1021-4437/02/4905- $27.00 © 2002
Russian Journal of Plant Physiology, Vol. 49, No. 5, 2002, pp. 657–664. Translated from Fiziologiya Rastenii, Vol. 49, No. 5, 2002, pp. 735–743.
Original Russian Text Copyright © 2002 by Ermishev, Naroditsky, Khavkin.
Among the transcriptional regulators of plant devel-
opment, the superfamily of
genes that con-
trol ﬂowering time, ﬂower identity, and fruit formation
[1, 2] has been investigated most extensively. These
traits are important agronomic characteristics that
determine earliness and yield structure in cereal crops.
Yet the structural and functional studies of
genes in grasses, except in rice and maize, lag behind
those in dicots.
Previously, we described short fragments of rye
genes corresponding to the MADS-box and
K-box domains of the transcription factors. In addition,
we observed shorter DNA fragments of the size corre-
sponding to the sum total of the exons 3 to 5. We believe
that the latter resulted from the ampliﬁcation of the
retrogenes . Here, we report rye
fragments, which comprise the
complete sequences of exons 1 to 5 and lack the corre-
sponding introns. Apparently, these fragments are pro-
cessed pseudogenes, or retropseudogenes.
MATERIALS AND METHODS
Plants of perennial rye
and winter rye
L., cv. Vyatka, were studied. Genomic DNA was iso-
lated from leaves of 15-day-old seedlings following the
protocol based on the method by Saghai-Maroof
. All subsequent manipulations with the DNA prep-
aration were performed as described previously .
DNA ampliﬁcation, cloning, and sequencing.
order to amplify and reamplify the sequences of the
genes, we used degenerate
primers AgF and AgR, designed to match the consensus
stretches at the start of the exon 1 and the end of the
exon 5 (Fig. 1, Table 1). The consensus stretches were
obtained by aligning the sequences of the maize genes
zag1, zag2, zag4, zmm1
accession nos. L18924, X80206, L46399, X81199, and
X81200) and the rice gene
order to reamplify the products of the ﬁrst reaction, we
used an inner primer MF1 together with AgR (see
Fig. 1 and Table 1). The MF1 primer recognizes the
consensus stretch within the exon 1 obtained by align-
ing the genes belonging to various classes of maize
zag1, zag5, zmm1, zmm2
(Genbank accession nos. L18924, L46398, X81199,
X81200, and L46400). The reverse primer AgR2 inside
exon 5 was designed on the basis of the already identi-
sequence from annual rye.
In the case of
genes, degenerate prim-
ers AglF and AglR recognize the consensus stretches at
the start of the exon 1 and the end of the exon 5 (see
Fig. 1 and Table 1). These primers were designed by
genes of rice (
Genbank accession nos. L34271, U78890, U78782,
U78891, U78892, and U31994), maize (
Genbank accession nos. L46397 and L46398), wheat
; Genbank accession no. AB007505), and
; Genbank accession no. U49734).
For reampliﬁcation, we combined the primers recog-
wheat gene and the universal
Retropseudogenes in Rye (
V. Yu. Ermishev, B. S. Naroditsky, and E. E. Khavkin
Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences,
Timiryazevskaya ul. 42, Moscow, 127550 Russia;
fax: 7 (095) 977-0947; e-mail: firstname.lastname@example.org
Received July 11, 2001
—The fragments of
genes belonging to the
were isolated by direct ampliﬁcation of genomic DNA from annual rye (
L.) and perennial rye
Guss.). The characterized fragments (deposited in the Genbank as the accession nos.
AF332885–AF332887 and AF346894) comprise the complete sequences of exons 1 to 5 and lack correspond-
ing introns. Their nearest homologs are the maize genes
(the Genbank accession nos. L18924
and L46398). One more
fragment isolated from annual rye (AF362364) is similar to the
wheat gene (AB007505). The fragment comprises exons 3–5 and contains a 105-bp insert between
the exons 3 and 4; this insert does not resemble any
introns presently known. We assume that all
these fragments of
genes are retropseudogenes.
Key words: Arabidopsis thaliana - Oryza sativa - Secale cereale - Secale montanum - Triticum aestivum - Zea
mays - MADS-box genes - pseudogenes - retrotransposons
: PCR—polymerase chain reaction.