The Spirodela genome is completed by the
cooperation of the international consortium. The
availability of whole-genome sequence relies on
the technologies of high-throughput sequencing,
BAC-end sequencing, and the physical map. The
duckweed collection provides the germplasm
with the broadly genetic diversity. Resequencing
more Spirodela genomes would decipher the
genomic variation associated with the phenotypic
change.
7.7 Sequencing Overview
Spirodela polyrhiza 7498 (Sp7498) has a small
plant genome of 158 Mb (Wang et al. 2011),
similar to Arabidopsis (Bennett et al. 2003) but
nearly half as many as the rice genome (Matsumoto et al. 2005) that was subjected to
whole-genome shotgun sequence by using
next-generation sequencing technology of Roche
454 (Fig. 7.2) (Wang et al. 2014). Nine million
single-end and 1.4 million paired-end reads were
generated, which resulted in 21 times of genome
coverage. In addition, the Sanger sequencing
produced one sequencing depth of BAC-end
sequencing from the 15,360 BAC clones
(Fig. 7.2). The reads were de novo assembled by
Newbler version 2.6 with default parameters after
trimming poor bases from ends and masking
vector sequences. The contig N50 was
18,927 bp, and scaffold N50 was 3,759,109 bp,
respectively. Of the 158 Mb genome, as measured by flow cytometry, 90% was assembled
into contigs, 97% of which was assembled in 252
scaffolds, and 94.1% in the top 50 largest scaffolds (Wang et al. 2014).
7.8 Construction of Physical Map
A BAC library with 100 Kb insertion was constructed with 40 times of genome coverage.
A total of 15,360 clones were subjected to DNA
fingerprinting, generating a physical map
(Fig. 7.2). We also used BAC-end sequences
(BES) to anchor the assembly with the physical
map, leading to the scaffolds joined into 32
pseudomolecules (Fig. 7.2). Gaps in sequences
like centromeres amounted to 10.7% of the
genome and remained in unnamed bases
(Ns) (Wang et al. 2014). To examine how the 32
pseudomolecules relate to the 20 chromosomes
of the haploid genome of Spirodela polyrhiza, a
fluorescence in situ hybridization (FISH) was
conducted by selecting those BACs that were
low in repeat sequences (Cao et al. 2016). A cytogenetic map with an average distance of
0.89 Mb was constructed by consecutive FISH
analyses. Seven ancestral blocks emerged from
duplicated chromosome segments of 19 Spirodela chromosomes were elucidated. The chromosomally integrated genome of Sp7498
established a framework for comparative genomics and karyotype evolution of duckweed species (Cao et al. 2016).
7.9 Spirodela Genes
Whole-genome sequence provides access to the
total number of genes that contribute to the
growth, development, and stress response.
Increasing studies of individual genes and their
corresponding gene families have elucidated
their functions in diverse molecular, physiological, and biological processes and have provided
novel clues on their regulation and gene
expression. A number of 19,623 protein-coding
genes were annotated by an integrated pipeline,
showing 28% less copies than Arabidopsis
(27,416) (Bennett et al. 2003) and 50% less
copies than rice (37,544) (Matsumoto et al.
2005). The small duckweed genome turns out
many missing genes, including those for plant
maturation and production of cellulose and lignin, whereas it retains more genes for starch
production than comparable genomes. The most
surprising finding was the insight into the
molecular basis involved in maintaining a
forever-young lifestyle. Spirodela had fewer
genes to promote and more genes to repress the
switch from juvenile to mature growth.
Spirodela appears to have a significantly
lower number of tandem gene clusters (948) than
rice (2,602) (Matsumoto et al. 2005), tomato
80
D. An and W. Wang
cooperation of the international consortium. The
availability of whole-genome sequence relies on
the technologies of high-throughput sequencing,
BAC-end sequencing, and the physical map. The
duckweed collection provides the germplasm
with the broadly genetic diversity. Resequencing
more Spirodela genomes would decipher the
genomic variation associated with the phenotypic
change.
7.7 Sequencing Overview
Spirodela polyrhiza 7498 (Sp7498) has a small
plant genome of 158 Mb (Wang et al. 2011),
similar to Arabidopsis (Bennett et al. 2003) but
nearly half as many as the rice genome (Matsumoto et al. 2005) that was subjected to
whole-genome shotgun sequence by using
next-generation sequencing technology of Roche
454 (Fig. 7.2) (Wang et al. 2014). Nine million
single-end and 1.4 million paired-end reads were
generated, which resulted in 21 times of genome
coverage. In addition, the Sanger sequencing
produced one sequencing depth of BAC-end
sequencing from the 15,360 BAC clones
(Fig. 7.2). The reads were de novo assembled by
Newbler version 2.6 with default parameters after
trimming poor bases from ends and masking
vector sequences. The contig N50 was
18,927 bp, and scaffold N50 was 3,759,109 bp,
respectively. Of the 158 Mb genome, as measured by flow cytometry, 90% was assembled
into contigs, 97% of which was assembled in 252
scaffolds, and 94.1% in the top 50 largest scaffolds (Wang et al. 2014).
7.8 Construction of Physical Map
A BAC library with 100 Kb insertion was constructed with 40 times of genome coverage.
A total of 15,360 clones were subjected to DNA
fingerprinting, generating a physical map
(Fig. 7.2). We also used BAC-end sequences
(BES) to anchor the assembly with the physical
map, leading to the scaffolds joined into 32
pseudomolecules (Fig. 7.2). Gaps in sequences
like centromeres amounted to 10.7% of the
genome and remained in unnamed bases
(Ns) (Wang et al. 2014). To examine how the 32
pseudomolecules relate to the 20 chromosomes
of the haploid genome of Spirodela polyrhiza, a
fluorescence in situ hybridization (FISH) was
conducted by selecting those BACs that were
low in repeat sequences (Cao et al. 2016). A cytogenetic map with an average distance of
0.89 Mb was constructed by consecutive FISH
analyses. Seven ancestral blocks emerged from
duplicated chromosome segments of 19 Spirodela chromosomes were elucidated. The chromosomally integrated genome of Sp7498
established a framework for comparative genomics and karyotype evolution of duckweed species (Cao et al. 2016).
7.9 Spirodela Genes
Whole-genome sequence provides access to the
total number of genes that contribute to the
growth, development, and stress response.
Increasing studies of individual genes and their
corresponding gene families have elucidated
their functions in diverse molecular, physiological, and biological processes and have provided
novel clues on their regulation and gene
expression. A number of 19,623 protein-coding
genes were annotated by an integrated pipeline,
showing 28% less copies than Arabidopsis
(27,416) (Bennett et al. 2003) and 50% less
copies than rice (37,544) (Matsumoto et al.
2005). The small duckweed genome turns out
many missing genes, including those for plant
maturation and production of cellulose and lignin, whereas it retains more genes for starch
production than comparable genomes. The most
surprising finding was the insight into the
molecular basis involved in maintaining a
forever-young lifestyle. Spirodela had fewer
genes to promote and more genes to repress the
switch from juvenile to mature growth.
Spirodela appears to have a significantly
lower number of tandem gene clusters (948) than
rice (2,602) (Matsumoto et al. 2005), tomato
80
D. An and W. Wang