Sequence Variation and Comparison of the 5S rRNA Sequences in <Emphasis Type="Italic">Allium</Emphasis> Species and their Chromosomal Distribution in Four <Emphasis Type="Italic">Allium</Emphasis> Species |
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Authors: | Jae-Han Son Kyong-Cheul Park Sung-Il Lee Eun-Jin Jeon Hyun-Hee Kim Nam-Soo Kim |
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Institution: | (1) Department of Molecular Biosciences, BK21 Training Team, Kangwon National University, Chuncheon, 200-701, South Korea;(2) Institute of Biosciences and Biotechnology, Kangwon National University, Chuncheon, 200-701, South Korea;(3) Department of Life Science, Sahmyook University, Seoul, 139-742, South Korea; |
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Abstract: | 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. |
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