Plant Molecular Biology 48: 5–20, 2002.
© 2002 Kluwer Academic Publishers. Printed in the Netherlands.
Through a genome, darkly: comparative analysis of plant chromosomal
Graham J. King
Comparative Genomics and Genetics Group, HRI, Wellesbourne, Warwick CV35 9EF, UK (e-mail gra-
Key words: plant genomes, DNA, comparative genomics, genetics, genome organisation, genome size, collinearity
Plant nuclear genomes encompass a wide range of variation in size and nucleotide composition with diverse
arrangements of chromosomal segments, repetitive sequences and distribution of genes. Comparative genomic
analysis may be undertaken at different levels of organisation, which are reﬂected in this review, together with a
focus on the genetic and functional signiﬁcance of the observed variation. Patterns of genome organisation have
been revealed which reﬂect the different underlying mechanisms and constraints driving change. Thus comparative
issues of genome size, nucleotide sequence composition and genome heterogeneity are provided as a background
to understanding the different levels of segmental and repetitive sequence duplication and distribution of genes.
The extent of synteny and collinearity revealed by recent genetic and sequence comparisons is discussed, together
with a consideration of problems associated with such analyses. The possible origins and mechanisms of variation
in genome size and organisation are covered, including the prevalence of duplication at different levels of organ-
isation. The likely genetic, functional and adaptive consequences of replicated loci are discussed with evidence
from comparative studies. The scope for comparative analysis of epigenetic plant genome variation is considered.
Finally, opportunities for applying comparative genomics to isolating genes and understanding complex crop
genomes are addressed.
For now we see through a glass, darkly, but then face
to face; now I know in part, but then shall I know even
as I am known. I Corinthians 13:12, King James Bible.
Plant nuclear genomes are overlapping hierarchies of
information residing in the large nucleoprotein struc-
tures of chromosomes. The construction and organi-
sation of DNA sequences varies, with contemporary
genome structures resulting from a combination of
molecular and evolutionary processes acting within
physical and biological constraints. Functionally, their
organisation enables genetic information to be embed-
ded in, and retrieved from, the chromosomal structure.
The information content of the primary duplex DNA
molecule within each chromosome represents a mul-
tiplexed signal which simultaneously carries many
codes for functions such as amino acid selection, gene-
splicing, transcription, and nucleosome positioning
At the macromolecular level, genomes primar-
ily evolve at different levels of organisation through
the processes of translocation, inversion, duplication,
recombination, deletion and substitution. Thus our
current approach to genome analysis in some respects
may be regarded as a form of ’molecular stratigra-
phy’, akin to interpretation of the geological record.
In the absence of a chromosome theory (Lima de
Faria, 1983) comparative methods are particularly use-
ful in identifying key constraints on DNA sequence
construction and evolution (Miramontes et al., 1995).
It is widely accepted that eukaryotes and their nu-
clear genomes arose from a common origin in symbio-
sis with organelles, and that the major divergence of
angiosperm plants into monocotyledons and dicotyle-
dons occurred some 130–200 million years ago. There