repeat families composed of only or two representatives (Wegrzyn et al. 2013;
Perera et al. 2018; Pellicer et al. 2018; Guan et al. 2016). Interestingly, while
possessing relatively small genomes, the gnetophyte gymnosperm, Gnetum
montanum (1C ¼ 4.2 Gb), and Amborella trichopoda (1C ¼ 0.87 Gb), the sole
surviving member of a sister group to all extant angiosperms (see Fig. 10), also are
characterized by ancient, highly diverged repeats (Wan et al. 2018; Amborella
Genome Project 2013).
8 Genomes as Maps
What is a map? In general, a map is a simplified representation of something that is
much more complex. Its most common purpose is to serve as a tractable guide by
which its user can find and/or explore previously studied places while avoiding
obstacles/dangers. Maps typically start off quite crude and simple. However, with
increased research and improvements in technology, maps become more accurate
and informative (Fig. 12). Nonetheless, maps must not be confused with what they
represent. A map of Europe is not equivalent to Europe itself; the map provides only
a little bit of information about Europe, most notably the relative locations of towns
and geographical landmarks. Certainly, more and more information can be added to
a map, but a map that contains too much detail as to be difficult to read is as
frustrating as a map that is not detailed enough.
Geneticists and molecular biologists have long utilized the word “map.” Genetic,
molecular, recombination, physical, QTL (quantitative trait loci), cytomolecular,
proteogenomic, and optical are just a few of the examples of maps utilized in
studying plants and other eukaryotes. Oftentimes, the aforementioned map types
are utilized to position DNA sequences along chromosomes.
So is a genome sequence a map or has it moved out of the realm of mapdom?
A genome sequence is still very much a map. It provides information on the linear
order of nucleotides along chromosomal strands of DNA and, when annotated,
shows the locations of landmarks and their potential functions. However, just as a
map of Europe represents something many, many orders of magnitude more complex than the map itself, a plant genome sequence also is but a crude glimpse into a
plant, one of the amazing products of billions of years of evolution.
There is a very important function of maps that has not yet been mentioned. Maps
are used by those seeking adventures, those looking to learn more about features on the
map, and those seeking to find novel, exciting things that others have overlooked or
not seen. Genome sequence maps are crude sketches of largely unexplored territories.
All of these territories are beautiful and wondrous. Some are ancient; some are
relatively new. Methods like Hi-C that provide a glimpse into how chromatin/chromosome interacts in living cells will help give a more accurate assessment of how
genomes function and evolve. Functional genomics and biochemistry will be needed
to understand the roles of coding and noncoding sequences and study their interactions. Integrating the numerous environmental, developmental, and epigenetic signals
Sequencing Plant Genomes
173
Perera et al. 2018; Pellicer et al. 2018; Guan et al. 2016). Interestingly, while
possessing relatively small genomes, the gnetophyte gymnosperm, Gnetum
montanum (1C ¼ 4.2 Gb), and Amborella trichopoda (1C ¼ 0.87 Gb), the sole
surviving member of a sister group to all extant angiosperms (see Fig. 10), also are
characterized by ancient, highly diverged repeats (Wan et al. 2018; Amborella
Genome Project 2013).
8 Genomes as Maps
What is a map? In general, a map is a simplified representation of something that is
much more complex. Its most common purpose is to serve as a tractable guide by
which its user can find and/or explore previously studied places while avoiding
obstacles/dangers. Maps typically start off quite crude and simple. However, with
increased research and improvements in technology, maps become more accurate
and informative (Fig. 12). Nonetheless, maps must not be confused with what they
represent. A map of Europe is not equivalent to Europe itself; the map provides only
a little bit of information about Europe, most notably the relative locations of towns
and geographical landmarks. Certainly, more and more information can be added to
a map, but a map that contains too much detail as to be difficult to read is as
frustrating as a map that is not detailed enough.
Geneticists and molecular biologists have long utilized the word “map.” Genetic,
molecular, recombination, physical, QTL (quantitative trait loci), cytomolecular,
proteogenomic, and optical are just a few of the examples of maps utilized in
studying plants and other eukaryotes. Oftentimes, the aforementioned map types
are utilized to position DNA sequences along chromosomes.
So is a genome sequence a map or has it moved out of the realm of mapdom?
A genome sequence is still very much a map. It provides information on the linear
order of nucleotides along chromosomal strands of DNA and, when annotated,
shows the locations of landmarks and their potential functions. However, just as a
map of Europe represents something many, many orders of magnitude more complex than the map itself, a plant genome sequence also is but a crude glimpse into a
plant, one of the amazing products of billions of years of evolution.
There is a very important function of maps that has not yet been mentioned. Maps
are used by those seeking adventures, those looking to learn more about features on the
map, and those seeking to find novel, exciting things that others have overlooked or
not seen. Genome sequence maps are crude sketches of largely unexplored territories.
All of these territories are beautiful and wondrous. Some are ancient; some are
relatively new. Methods like Hi-C that provide a glimpse into how chromatin/chromosome interacts in living cells will help give a more accurate assessment of how
genomes function and evolve. Functional genomics and biochemistry will be needed
to understand the roles of coding and noncoding sequences and study their interactions. Integrating the numerous environmental, developmental, and epigenetic signals
Sequencing Plant Genomes
173