Ancestral and More Recently Acquired Syntenic Relationships of MADS-box Genes Uncovered by the
Physcomitrella patens Pseudochromosomal Genome Assembly
Plant Cell Reports
E. I. Barker N. W. Ashton
Department of Biology, University of Regina, Regina, SK, S4S 0A2, Canada
Author for correspondence:
Neil W. Ashton
e-mail: physcomitrella@gmail.com
OR1 Terminology and shorthand notation
Terms
Synteny (syntenic), “same thread”, refers to two or more gene loci on the same chromosome. This is the
original definition of this term attributable to J.H. Renwick to describe a situation in which recombination
analysis is unable to demonstrate genetic linkage between genes shown by other methods to reside on the same
chromosome (Renwick 1971).
Shared synteny refers here to paralogous blocks of genes on different chromosomes within a single genome
that arose from a common ancestral chromosome or block of genes. The degree of preservation of colocalisation and co-linearity, i.e. gene order, orientation and spacing, within extant blocks varies according to
the time passed since their ancestor was duplicated and the rate at which chromosomal rearrangements
occurred. Shared synteny also refers to orthologous blocks of genes on chromosomes in different species
that arose from a common ancestral chromosome or block of genes.
Conserved synteny is synonymous with shared synteny.
Shared (or conserved) macrosynteny refers to synteny preserved over long sections of two or more
chromosomes.
Shared (or conserved) microsynteny refers to synteny preserved over short sections (comprising a few genes
only) of two or more chromosomes.
Supplementary Reference
Renwick JH (1971) The mapping of human chromosomes. Annu Rev Genet 5:8-20
Shorthand notation for gene duplication
The left-hand diagram in row a) of the figure below illustrates a hypothetical ancestral gene, Gene A,
that duplicates to produce identical genes, Gene A' and Gene A''. The sequences of Gene A' and Gene A''
diverge over time, resulting in the sequences of extant genes, Gene B and Gene C respectively. The right-hand
diagram illustrates our shorthand notation for this series of events. In our duplication model (Fig. 3), for the
sake of economy and clarity, we use the gene names for the extant genes (the equivalents of Genes B and C)
and for each of their ancestors along their separate lineages (the equivalents of Gene A' and Gene A"). The
name of one of the extant genes is applied to their MRCA (the equivalent of Gene A). In the text we refer to
the ancestral genes as “the ancestor of” plus the name of the extant gene or “the MRCA of” with the names of
the descendants. In some cases, we merely apply the name of the extant gene to its ancestor(s). This simplifies
the task of following the genes through their lineages.
The left-hand diagram in row b) shows, as an example, a series of events in which the MRCA of
PPTIM2 and PPTIM3 duplicated to give rise to two ancestral genes that evolved into the extant genes, with
our simplified gene nomenclature as described in the preceding paragraph. In our model (Fig. 3) the arrow
between PPTIM2 and PPTIM3 (see the right-hand box) indicates the same event. Examples of our choices of
which genes to depict first in the model (the equivalents of “Gene A”) are given in Online Resource 5 where
we describe the process of constructing the model. We use arrows to provide directionality to these events.