Nevertheless, some clades of MIKC
C -group
genes were lost, some even more than once.
Among the at least 12 clades of MIKC
C -group
genes that had been established in the MRCA of
extant seed plants, one, named GpMADS4-like
genes, may have been lost in the lineage that led
to extant flowering plants (Gramzow et al. 2014).
Of the 17 clades of MIKC
C -group genes that
probably existed in the MRCA of extant
angiosperms, three (AGL12-, AGL15-, and STKlike genes) have been lost at least once, two
(AGL9- and OsMADS32-like genes) have been
lost at least twice, and two have been lost at least
five (TM8-like genes) or six (FLC-like genes)
times independently throughout angiosperm
evolution (Gramzow and Theißen 2015).
Because of the limited genome sampling, these
are very conservative estimates, and the real
numbers are probably much higher. Interestingly,
a subclade of B sister genes, termed GORDITAlike genes, has been lost several times in parallel
in crucifers alone (Hoffmeier et al. 2018).
The reasons why some clades of MIKC
C -
group genes become dispensable during evolution and hence get lost in some lineages are all
but clear. Which roles do genetic drift based on
low purifying selection on the one hand and
adaptive advantage on the other hand play?
It would be interesting to relate gene loss to
the organismal context in which it happens.
A well-known example is gene loss as a consequence of parasitism, since many parasites
receive functions from their hosts rather than to
encode them in their own genomes. Indeed, it has
been reported that the dodder species Cuscuta
australis, a root- and leafless-parasitic plant from
the family Convolvulaceae, has no FLC-,
StMADS11-(SVP-), and AGL17-like MIKC
C -
group genes (Sun et al. 2018). Whether the loss
of these genes can be attributed to the loss of
major plant organs remains to be seen. However,
not only some kinds of parasitism, but also other
evolutionary processes in angiosperms involved
the loss of organs. An obvious case in point is
duckweeds.
9.4 Previous Studies on the Loss
of MADS-Box Genes
in Alismatales
Preliminary analyses made possible because a
genome sequence of Spirodela polyrhiza (clone
7498) had become available (Wang et al. 2014)
suggested that four clades of MIKC
C -group
genes that were established in the stem group of
extant angiosperms (AGL9-, AGL12-, FLC-, and
OsMADS32-like genes), are missing in the genome of this duckweed species; they thus have
possibly been lost in the lineage that led to
Spirodela polyrhiza (Gramzow and Theißen
2015). An independent analysis confirmed the
absence of these gene clades, and reported also
the absence of MIKC*-group genes (which had
not been investigated in the previous study)
(Olsen et al. 2016). Thus, Spirodela polyrhiza
may have lost the highest number of clades of
MIKC-type genes of all investigated species
(Gramzow and Theißen 2015). It was tempting to
hypothesize, therefore, that the relatively high
number of possibly lost clades is causally linked
to the simplification of the duckweed body plan
during evolution. Maybe duckweeds such as
Spirodela polyrhiza lost some ancestral clades of
MIKC-type genes because they were not
required anymore to control developmental processes that had been significantly simplified or
even abolished (Gramzow and Theißen 2015).
The only other species from Alismatales
except duckweeds for which a genome sequence
is currently available is Zostera marina (Zosteraceae), which is phylogenetically more derived
than duckweeds (Olsen et al. 2016). The finding
that AGL12-, AGL9-, OsMADS32-like, and
MIKC*-group genes have been found in that
species (Olsen et al. 2016) suggests that these
gene clades have been lost in the lineage that led
to duckweeds after the lineage that led to more
derived Alismatales had branched-off. Probably
these gene losses are duckweed-specific. In
contrast, FLC-like genes were reported to be
missing in both Spirodela polyrhiza and Zostera
96
L. Gramzow and G. Theißen
C -group
genes were lost, some even more than once.
Among the at least 12 clades of MIKC
C -group
genes that had been established in the MRCA of
extant seed plants, one, named GpMADS4-like
genes, may have been lost in the lineage that led
to extant flowering plants (Gramzow et al. 2014).
Of the 17 clades of MIKC
C -group genes that
probably existed in the MRCA of extant
angiosperms, three (AGL12-, AGL15-, and STKlike genes) have been lost at least once, two
(AGL9- and OsMADS32-like genes) have been
lost at least twice, and two have been lost at least
five (TM8-like genes) or six (FLC-like genes)
times independently throughout angiosperm
evolution (Gramzow and Theißen 2015).
Because of the limited genome sampling, these
are very conservative estimates, and the real
numbers are probably much higher. Interestingly,
a subclade of B sister genes, termed GORDITAlike genes, has been lost several times in parallel
in crucifers alone (Hoffmeier et al. 2018).
The reasons why some clades of MIKC
C -
group genes become dispensable during evolution and hence get lost in some lineages are all
but clear. Which roles do genetic drift based on
low purifying selection on the one hand and
adaptive advantage on the other hand play?
It would be interesting to relate gene loss to
the organismal context in which it happens.
A well-known example is gene loss as a consequence of parasitism, since many parasites
receive functions from their hosts rather than to
encode them in their own genomes. Indeed, it has
been reported that the dodder species Cuscuta
australis, a root- and leafless-parasitic plant from
the family Convolvulaceae, has no FLC-,
StMADS11-(SVP-), and AGL17-like MIKC
C -
group genes (Sun et al. 2018). Whether the loss
of these genes can be attributed to the loss of
major plant organs remains to be seen. However,
not only some kinds of parasitism, but also other
evolutionary processes in angiosperms involved
the loss of organs. An obvious case in point is
duckweeds.
9.4 Previous Studies on the Loss
of MADS-Box Genes
in Alismatales
Preliminary analyses made possible because a
genome sequence of Spirodela polyrhiza (clone
7498) had become available (Wang et al. 2014)
suggested that four clades of MIKC
C -group
genes that were established in the stem group of
extant angiosperms (AGL9-, AGL12-, FLC-, and
OsMADS32-like genes), are missing in the genome of this duckweed species; they thus have
possibly been lost in the lineage that led to
Spirodela polyrhiza (Gramzow and Theißen
2015). An independent analysis confirmed the
absence of these gene clades, and reported also
the absence of MIKC*-group genes (which had
not been investigated in the previous study)
(Olsen et al. 2016). Thus, Spirodela polyrhiza
may have lost the highest number of clades of
MIKC-type genes of all investigated species
(Gramzow and Theißen 2015). It was tempting to
hypothesize, therefore, that the relatively high
number of possibly lost clades is causally linked
to the simplification of the duckweed body plan
during evolution. Maybe duckweeds such as
Spirodela polyrhiza lost some ancestral clades of
MIKC-type genes because they were not
required anymore to control developmental processes that had been significantly simplified or
even abolished (Gramzow and Theißen 2015).
The only other species from Alismatales
except duckweeds for which a genome sequence
is currently available is Zostera marina (Zosteraceae), which is phylogenetically more derived
than duckweeds (Olsen et al. 2016). The finding
that AGL12-, AGL9-, OsMADS32-like, and
MIKC*-group genes have been found in that
species (Olsen et al. 2016) suggests that these
gene clades have been lost in the lineage that led
to duckweeds after the lineage that led to more
derived Alismatales had branched-off. Probably
these gene losses are duckweed-specific. In
contrast, FLC-like genes were reported to be
missing in both Spirodela polyrhiza and Zostera
96
L. Gramzow and G. Theißen