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
OR5 Our process of constructing the MADS-box gene duplication model
We began by placing the pairs of genes at the tips of the branches of the phylogenetic trees (Online
Resource 3) in Step 4 of our model (Fig. 3) because these gene pairs represent the most recent duplication
events. PPTIM2 (C16) and PPTIM3 (C25) make a particularly good example because they are closely
related and located in conserved microsyntenic clusters. Ever less closely related gene pairs were placed at
increasingly earlier steps of the model. When decisions were arbitrary, we placed duplicate genes in an order
that would provide an uninterrupted flow through the diagram.
We used the extant gene names (as described in Online Resource 1), gene orientations and relative
chromosomal positions in Step 4. We carried the names, orientations and locations backward through the
model. As an alternative, we could have constructed hypothetical ancestral chromosomes and given each
hypothetical gene ancestor a unique name. However, this would have sacrificed clarity, simplicity and
economy.
For Step 1, we chose C3 and C16 because, taken together, they harbour members of the MIKCC,
MIKC*, Mα and Mβ clades. These are the four clades of MADS-box genes that are shared by Physcomitrella
and other plants and, therefore, were present when the lineage leading to Physcomitrella branched off from
that leading to other plants.
Like C3, C1 and C14 each contain one MIKCC gene and two MIKC* genes. However, C3 harbours
one member of each of the major clades of MIKC* genes (the PpMADS2 clade and the PPMA9 clade) while
the other two chromosomes contain MIKC* genes from the PPMA9 clade only. Another factor is that the
relative orientations of the three genes on C3 are consistent with those of the majority of MIKC gene clusters
in Physcomitrella.
In Step 2, we chose C1 as an early duplicate of C3 primarily because PPM2 and PpMADS-S are
members of different MIKCC clades. Additionally, C1 belongs to the group of chromosomes in which a
longer distance separates the MIKCC and MIKC* genes whereas C3 belongs to the group in which a shorter
distance separates the MIKCC and MIKC* genes.
We could have chosen C14 or C17 in Step 2 because they each harbour one member of the PpMADSS clade and on both chromosomes the MIKCC and MIKC* genes are relatively distantly separated. However,
if we had chosen C14, two MIKC* genes would appear to have reversed their orientation relative to that of
the MIKCC genes in Step 2 and to have returned to their original orientation in a later step. Choosing C17
would invoke the apparent loss of one of the two MIKC* genes and the reappearance of the second MIKC*
gene on C1 or C14 at a later step. We do not know when, during the course of evolution of Physcomitrella,
genes were lost or their orientations reversed. However, where possible we have adopted a parsimonious
approach involving a minimum number of gene losses and reversals in gene orientation.
In Step 3, duplication of the MRCA of PPTIM2 and PPTIM1 is shown as PPTIM2 (C16) producing
PPTIM1 (C17). The common ancestor of the Mα clade and the clade containing PPTIM1, PPTIM4 and
PPTIM5 is expected to be an Mα gene. If we had placed PPTIM1 in Step 1 to represent the common
ancestor, this fact would be unclear.