8
Repetitive Sequences: Impacts
and Uses in the Spirodela Genome
Paul Fourounjian
Abstract
Repetitive DNA, consisting of small and large
satellite repeats and transposable elements,
comprises over 50% of most plant genomes.
The Lemnaceae family demonstrates a
*12-fold difference in genome size and
relatively similar number of genes, indicating
a wide variability in repeat content. The best
studied genome of the family Spirodela
polyrhiza had a normal total satellite DNA
content, yet a surprisingly high 50% of those
were dinucleotide microsatellite repeats. The
telomeres and 119 bp centromere repeats were
typical, although ribosomal repeats appear
scarce. Genomic studies showed a small
number of 24nt heterochromatic siRNAs
accompanied by the lowest rate of DNA
methylation seen in any plant sequenced at
9% and low rates of heterochromatin formation. Despite this low level of regulation, the
transposable elements are unexpectedly rare
and old. In fact, they even show high rates of
DNA methylation and high rates of inactivation through illegitimate recombination. This
suggests that the scarce 24nt siRNAs are
surprisingly effective and an intriguing topic
of further research.
In the early years of DNA and chromosome
research, structural components of chromosomes
were noticed as patterns in DNA and protein
stains, often in the centromeric or telomeric
regions. Once DNA sequencing began it was
uncovered that virtually all eukaryotic genomes
contain significant portions of repetitive DNA,
previously thought of as “junk DNA” (Biscotti
et al. 2015). In plants, repetitive elements comprise the majority of most genomes sequenced,
ranging from a mere 14% in the grain teff to 85%
in maize (Wendel et al. 2016). These repetitive
elements can be categorized into tandem repeats
which aid in chromosome structure, and longer
interspersed repeats derived from transposable
elements (TEs). As of 2018 there are two published sequences for Spirodela polyrhiza clones
7498 and 9509, and the Lemna minor 5500,
along with draft genomes of two Lemna species
minor and gibba and the Wolffia species australiana (Unpublished), (Wang et al. 2014; Van
Hoeck et al. 2015; Ernst and Martienssen 2016;
Michael et al. 2017). Similar to other angiosperms as a whole, these genomes vary considerably in size, but not significantly in gene
number (Table 8.1). The Lemnaceae family displays a 12-fold difference in genome size from
the smallest sequenced monocot Spirodela
polyrhiza to the 1881 megabase Wolffia arrhiza
(Wang et al. 2011). A recent review on plant
genome architecture summarized that these size
variations between genomes are due to common
whole genome duplication, followed by
P. Fourounjian (&)
Waksman Institute of Microbiology, Rutgers
University, Piscataway 08854, USA
e-mail: pjf99@scarletmail.rutgers.edu
© Springer Nature Switzerland AG 2020
X. H. Cao et al. (eds.), The Duckweed Genomes, Compendium of Plant Genomes,
https://doi.org/10.1007/978-3-030-11045-1_8
87
Repetitive Sequences: Impacts
and Uses in the Spirodela Genome
Paul Fourounjian
Abstract
Repetitive DNA, consisting of small and large
satellite repeats and transposable elements,
comprises over 50% of most plant genomes.
The Lemnaceae family demonstrates a
*12-fold difference in genome size and
relatively similar number of genes, indicating
a wide variability in repeat content. The best
studied genome of the family Spirodela
polyrhiza had a normal total satellite DNA
content, yet a surprisingly high 50% of those
were dinucleotide microsatellite repeats. The
telomeres and 119 bp centromere repeats were
typical, although ribosomal repeats appear
scarce. Genomic studies showed a small
number of 24nt heterochromatic siRNAs
accompanied by the lowest rate of DNA
methylation seen in any plant sequenced at
9% and low rates of heterochromatin formation. Despite this low level of regulation, the
transposable elements are unexpectedly rare
and old. In fact, they even show high rates of
DNA methylation and high rates of inactivation through illegitimate recombination. This
suggests that the scarce 24nt siRNAs are
surprisingly effective and an intriguing topic
of further research.
In the early years of DNA and chromosome
research, structural components of chromosomes
were noticed as patterns in DNA and protein
stains, often in the centromeric or telomeric
regions. Once DNA sequencing began it was
uncovered that virtually all eukaryotic genomes
contain significant portions of repetitive DNA,
previously thought of as “junk DNA” (Biscotti
et al. 2015). In plants, repetitive elements comprise the majority of most genomes sequenced,
ranging from a mere 14% in the grain teff to 85%
in maize (Wendel et al. 2016). These repetitive
elements can be categorized into tandem repeats
which aid in chromosome structure, and longer
interspersed repeats derived from transposable
elements (TEs). As of 2018 there are two published sequences for Spirodela polyrhiza clones
7498 and 9509, and the Lemna minor 5500,
along with draft genomes of two Lemna species
minor and gibba and the Wolffia species australiana (Unpublished), (Wang et al. 2014; Van
Hoeck et al. 2015; Ernst and Martienssen 2016;
Michael et al. 2017). Similar to other angiosperms as a whole, these genomes vary considerably in size, but not significantly in gene
number (Table 8.1). The Lemnaceae family displays a 12-fold difference in genome size from
the smallest sequenced monocot Spirodela
polyrhiza to the 1881 megabase Wolffia arrhiza
(Wang et al. 2011). A recent review on plant
genome architecture summarized that these size
variations between genomes are due to common
whole genome duplication, followed by
P. Fourounjian (&)
Waksman Institute of Microbiology, Rutgers
University, Piscataway 08854, USA
e-mail: pjf99@scarletmail.rutgers.edu
© Springer Nature Switzerland AG 2020
X. H. Cao et al. (eds.), The Duckweed Genomes, Compendium of Plant Genomes,
https://doi.org/10.1007/978-3-030-11045-1_8
87