Plant Molecular Biology 42: 151–166, 2000.
© 2000 Kluwer Academic Publishers. Printed in the Netherlands.
Knots in the family tree: evolutionary relationships and functions of knox
, Patricia S
and Sarah Hake
Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA (
correspondence; e-mail firstname.lastname@example.org);
Department of Integrative Biology and University and
Jepson Herbaria, University of California, Berkeley, CA 94720, USA
Key words: evolution, homeodomain protein, knox gene, meristem
Knotted-like homeobox (knox) genes constitute a gene family in plants. Class I knox genes are expressed in shoot
apical meristems, and (with notable exceptions) not in lateral organ primordia. Class II genes have more diverse
expression patterns. Loss and gain of function mutations indicate that knox genes are important regulators of
meristem function. Gene duplication has contributed to the evolution of families of homeodomain proteins in
metazoans. We believe that similar mechanisms have contributed to the diversity of knox gene function in plants.
Knox genes may have contributed to the evolution of compound leaves in tomato and could be involved in the
evolution of morphologicaltraits in other species. Alterations in cis-regulatory regions in some knox genes correlate
with novel patterns of gene expression and distinctive morphologies. Preliminary data from the analysis of class I
knox gene expression illustrates the evolution of complex patterns of knox expression is likely to have occurred
through loss and gain of domains of gene expression.
The primary architecture of plants derives from the
shoot apical meristem, which produces leaves, inter-
nodes and axillary buds. Seemingly simple differences
in organ initiation from the meristem, such as leaf
initiation in a spiral versus decussate phyllotaxy, can
result in dramatically divergent overall morphologies.
The organization and maintenance of the meristem re-
mains a fundamental question in plant development.
As new information emerges regarding the genetic
regulation of meristem organization and function, the
opportunity arises to explore the relationship between
gene expression in meristems during development and
in the evolution of plant form.
The establishment of phylogenetic relationships
provides a framework to analyze the evolution
of genes and gene families and to facilitate a
comparative-developmental approach. The assign-
ment of phylogenetic relationships is necessary for
resolving questions of homology both at the molecular
and morphological level [1, 2]. Characters are con-
sidered to be homologous if they are derived from a
common ancestor . Orthology and paralogy are
distinct forms of homology. Paralogous genes arise
from duplications within an organism whereas orthol-
ogous genes derive at the time of divergence between
taxa . Assignment of orthology can be compli-
cated when genes have duplicated and diverged within
an organism, making their relationships to similar
genes in other organisms difﬁcult to establish . To
distinguish between paralogous and orthologous genes
it is necessary to determine phylogenetic relationships
among all members of the gene family from the or-
ganisms being compared. Within the context of such a
phylogeny, ancestral conditions as well as trends in de-
rived characters, such as patterns of gene expression,
can be inferred. Several recent phylogenetic analyses
of the MADS-box family of transcription factors in
plants are excellent examples of how one can look at
evolution of a gene family and assess the potential for
function in morphological evolution [19, 64, 82].