp in SS-III that distinguished it from SS-II. The coding sequences of the 5S rRNA genes started with CGG and ended with either CCC or TCC. Both long and short spacers started with TTTT at their 5′-ends. However, the long spacers ended with a 3′-TGA sequence, whereas the short spacers terminated with various sequences, such as TTA, ATA, or TGA. GC content ranged from 27 to 41% in whole repeats, and the GC content in the long spacers was lower than in the short spacers. The nucleotide diversity in the coding regions was lower than in the spacers, and the nucleotide diversity in the coding regions did not correlate with that of the spacers. FISH analysis confirmed that each Allium species has either short spacers or long spacers. Although chromosomal locations of the 5S rRNA genes in Allium wakegi confirmed the allodiploid nature of A. cepa and A. fistulosum, spacer sequences revealed the absence of SS-II in A. cepa and in A. wakegi. The current study demonstrated that the 5S rRNA genes diverged in early stages in Allium species differentiation except of the allodiploid A. wakegi.


Allium 5S rRNA Nucleotide diversity Allodiploid 



This study was supported by the Bio-Green 21 Project (Grant 200804010340600080100) of the Rural Development Administration (RDA), Republic of Korea. JHS and SIL are the recipients of the BK21 Program supported by the Ministry of Education, Science and Technology (MEST), Republic of Korea. Authors express thanks to Dr. G. Fedak for critical reading of the manuscript.


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Copyright information

© The Botanical Society of Korea 2011

Authors and Affiliations

  • Jae-Han Son
    • 1
  • Kyong-Cheul Park
    • 2
  • Sung-Il Lee
    • 1
  • Eun-Jin Jeon
    • 3
  • Hyun-Hee Kim
    • 3
  • Nam-Soo Kim
    • 1
    • 2
    Email author
  1. 1.Department of Molecular Biosciences, BK21 Training TeamKangwon National UniversityChuncheonSouth Korea
  2. 2.Institute of Biosciences and BiotechnologyKangwon National UniversityChuncheonSouth Korea
  3. 3.Department of Life ScienceSahmyook UniversitySeoulSouth Korea

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