Plant Molecular Biology 48: 21–37, 2002.
© 2002 Kluwer Academic Publishers. Printed in the Netherlands.
Plant genome evolution: lessons from comparative genomics at the DNA
Max-Delbrück-Laboratorium in der Max-Planck-Gesellschaft, Carl-von-Linn´e-Weg 10, 50829 Cologne,
Germany; present address: Max-Planck-Institut für molekulare Pﬂanzenphysiologie, Am Mühlenberg 1, 14476
Golm, Germany (e-mail firstname.lastname@example.org)
Key words: collinearity, comparative mapping, comparative sequence analysis, genome, retroelement, sequence
Angiosperm genomes show tremendous variability in genome size and chromosome number. Nevertheless, com-
parative genetic mapping has revealed genome collinearity of closely related species. Sequence-based comparisons
were used to assess the conservation of gene arrangements. Numerous small rearrangements, insertions/deletions,
duplications, inversions and translocations have been detected. Importantly, comparative sequence analyses have
unambiguously shown micro-collinearity of distantly related plant species. Duplications and subsequent gene loss
have been identiﬁed as a particular important factor in the evolution of plant genomes.
Cytogenetic techniques allow insight into genome or-
ganisation at the chromosome level. Chromosome
numbers for different species have been established
by light microscopic analysis of chromosome spreads.
In angiosperms, plants with as few as 2n = 4(e.g.
Haplopappus gracilis) and as many as 2n = ca. 600
chromosomes (Voanioala gerardii) are known (Ben-
nett, 1998). The importance and prevalence of poly-
ploidy in angiosperms has also been recognized by
studying karyotypes of different plant species. It has
been estimated that 50–70% of ﬂowering plants have
experienced chromosome doubling at least once in
their evolutionary history (Wendel, 2000). Many of
the important crop plants are polyploids (e.g. wheat,
rapeseed, potato, cotton).
Different methods can be used to estimate genome
size. These include for example DNA reassociation ki-
netics, nuclear volume measurements and estimations
from sampling genomic clone libraries. Microdensito-
metry of Feulgen-stained nuclei (Bennett and Smith,
1976, 1991; Bennett et al., 1982) and ﬂow cytome-
try of isolated nuclei stained with propidium iodide
(Arumuganathan and Earle, 1991) were used for ex-
tensive surveys. A compilation of 2802 estimates for
angiosperm species has shown that haploid genome
sizes range over 1000-fold from ca. 0.1 pg to over
125 pg. About 50% of the ﬂowering plants analysed
to date have genome sizes between 0.1 and 3.5 pg
(Leitch et al., 1998). Arabidopsis has one of the small-
est genomes observed in higher plants, the analysis
of the DNA sequence of the nuclear genome supports
a value of 125 Mb (Arabidopsis Genome Initiative,
2000). In contrast, the particularly large genome of
Fritillaria assyriaca encompasses ca. 120 000 Mb
(Bennett and Smith, 1976). Even species belonging
to the same family show substantial differences in
genome size. In the Poaceae, values of ca. 450, 750,
2500, 5000 and 16 000 Mb have been established for
the rice, sorghum, maize, barley and wheat genomes,
respectively (Arumuganathan and Earle, 1991).
Reassociation kinetic studies provide an impor-
tant insight into the complexity of plant genomes.
These experiments have unequivocally shown that
plant genomes are composed of repeated and low or
single-copy DNA sequences. Comparing complexities
of large and small plant genomes, it has been estab-