4 representatives, respectively. The most species-rich angiosperm families (Asteraceae
or Compositae and Orchidaceae) have 1 and 0 representatives, respectively.
7 What Genome Sequencing Has Revealed About Plant
Genome Structure and Function
Sequencing of plant genomes has resulted in some new discoveries about plant
evolution and genetics and reinforced a number of previously observed trends.
7.1 Whole Genome Duplications Are Very Common
It has long been known that whole genome duplications (WGDs) are common in
angiosperms. However, it wasn’t until whole genome sequencing that the extent to
which plant genomes (angiosperms and other lineages) have been shaped by ancient
polyploidy events began to become apparent.
Intra- and inter-genome comparisons indicate that paleopolyploidy is a feature of
the evolutionary histories of all land plants and probably all eukaryotic organisms
13 ;
even the yeast Saccharomyces cerevisiae, with a genome one-fifth the size of the
smallest plant genome, is a paleopolyploid (Wong et al. 2002). In retrospect, this is
perhaps not that surprising. New genes rarely arise de novo, they are typically
derivations of duplicated existing genes, and whole genome duplication is ostensibly
one route that plants have used to increase their gene repertoires time and again.
As discussed by Garsmeur et al. (2014), whole genome duplication events
typically are followed by preferential loss of most duplicated genes via
intrachromosomal recombination. This process, called fractionation, can preferentially target one of the subgenomes (biased fractionation) or may be fairly balanced
between subgenomes (unbiased fractionation). Fractionation and divergence of gene
duplicates (whether they are homologs, homeologs, orthologs, or paralogs) are
critical parts of diploidization (Paterson et al. 2004).
The actual number of times a plant lineage has experienced whole genome
duplications is not straightforward. Very ancient paleopolyploid events have likely
become undetectable. Likewise, allopolyploidy events may not involve parental
species with the same ploidy level, a fact that can complicate paleopolyploidy
research.
Figure 10 shows WGDs in plants based on DNA sequence data. The figure was
last modified on April 3, 2013, so it is missing information from plants that have had
their genomes sequenced since then. Recent sequence analysis suggests that
13 Even the yeast Saccharomyces cerevisiae, with a genome one-fifth the size of the smallest plant
genome, is a paleopolyploid (Wong et al. 2002).
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D. G. Peterson and M. Arick
or Compositae and Orchidaceae) have 1 and 0 representatives, respectively.
7 What Genome Sequencing Has Revealed About Plant
Genome Structure and Function
Sequencing of plant genomes has resulted in some new discoveries about plant
evolution and genetics and reinforced a number of previously observed trends.
7.1 Whole Genome Duplications Are Very Common
It has long been known that whole genome duplications (WGDs) are common in
angiosperms. However, it wasn’t until whole genome sequencing that the extent to
which plant genomes (angiosperms and other lineages) have been shaped by ancient
polyploidy events began to become apparent.
Intra- and inter-genome comparisons indicate that paleopolyploidy is a feature of
the evolutionary histories of all land plants and probably all eukaryotic organisms
13 ;
even the yeast Saccharomyces cerevisiae, with a genome one-fifth the size of the
smallest plant genome, is a paleopolyploid (Wong et al. 2002). In retrospect, this is
perhaps not that surprising. New genes rarely arise de novo, they are typically
derivations of duplicated existing genes, and whole genome duplication is ostensibly
one route that plants have used to increase their gene repertoires time and again.
As discussed by Garsmeur et al. (2014), whole genome duplication events
typically are followed by preferential loss of most duplicated genes via
intrachromosomal recombination. This process, called fractionation, can preferentially target one of the subgenomes (biased fractionation) or may be fairly balanced
between subgenomes (unbiased fractionation). Fractionation and divergence of gene
duplicates (whether they are homologs, homeologs, orthologs, or paralogs) are
critical parts of diploidization (Paterson et al. 2004).
The actual number of times a plant lineage has experienced whole genome
duplications is not straightforward. Very ancient paleopolyploid events have likely
become undetectable. Likewise, allopolyploidy events may not involve parental
species with the same ploidy level, a fact that can complicate paleopolyploidy
research.
Figure 10 shows WGDs in plants based on DNA sequence data. The figure was
last modified on April 3, 2013, so it is missing information from plants that have had
their genomes sequenced since then. Recent sequence analysis suggests that
13 Even the yeast Saccharomyces cerevisiae, with a genome one-fifth the size of the smallest plant
genome, is a paleopolyploid (Wong et al. 2002).
168
D. G. Peterson and M. Arick