Sequence Variation and Comparison of the 5S rRNA Sequences in Allium Species and their Chromosomal Distribution in Four Allium Species
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.
KeywordsAllium 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.
- Appel R, Honeycutt RL (1986) rDNA: evolution over a billion years. In: Dutta SK (ed) DNA systematic, vol II. CRC Press, Boca Raton, FL, pp 81–155Google Scholar
- Arnheim N (1983) Concerted evolution of multigene families. In: Nei M, Koehn RK (eds) Evolution of genes and proteins. Sinauer Associates, Sunderland, MA, USA, pp 36–61Google Scholar
- Drouin G, Moniz de Sa M (1995) The concerted evolution of 5S ribosomal genes linked to the repeat units of other multigene families. MolBiolEvol 12:481–493Google Scholar
- Friesen N, Fritsch R, Blattner FR (2006) Phylogeny and new intragenic classification of Allium (Alliaceae) based on nuclear ribosomal DNA ITS sequences. Aliso 22:372–395Google Scholar
- Fritsch RM, Blattner FR, Gurushidze M (2010) New classification of Allium L. Subg. Melanocrommyum (Webb &Berthel) Rouy (Alliaceae) based on molecular and morphological characters. Phyton 49:145–220Google Scholar
- Harvey MJ (1995) Onion and other cultivated alliums. Allium spp. (Liliaceae). In Evolution of crop plants, Smartt J and Simmonds NW, eds., 2nd ed., Wiley Pub.Co. New York pp. 344–350Google Scholar
- Lee SH, Seo BB (1997) Chromosomal localization of 5S and 18S–26S rRNA genes using fluorescence in situ hybridization in Allium wakegi. Kor J Genet 19:19–26Google Scholar
- Li Q-Q, Zhou S-D, He X-J, Yu Y, Zhang Y-C, Wei X-Q (2010) Phylogeny and biogeography of Allium (Armaryllidaceae: Alliaceae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Annals Bot 106:709–733CrossRefGoogle Scholar
- Sanderson MJ, Doyle JJ (1992) Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. SystBiol 41:4–17Google Scholar