3D space of the nucleus (Denker and De Laat 2016). Chromatin contacts within a
TAD are greatly preferred over interactions between sequences in different TADs
(Liu and Weigel 2015). An understanding of TADs and how they function and
evolve will be essential to understanding how plant genomes function and evolve.
2.8 Diploidy and Polyploidy
Most plants are functionally diploid meaning that each chromosome in their 2n cells
has one (and only one) homolog with which it will pair, synapse, and recombine
during meiosis. Being a diploid or behaving like a diploid during meiosis is key to
maintaining the ability to reproduce sexually. The majority of plants maintain sexual
reproduction even if their seeds/spores are typically outcompeted by asexual propagules; e.g., poplar trees are an example of plants that primarily reproduce via root
sprouts but maintain sexual reproduction (DiFazio et al. 2011). The advantages of
sexual reproduction in plants are not as well understood as one might think, yet the
fact that only about 0.1% of flowering plants have lost their ability to reproduce
sexually is indicative of the importance of meiosis and sex to this clade
(Charlesworth 2006).
Polyploidy is a phenomenon through which a genome grows in size through the
addition of another complete genome. While most plants are functionally diploids, it
appears that all plant genomes have undergone polyploidy events in their evolutionary past (Dodsworth et al. 2016). Sometimes these events happened so long ago that
they can only be detected through careful whole genome sequence analyses. Species
that have had polyploidy events in their ancient past are said to be paleopolyploids.
Other species have had polyploidy events happen more recently.
If a species is a true diploid or a paleopolyploid, its diploid cells are said to have
the 2x ploidy level and its gametes have the 1x ploidy level. Such organisms would
have 2C ¼ 2n ¼ 2x somatic cells and 1C ¼ 1n ¼ 1x gametes. Plants with 3, 4, 5, 6,
7, 8, 9, 10, 11, or 12 sets of chromosomes in their somatic cells are called triploids,
tetraploids, pentaploids, hexaploids, heptaploids, octoploids, nonaploids,
decaploids, undecaploids, and dodecaploids, respectively. For higher levels of
polyploidy, a number followed by ploid may be used (e.g., 30-ploid). Species that
have an odd number ploidy level are infertile. Species with even number ploidy
levels may or may not be fertile depending upon how they became polyploids. There
are two primary means by which organisms become polyploids: specifically,
allopolyploidy and autopolyploidy.
2.9 Allopolyploidy
Allopolyploidy is one mechanism by which polyploidy occurs. It is initiated via
hybridization between two related but sexually incompatible species. The species
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TAD are greatly preferred over interactions between sequences in different TADs
(Liu and Weigel 2015). An understanding of TADs and how they function and
evolve will be essential to understanding how plant genomes function and evolve.
2.8 Diploidy and Polyploidy
Most plants are functionally diploid meaning that each chromosome in their 2n cells
has one (and only one) homolog with which it will pair, synapse, and recombine
during meiosis. Being a diploid or behaving like a diploid during meiosis is key to
maintaining the ability to reproduce sexually. The majority of plants maintain sexual
reproduction even if their seeds/spores are typically outcompeted by asexual propagules; e.g., poplar trees are an example of plants that primarily reproduce via root
sprouts but maintain sexual reproduction (DiFazio et al. 2011). The advantages of
sexual reproduction in plants are not as well understood as one might think, yet the
fact that only about 0.1% of flowering plants have lost their ability to reproduce
sexually is indicative of the importance of meiosis and sex to this clade
(Charlesworth 2006).
Polyploidy is a phenomenon through which a genome grows in size through the
addition of another complete genome. While most plants are functionally diploids, it
appears that all plant genomes have undergone polyploidy events in their evolutionary past (Dodsworth et al. 2016). Sometimes these events happened so long ago that
they can only be detected through careful whole genome sequence analyses. Species
that have had polyploidy events in their ancient past are said to be paleopolyploids.
Other species have had polyploidy events happen more recently.
If a species is a true diploid or a paleopolyploid, its diploid cells are said to have
the 2x ploidy level and its gametes have the 1x ploidy level. Such organisms would
have 2C ¼ 2n ¼ 2x somatic cells and 1C ¼ 1n ¼ 1x gametes. Plants with 3, 4, 5, 6,
7, 8, 9, 10, 11, or 12 sets of chromosomes in their somatic cells are called triploids,
tetraploids, pentaploids, hexaploids, heptaploids, octoploids, nonaploids,
decaploids, undecaploids, and dodecaploids, respectively. For higher levels of
polyploidy, a number followed by ploid may be used (e.g., 30-ploid). Species that
have an odd number ploidy level are infertile. Species with even number ploidy
levels may or may not be fertile depending upon how they became polyploids. There
are two primary means by which organisms become polyploids: specifically,
allopolyploidy and autopolyploidy.
2.9 Allopolyploidy
Allopolyploidy is one mechanism by which polyploidy occurs. It is initiated via
hybridization between two related but sexually incompatible species. The species
Sequencing Plant Genomes
121