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

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.

Karyotype analysis of eight cultivated Allium species

“…The number and localization of the rDNA sites that were obtained for A . fistulosum consents with most of the earlier reports (Kirov et al 2017 ; Lee et al 1999 ; Son et al 2012 ). However, Gernand et al ( 2007 ) reported additional one or four minor polymorphic sites of 35S rDNA on A .…”

“…Only two pairs of 5S rDNA sites were observed on the short arm of one chromosome pair in A . sativum , although earlier reports showed three pairs of sites of 5S rDNA in this species (one on the long arm and two on the short arm of the same chromosome pair; Lee et al 1999 ; Son et al 2012 ). Such phenomenon, the intraspecific polymorphisms in the rDNA sites number, has also been observed in many species including Amaranthus , Chenopodium , and Prospero (Jang et al 2013 ; Kolano et al 2013 ; Kolano et al 2015 ).…”

Garlic (A. sativum L.) alliinase gene family polymorphism reflects bolting types and cysteine sulphoxides content

“…Jovan). This finding is similar to the expected ratio and is in line with reports involving other Allium genes [ 29 ]. Similar variability ratios were found for the other three accessions used in our alliinase variability analysis (Djambul1, Marhfeld, and Japo).…”

Diverse evolutionary pathways shaped 5S rDNA of species of tribe Anemoneae (Ranunculaceae) and reveal phylogenetic signal

“…However, when inter-chromosome exchange is missing, 5S rDNA arrays located on different chromosomes could evolve independently. In other words, new variants formed via mutations and homogenization events could lead to development of chromosome-specific 5S rDNA arrays (Volkov et al, 2001;Son et al, 2012). Chromosome-specific arrays are also characteristic of polyploid species in which the outcome of concerted evolution depends on the frequency of genetic exchanges between homologous sequences on homoeologous chromosomes.…”