16
Small RNAs in Duckweeds
Paul Fourounjian
Abstract
Within eukaryotic genomes, there are several
types of small RNAs including sn, sno, si, and
miRNAs. With respect to the Lemnaceae
family, the vast majority of the research to date
has been conducted in Spirodela polyrhiza,
focused mainly on the miRNAs. This research
consists of three small RNA-sequencing experiments in strains from China, Germany, and the
USA, with each experiment identifying conserved miRNAs and predicting novel miRNAs
and targets. While the novel miRNAs and
recently discovered miRNAs fluctuated, the
family size and expression of well-known
miRNA families was consistent between the
three experiments. While miRBase likely contains many incorrect annotations, these miRNAs were annotated according to strict criteria
and analyzed for the miRBase high confidence
list. They were further characterized through
degradome sequencing, which confirmed half
of the conserved miRNAs and a third of the
novel. Finally, Spirodela polyrhiza has a
surprisingly low abundance of 24nt sRNAs,
which are required to suppress transposon
proliferation.
As scientists moved from sequencing the /X174
virus in 1977 to prokaryote genomes, simple
eukaryotes, and then the first plant, Arabidopsis
thaliana in the year 2000, they saw that these
larger complex genomes were made of so much
more than genes. We now know that eukaryotic
genomes contain a host of structural repeats such
as the centromere and telomere regions. There
are also large stretches of tandem repeats, also
called satellite DNA. Then, there are the
virus-like transposable elements that are often
copied and spread across the genome. Many of
the transcribed RNA sequences are small RNAs
like small interfering, micro, and small nucleolar
RNAs (si, mi, and snoRNAs) that bind to protein
complexes to regulate gene expression and
assemble ribosomes. Larger RNA transcripts
include long non-coding RNAs and the high
copy number ribosomal and transfer RNAs (lnc,
r, and tRNAs) that translate mRNAs to proteins.
Each genome also contains plenty of pseudogenes, which are non-functional due to mutations.
Finally, the genome contains the protein-coding
genes themselves, with all their introns, exons,
cis- and trans-regulatory elements and terminators, which are 2% of the human genome and
roughly 20% of a typical angiosperm genome,
with wide variation due to genome size
differences.
Within this genome, there are several types of
transcribed RNAs, with the longer varieties
including m, r, t, and lncRNA. While the first
three types are well characterized, long
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_16
157
Small RNAs in Duckweeds
Paul Fourounjian
Abstract
Within eukaryotic genomes, there are several
types of small RNAs including sn, sno, si, and
miRNAs. With respect to the Lemnaceae
family, the vast majority of the research to date
has been conducted in Spirodela polyrhiza,
focused mainly on the miRNAs. This research
consists of three small RNA-sequencing experiments in strains from China, Germany, and the
USA, with each experiment identifying conserved miRNAs and predicting novel miRNAs
and targets. While the novel miRNAs and
recently discovered miRNAs fluctuated, the
family size and expression of well-known
miRNA families was consistent between the
three experiments. While miRBase likely contains many incorrect annotations, these miRNAs were annotated according to strict criteria
and analyzed for the miRBase high confidence
list. They were further characterized through
degradome sequencing, which confirmed half
of the conserved miRNAs and a third of the
novel. Finally, Spirodela polyrhiza has a
surprisingly low abundance of 24nt sRNAs,
which are required to suppress transposon
proliferation.
As scientists moved from sequencing the /X174
virus in 1977 to prokaryote genomes, simple
eukaryotes, and then the first plant, Arabidopsis
thaliana in the year 2000, they saw that these
larger complex genomes were made of so much
more than genes. We now know that eukaryotic
genomes contain a host of structural repeats such
as the centromere and telomere regions. There
are also large stretches of tandem repeats, also
called satellite DNA. Then, there are the
virus-like transposable elements that are often
copied and spread across the genome. Many of
the transcribed RNA sequences are small RNAs
like small interfering, micro, and small nucleolar
RNAs (si, mi, and snoRNAs) that bind to protein
complexes to regulate gene expression and
assemble ribosomes. Larger RNA transcripts
include long non-coding RNAs and the high
copy number ribosomal and transfer RNAs (lnc,
r, and tRNAs) that translate mRNAs to proteins.
Each genome also contains plenty of pseudogenes, which are non-functional due to mutations.
Finally, the genome contains the protein-coding
genes themselves, with all their introns, exons,
cis- and trans-regulatory elements and terminators, which are 2% of the human genome and
roughly 20% of a typical angiosperm genome,
with wide variation due to genome size
differences.
Within this genome, there are several types of
transcribed RNAs, with the longer varieties
including m, r, t, and lncRNA. While the first
three types are well characterized, long
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_16
157