or missing chromosomes (aneuploidy), interspecific hybridization, large-scale chromosome rearrangements, and massive epigenetic changes are common in plants
(Leitch and Leitch 2008). The plasticity of plant genomes appears to be central to the
evolutionary success of plants, most notably the angiosperms which account for
roughly 90% of plant species (Chapman 2009). It can also make plant genome
research (including genome sequencing) extremely challenging.
In this chapter, we will discuss the history and current state of plant genome
sequencing. In addition, we will provide an overview of terminology used in
discussing genomes and genome sequencing, a review of technology and techniques
utilized in sequencing and assembling genomes, and a brief overview of what has
been learned from plant genome sequencing projects.
2 Fundamental Concepts When Considering Genomes
and Genome Sequences
2.1 What Is a Genome?
This is actually not an easy question to answer. In broad terms, a genome is nucleic
acid that contains within its nucleotide sequence the genetic information that defines
an entity and through which that entity transmits, in full or part, its genetic information to future generations. Note that we italicized three particular wording
choices, specifically, entity, nucleic acid, and in full or part. Here is why.
• Entity – We use the term entity in the definition because the more obvious word
choice, organism, implies life, and not all things that have a genome are alive.
While it is true that all living creatures possess genomes, viruses and viroids are
nonliving infectious agents with their own genomes. Likewise, although plastids
and mitochondria evolved from bacteria (i.e., living cells), they are now “lifeless”
eukaryotic organelles with genomes that have been stripped of most of the genes
required for independent existence. Lastly, while death is typically associated
with degeneration of nucleic acids, genomes do not decay immediately and, in
certain environmental situations, may be partially preserved for extremely long
periods of time. The relative stability of DNA in particular allows the genomes of
deceased cells to be used in forensic identification of victims and/or potential
culprits of violent crime (e.g., semen, blood, and/or skin tissues left at crime
scenes can be used to narrow down suspects in rape and murder cases) (Butler
2015). Moreover, well-preserved tissues may allow study of the genomes of
ancient and/or extinct organisms (see Shapiro and Hofreiter 2014, for review).
• Nucleic acid – While all known living creatures have genomes composed of
DNA, all viroids and the majority of viruses possess RNA genomes (Gelderblom
1996). Indeed, the genomes of viruses may be composed of double-stranded
DNA (dsDNA), single-stranded DNA (ssDNA), single-stranded RNA (ssRNA),
or double-stranded RNA (dsRNA) (van Regenmortel and Mahy 2004).
Sequencing Plant Genomes
115
(Leitch and Leitch 2008). The plasticity of plant genomes appears to be central to the
evolutionary success of plants, most notably the angiosperms which account for
roughly 90% of plant species (Chapman 2009). It can also make plant genome
research (including genome sequencing) extremely challenging.
In this chapter, we will discuss the history and current state of plant genome
sequencing. In addition, we will provide an overview of terminology used in
discussing genomes and genome sequencing, a review of technology and techniques
utilized in sequencing and assembling genomes, and a brief overview of what has
been learned from plant genome sequencing projects.
2 Fundamental Concepts When Considering Genomes
and Genome Sequences
2.1 What Is a Genome?
This is actually not an easy question to answer. In broad terms, a genome is nucleic
acid that contains within its nucleotide sequence the genetic information that defines
an entity and through which that entity transmits, in full or part, its genetic information to future generations. Note that we italicized three particular wording
choices, specifically, entity, nucleic acid, and in full or part. Here is why.
• Entity – We use the term entity in the definition because the more obvious word
choice, organism, implies life, and not all things that have a genome are alive.
While it is true that all living creatures possess genomes, viruses and viroids are
nonliving infectious agents with their own genomes. Likewise, although plastids
and mitochondria evolved from bacteria (i.e., living cells), they are now “lifeless”
eukaryotic organelles with genomes that have been stripped of most of the genes
required for independent existence. Lastly, while death is typically associated
with degeneration of nucleic acids, genomes do not decay immediately and, in
certain environmental situations, may be partially preserved for extremely long
periods of time. The relative stability of DNA in particular allows the genomes of
deceased cells to be used in forensic identification of victims and/or potential
culprits of violent crime (e.g., semen, blood, and/or skin tissues left at crime
scenes can be used to narrow down suspects in rape and murder cases) (Butler
2015). Moreover, well-preserved tissues may allow study of the genomes of
ancient and/or extinct organisms (see Shapiro and Hofreiter 2014, for review).
• Nucleic acid – While all known living creatures have genomes composed of
DNA, all viroids and the majority of viruses possess RNA genomes (Gelderblom
1996). Indeed, the genomes of viruses may be composed of double-stranded
DNA (dsDNA), single-stranded DNA (ssDNA), single-stranded RNA (ssRNA),
or double-stranded RNA (dsRNA) (van Regenmortel and Mahy 2004).
Sequencing Plant Genomes
115