(2,340) (Sato et al. 2012), and Arabidopsis
(1,938) (Lamesch et al. 2012), but it is surprisingly close to banana (1,048) (D’Hont et al.
2012), which has 1.9 times of the Spirodela gene
number (Wang et al. 2014).
7.10 Resequencing of Spirodela
Genome
The investigation for specific turion (dormant
stage) yields appeared that many factors including phosphate deficiency and temperature could
affect the dormant organ development (Appenroth and Adamec 2015). Spirodela polyrhiza
9509 (Sp9509) was shown to have a low turion
yield. To obtain genome-wide information on
intraspecific variations between different Spirodela populations, Sp9509 was resequenced by
using high-depth short-read sequencing and
high-throughput genome mapping technologies
(Fig. 7.2) (Michael et al. 2017). The draft genome of Sp9509 was assembled and was further
defined into 20 chromosomes with the BioNano
physical map.
The genome comparison between Sp7498 and
Sp9509 revealed conflicts and identified potential
misassembled sites in each genome, indicating
that PCR validations or long reads spanning over
the junctions were required. There were 96
high-confidence structure variations (SVs) with
the range of 1000–100,000 bp between the two
BioNano genome maps of Sp9509 and Sp7498.
The copy number of the rDNA repeats units in
Sp9509, as well as four different accessions of S.
polyrhiza was significantly shrunk less than 100,
which was even fewer than that of yeast (Michael
et al. 2017). There was 25.25% repeat content
with 271 full-length long terminal repeats (LTRs)
in the Sp9509 genome, compared with *17% of
Sp7498 (Wang et al. 2014). The transposon
similarity in Sp9509 was very low against other
species of Brachypodium, rice, and sorghum,
indicating a large evolutionary distance between
them. The overall DNA methylation level in
Spirodela was the lowest (9%) among the tested
plants of A. thaliana (32%), rice (39%), Setaria
italica (44%), and B. distachyon (54%) (Michael
et al. 2017). The high copy number of tandem
repeats (TRs) generally occurs in the chromosome centromeres (Melters et al. 2013). The
Sp7498 genome was predicted to have a 138 bp
centromere repeat-like sequence, whereas
Sp9509 was found a 119 bp TR on 19 out of the
20 chromosomes with high DNA methylation
levels (Michael et al. 2017). The distribution of
the 119 bp centromere repeat across some of the
Spirodela chromosomes suggested that they were
holocentric. This result was consistent with a
dispersed heterochromatin signal observed in
cytological studies (Cao et al. 2015). The bioinformatics analysis predicted that there were 59
conserved microRNAs (miRNAs) of 22 families
and
25
novel
miRNAs.
The
small
RNA-sequencing validated 29 Spirodela-specific
miRNAs in the genome of Sp9509. The
sequence-based annotation identified five and
three loci for miRNA156 and miRNA159 in
Sp9509, respectively (Michael et al. 2017). In
contrast, the Sp7498 genome included 24 loci
encoded for miRNA156 and one locus encoded
for miRNA159 (Wang et al. 2014).
7.11 Going Back to the Native
Ecotypes
Genetic diversity represents a great resource for
the improvement of breeding. Dr. Landolt collected more than 1,000 native ecotypes all over
the world and shifted the biggest collection to
Rutgers duckweed stock cooperative (http://
www.ruduckweed.org) (Fig. 7.2). There are five
genera of duckweeds including 37 species. The
best marker to identify duckweed species is the
atpF-atpH intergenic region (Wang et al. 2010).
Intriguing the large native collection would shed
new light on their charming and thus make the
most use of duckweeds as biofeed, biofuel, and
bioremediator.
7 The Journey of Spirodela Whole-Genome Sequencing
81
(1,938) (Lamesch et al. 2012), but it is surprisingly close to banana (1,048) (D’Hont et al.
2012), which has 1.9 times of the Spirodela gene
number (Wang et al. 2014).
7.10 Resequencing of Spirodela
Genome
The investigation for specific turion (dormant
stage) yields appeared that many factors including phosphate deficiency and temperature could
affect the dormant organ development (Appenroth and Adamec 2015). Spirodela polyrhiza
9509 (Sp9509) was shown to have a low turion
yield. To obtain genome-wide information on
intraspecific variations between different Spirodela populations, Sp9509 was resequenced by
using high-depth short-read sequencing and
high-throughput genome mapping technologies
(Fig. 7.2) (Michael et al. 2017). The draft genome of Sp9509 was assembled and was further
defined into 20 chromosomes with the BioNano
physical map.
The genome comparison between Sp7498 and
Sp9509 revealed conflicts and identified potential
misassembled sites in each genome, indicating
that PCR validations or long reads spanning over
the junctions were required. There were 96
high-confidence structure variations (SVs) with
the range of 1000–100,000 bp between the two
BioNano genome maps of Sp9509 and Sp7498.
The copy number of the rDNA repeats units in
Sp9509, as well as four different accessions of S.
polyrhiza was significantly shrunk less than 100,
which was even fewer than that of yeast (Michael
et al. 2017). There was 25.25% repeat content
with 271 full-length long terminal repeats (LTRs)
in the Sp9509 genome, compared with *17% of
Sp7498 (Wang et al. 2014). The transposon
similarity in Sp9509 was very low against other
species of Brachypodium, rice, and sorghum,
indicating a large evolutionary distance between
them. The overall DNA methylation level in
Spirodela was the lowest (9%) among the tested
plants of A. thaliana (32%), rice (39%), Setaria
italica (44%), and B. distachyon (54%) (Michael
et al. 2017). The high copy number of tandem
repeats (TRs) generally occurs in the chromosome centromeres (Melters et al. 2013). The
Sp7498 genome was predicted to have a 138 bp
centromere repeat-like sequence, whereas
Sp9509 was found a 119 bp TR on 19 out of the
20 chromosomes with high DNA methylation
levels (Michael et al. 2017). The distribution of
the 119 bp centromere repeat across some of the
Spirodela chromosomes suggested that they were
holocentric. This result was consistent with a
dispersed heterochromatin signal observed in
cytological studies (Cao et al. 2015). The bioinformatics analysis predicted that there were 59
conserved microRNAs (miRNAs) of 22 families
and
25
novel
miRNAs.
The
small
RNA-sequencing validated 29 Spirodela-specific
miRNAs in the genome of Sp9509. The
sequence-based annotation identified five and
three loci for miRNA156 and miRNA159 in
Sp9509, respectively (Michael et al. 2017). In
contrast, the Sp7498 genome included 24 loci
encoded for miRNA156 and one locus encoded
for miRNA159 (Wang et al. 2014).
7.11 Going Back to the Native
Ecotypes
Genetic diversity represents a great resource for
the improvement of breeding. Dr. Landolt collected more than 1,000 native ecotypes all over
the world and shifted the biggest collection to
Rutgers duckweed stock cooperative (http://
www.ruduckweed.org) (Fig. 7.2). There are five
genera of duckweeds including 37 species. The
best marker to identify duckweed species is the
atpF-atpH intergenic region (Wang et al. 2010).
Intriguing the large native collection would shed
new light on their charming and thus make the
most use of duckweeds as biofeed, biofuel, and
bioremediator.
7 The Journey of Spirodela Whole-Genome Sequencing
81