10
Duckweed Chloroplast Genome
Sequencing and Annotation
Yating Zhang and Wenqin Wang
Abstract
Duckweed chloroplasts make great contributions to their rapid growth and abundant starch
accumulation. The availability of chloroplast
genomes will greatly facilitate the understanding of duckweed traits and further genetic
chloroplast bioengineering. Here, we summarized the progress of duckweed chloroplast
genome sequencing, together with the developments of sequencing technology and bioinformatics tools. The high-quality chloroplast DNA
preparation was specifically emphasized in this
chapter due to the key of genome sequencing.
We also highlighted the potential applications of
chloroplast genomes in the phylogenetic studies
and the improvement of plant desirable traits.
10.1 Introduction
Lemnaceae (duckweeds) is comprised of five
genera of 37 species: Spirodela, Landoltia,
Lemna, Wolffiella, and Wolffia. Their taxonomy
belongs to the basal monocotyledon of flower
plants. They have a list of appealing characteristics in plant science, attracting tremendous
attentions in recent years. As one of the ideal
experimental plants, duckweeds could survive in
an aquatic environment with little nutrients and
even limited space when the high density of
individuals is arrived. They grow quickly often
by the way of asexually reproduction and double
their biomass within two days.
Duckweeds have shown invaluable utilization
in wastewater treatment, source of biofeed and
biofuel (Cheng and Stomp 2009; Stomp and
El-Gewely 2005). The exploration of more native
duckweed ecotypes with the diverse genetic
background is critical in duckweed breeding.
However, the duckweed is a minimalist with an
extremely simple morphology containing few
leaves (called fronds) with or without roots
(Stomp and El-Gewely 2005). The frond size is
less than one centimeter by average. Professor
Elias Landolt from the ETH Zurich, Switzerland
is the father of duckweeds, and he is the only
person who could recognize all 37 species of
duckweeds based on a morphological basis
(Landolt 1986). An expert who does not get a
deep training may hardly distinguish the duckweed sister species. Thus, the highly morphological degeneration becomes a bottleneck to
identify duckweeds efficiently until the appearance of DNA barcode. The Consortium for the
Barcode of Life (CBOL) plant-working group
proposed seven leading candidate sequences all
from the chloroplast genome were the best
promising barcoding markers (Group CPW
2009). A comprehensive study was carried out to
Y. Zhang Á W. Wang (&)
School of Agriculture and Biology, Shanghai Jiao
Tong University, 800 Dong Chuan Road, Shanghai
200240, China
e-mail: wang2015@sjtu.edu.cn
© 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_10
103
Duckweed Chloroplast Genome
Sequencing and Annotation
Yating Zhang and Wenqin Wang
Abstract
Duckweed chloroplasts make great contributions to their rapid growth and abundant starch
accumulation. The availability of chloroplast
genomes will greatly facilitate the understanding of duckweed traits and further genetic
chloroplast bioengineering. Here, we summarized the progress of duckweed chloroplast
genome sequencing, together with the developments of sequencing technology and bioinformatics tools. The high-quality chloroplast DNA
preparation was specifically emphasized in this
chapter due to the key of genome sequencing.
We also highlighted the potential applications of
chloroplast genomes in the phylogenetic studies
and the improvement of plant desirable traits.
10.1 Introduction
Lemnaceae (duckweeds) is comprised of five
genera of 37 species: Spirodela, Landoltia,
Lemna, Wolffiella, and Wolffia. Their taxonomy
belongs to the basal monocotyledon of flower
plants. They have a list of appealing characteristics in plant science, attracting tremendous
attentions in recent years. As one of the ideal
experimental plants, duckweeds could survive in
an aquatic environment with little nutrients and
even limited space when the high density of
individuals is arrived. They grow quickly often
by the way of asexually reproduction and double
their biomass within two days.
Duckweeds have shown invaluable utilization
in wastewater treatment, source of biofeed and
biofuel (Cheng and Stomp 2009; Stomp and
El-Gewely 2005). The exploration of more native
duckweed ecotypes with the diverse genetic
background is critical in duckweed breeding.
However, the duckweed is a minimalist with an
extremely simple morphology containing few
leaves (called fronds) with or without roots
(Stomp and El-Gewely 2005). The frond size is
less than one centimeter by average. Professor
Elias Landolt from the ETH Zurich, Switzerland
is the father of duckweeds, and he is the only
person who could recognize all 37 species of
duckweeds based on a morphological basis
(Landolt 1986). An expert who does not get a
deep training may hardly distinguish the duckweed sister species. Thus, the highly morphological degeneration becomes a bottleneck to
identify duckweeds efficiently until the appearance of DNA barcode. The Consortium for the
Barcode of Life (CBOL) plant-working group
proposed seven leading candidate sequences all
from the chloroplast genome were the best
promising barcoding markers (Group CPW
2009). A comprehensive study was carried out to
Y. Zhang Á W. Wang (&)
School of Agriculture and Biology, Shanghai Jiao
Tong University, 800 Dong Chuan Road, Shanghai
200240, China
e-mail: wang2015@sjtu.edu.cn
© 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_10
103