• In full or part – Viruses, plastids, mitochondria, and prokaryotes normally
reproduce by generating exact replicates of their genomes which they pass to
their progeny. Granted, mistakes in replication, recombination events, and
improper genome partitioning/packaging can lead to progeny with mutations,
but passing a full genome complement to progeny is the norm in the aforementioned entities. In most eukaryotes there are two types of cell division – mitosis
and meiosis. The majority of eukaryotes are functionally diploid meaning they
have two sets of homologous chromosomes in their somatic cells. Mitosis, the
eukaryotic form of asexual reproduction, results in two daughter cells identical to
the parental cell; the full parental genome (including each homologous pair) is
passed to both daughter cells. Meiosis, which involves a highly modified first cell
division followed by a fairly standard mitotic division, results in the production of
gametes, each containing half the number of chromosomes from which they were
derived. Sex involves the fusion of two gametes, often, but not always, from
different individuals of the same species; this restores the chromosome number in
the resulting zygote to that of the parents. In asexual reproduction, the genome of
an entity is passed to its progeny in full, while in sexual reproduction, only part of
a cell’s genetic information (ca. one-half) is passed to its offspring.
2.2 Which Genome Is the Plant Genome?
Plants have three distinct genomes: a nuclear genome, a chloroplast genome, and a
mitochondrial genome. While mitochondrial and chloroplasts are derived from once
free-living bacteria, these organellar genomes have evolved within the environment
of the plant cell and are essential to plant survival. Hence, they are truly plant
genomes and can be used in plant phylogenetic research. However, when one says
they are sequencing the genome of Zea mays, it is assumed that they are sequencing
the Zea mays nuclear genome. If they are sequencing a chloroplast or mitochondrial
genome, they are expected to indicate this (e.g., Zea mays mitochondrial genome).
With regard to the remainder of this review, all discussions will focus on nuclear
genomes.
2.3 What Are C Value and n Value?
A complication when discussing plant nuclear genomes is rooted in the fact that the
amount of DNA in a cell and the number of chromosomes in the cell nucleus differ
based upon the cell’s stage in the cell cycle and/or its developmental fate. Cells in G 1
are said to contain the 2C DNA amount (where “C” stands for constant) (Bennett and
Leitch 2005) and two homologous chromosome sets (i.e., they have the 2n chromosome number where “n” stands for number). A shorthand way of writing this is
2C ¼ 2n or 2n ¼ 2C. Cells that have completed S phase (DNA replication) are
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reproduce by generating exact replicates of their genomes which they pass to
their progeny. Granted, mistakes in replication, recombination events, and
improper genome partitioning/packaging can lead to progeny with mutations,
but passing a full genome complement to progeny is the norm in the aforementioned entities. In most eukaryotes there are two types of cell division – mitosis
and meiosis. The majority of eukaryotes are functionally diploid meaning they
have two sets of homologous chromosomes in their somatic cells. Mitosis, the
eukaryotic form of asexual reproduction, results in two daughter cells identical to
the parental cell; the full parental genome (including each homologous pair) is
passed to both daughter cells. Meiosis, which involves a highly modified first cell
division followed by a fairly standard mitotic division, results in the production of
gametes, each containing half the number of chromosomes from which they were
derived. Sex involves the fusion of two gametes, often, but not always, from
different individuals of the same species; this restores the chromosome number in
the resulting zygote to that of the parents. In asexual reproduction, the genome of
an entity is passed to its progeny in full, while in sexual reproduction, only part of
a cell’s genetic information (ca. one-half) is passed to its offspring.
2.2 Which Genome Is the Plant Genome?
Plants have three distinct genomes: a nuclear genome, a chloroplast genome, and a
mitochondrial genome. While mitochondrial and chloroplasts are derived from once
free-living bacteria, these organellar genomes have evolved within the environment
of the plant cell and are essential to plant survival. Hence, they are truly plant
genomes and can be used in plant phylogenetic research. However, when one says
they are sequencing the genome of Zea mays, it is assumed that they are sequencing
the Zea mays nuclear genome. If they are sequencing a chloroplast or mitochondrial
genome, they are expected to indicate this (e.g., Zea mays mitochondrial genome).
With regard to the remainder of this review, all discussions will focus on nuclear
genomes.
2.3 What Are C Value and n Value?
A complication when discussing plant nuclear genomes is rooted in the fact that the
amount of DNA in a cell and the number of chromosomes in the cell nucleus differ
based upon the cell’s stage in the cell cycle and/or its developmental fate. Cells in G 1
are said to contain the 2C DNA amount (where “C” stands for constant) (Bennett and
Leitch 2005) and two homologous chromosome sets (i.e., they have the 2n chromosome number where “n” stands for number). A shorthand way of writing this is
2C ¼ 2n or 2n ¼ 2C. Cells that have completed S phase (DNA replication) are
116
D. G. Peterson and M. Arick