ISSN 10227954, Russian Journal of Genetics, 2014, Vol. 50, No. 10, pp. 1120–1124. © Pleiades Publishing, Inc., 2014.
Original Russian Text © M.A. Filyushin, E.Z. Kochieva, 2014, published in Genetika, 2014, Vol. 50, No. 10, pp. 1263–1268.
All higher plants possess genes encoding ribosomal
RNAs (except for the 5S gene) in the nuclear genome,
which are represented by hundreds and thousands tan
dem repeats of cistron 18SITS15.8SITS226S .
Cistron copies might be localized on several frequently
nonhomologous chromosomes, and cistron sequences
are usually invariable within one species. Such homo
geneity in sequences appears to be due to consistent
evolution, which is assumed to be caused by the mech
anisms of gene conversion and unequal crossover .
However, the cistron sequence is variable, a fact that is
frequently used for molecularphylogenetic analysis of
different plant genera [3, 4]. At the same time, several
types of cistron sequences have been identified in dis
tinct plant groups, including both gymnosperms and
angiosperms, accompanied by the accumulation of
mutations destabilizing the secondary structure of
rRNA molecules and intergenic spacers, which might
result in pseudogene formation [5, 6].
Ribosomal RNAs form specific secondary struc
tures associated with ribosomal proteins. Formed 3D
riboprotein complexes have great significance in the
process of correct ribosome assembly and subsequent
translation. The secondary structure of 5.8S rDNA
consists of four loops (1a, 1b, 2, and 3) , or five
loops (B4, B5, B6, B7, and B8) if assumes 1a and 1b to
be based on a separate loop , and contains three
conserved motifs . Loop 1b (B6) includes the highly
conserved 14nucleotide motif 5'GAAUUGCA
GAAUCC3' common for all higher plants that bind
with ribosomal protein during the assembly of the
major ribosomal subunit, as well as two motifs neces
sary for the maintenance of the correct secondary
structure of the 5.8S RNA molecule [9, 10].
genus represents the major genus of Amaryl
lidaceae family (order Asparagales) and consists of
more than 800 species of perennial plants with subter
ranean storage organs—bulbs and rhizomes. Earlier
Friesen et al.  systematized
genus and iso
lated 15 subgenera followed by their division into three
evolutionary groups. The third evolutionary group
includes seven subgenera (
) consisting of 37 sections.
comprising of 15 sections appears to be the most
numerous and includes such highly economically
valuable species as garlic
garden forms of
(pearly, Egypt, and
bulb onions) and several other species.
The present study aimed to conduct a sequence
analysis of 5.8S rDNA and to study the possible effect
of nucleotide substitutions on the topology of the sec
ondary structure of this RNA molecule in the acces
sions of seven subgenera comprising the third evolu
tionary group, particularly in accessions of the
section of the
subgenus, which is known to be
the largest and most significant.
To analyze 5.8S rDNA sequences, a DNA collec
tion of accessions belonging to various subgenera of
genus was formed (table). Accessions of out
genera of order Asparagales were used as the out
(Amaryllidaceae family), and
(Asparagaceae family). The plant material was granted
by the Botanical Garden of the University of
(Germany), VNIISSOK (Lesnoy gorodok,
MR); geolocal garlic accessions were donated by VIR
(SaintPetersburg). Total DNA was isolated by stan
dard technique from the seedlings and herbarium
For amplification of the ITS15.8SITS2
sequence, PCR primers ITS4 and ITS5 were used .
5.8S rDNA Variability in
to the Third Evolutionary Group
M. A. Filyushin and E. Z. Kochieva
“Bioengineering” Center, Russian Academy of Sciences, Moscow, 117312 Russia
email: firstname.lastname@example.org, email@example.com
Received April 2, 2014; in final form April 17, 2014.
—Sequence analysis of 5.8S rDNA in 67 accessions of the subgenus
and six other subgenera
belonging to the third evolutionary group of
genus (Friesen et al., 2006) was performed. Nucleotide
substitutions in 5.8S rDNA sequences of
accessions were identified and studied for the first time. The
probable secondary structure of 5.8S rRNA was constructed. It was shown that mutations in 5.8S rDNA do
not involve conserved motifs, and they did not significantly affect the secondary structure of the RNA mole