6
Strategies and Tools for Sequencing
Duckweeds
Xiaoli Xiang and Changsheng Li
Abstract
Duckweeds belong to the smallest flowering
plants that undergo fast vegetative growth in an
aquatic environment. Due to their special plant
characteristics, they are commonly used in
wastewater treatment, biofuel, and animal feed.
Sequencing duckweed genomes will promote
their development in molecular biology and
functional genomics, thereby facilitating its
application in feed, energy, and environmental
protection. In addition to extremely fast growth
speed, the genome sizes of duckweeds are
varied from 150 to 1881 Mb with a roughly
13-fold change. But with the rapid development of sequencing technology and dramatic
decrease of sequencing cost, sequencing different kinds of duckweed genomes has become
feasible. Here, we review the strategies and
tools for sequencing and assembling duckweeds genomes. We introduce the platforms of
the next-generation sequencing (NGS) (Illumina paired-end sequencing with short reads)
and the third-generation sequencing (TGS)
(PacBio and Nanopore sequencing with long
reads) that are broadly applied in plant
genomics. We also overview the recent widely
used scaffolding technologies including Bionano, Hi-C, and 10X Genomics. Tools for de
novo assembling duckweeds genomes are
determined by the sequencing platforms that
give short reads or long reads. The programs of
SOAPdenovo and ALLPATHS-LG are sufficient to assemble Illumina short reads;
whereas, the assemblers of FALCON, CANU,
MECAT, and HGAP are broadly used in
assembling plant genomes sequenced by the
platforms of PacBio or Nanopore. The hybrid
assembly tool such as MaSuRCA is required
for the integration of short and long reads. We
expect that the strategies and tools will accelerate the duckweed genomics and promote
their industrial applications.
6.1 Strategies for Sequencing
Duckweeds
6.1.1 Illumina Paired-End Sequencing
for Low Complexity
Duckweed Genomes
Next-generation sequencing technologies (NGS),
also known as high-throughput sequencing technologies, can generate unprecedented amounts of
data, greatly facilitating research in genomics and
X. Xiang
Institute of Biotechnology and Nuclear Technology,
Sichuan Academy of Agricultural Sciences,
Chengdu, China
C. Li (&)
Institute of Plant Physiology & Ecology, Shanghai
Institutes for Biological Sciences, Chinese Academy
of Sciences, Beijing, China
e-mail: lcslyh@yahoo.com
© 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_6
67
Strategies and Tools for Sequencing
Duckweeds
Xiaoli Xiang and Changsheng Li
Abstract
Duckweeds belong to the smallest flowering
plants that undergo fast vegetative growth in an
aquatic environment. Due to their special plant
characteristics, they are commonly used in
wastewater treatment, biofuel, and animal feed.
Sequencing duckweed genomes will promote
their development in molecular biology and
functional genomics, thereby facilitating its
application in feed, energy, and environmental
protection. In addition to extremely fast growth
speed, the genome sizes of duckweeds are
varied from 150 to 1881 Mb with a roughly
13-fold change. But with the rapid development of sequencing technology and dramatic
decrease of sequencing cost, sequencing different kinds of duckweed genomes has become
feasible. Here, we review the strategies and
tools for sequencing and assembling duckweeds genomes. We introduce the platforms of
the next-generation sequencing (NGS) (Illumina paired-end sequencing with short reads)
and the third-generation sequencing (TGS)
(PacBio and Nanopore sequencing with long
reads) that are broadly applied in plant
genomics. We also overview the recent widely
used scaffolding technologies including Bionano, Hi-C, and 10X Genomics. Tools for de
novo assembling duckweeds genomes are
determined by the sequencing platforms that
give short reads or long reads. The programs of
SOAPdenovo and ALLPATHS-LG are sufficient to assemble Illumina short reads;
whereas, the assemblers of FALCON, CANU,
MECAT, and HGAP are broadly used in
assembling plant genomes sequenced by the
platforms of PacBio or Nanopore. The hybrid
assembly tool such as MaSuRCA is required
for the integration of short and long reads. We
expect that the strategies and tools will accelerate the duckweed genomics and promote
their industrial applications.
6.1 Strategies for Sequencing
Duckweeds
6.1.1 Illumina Paired-End Sequencing
for Low Complexity
Duckweed Genomes
Next-generation sequencing technologies (NGS),
also known as high-throughput sequencing technologies, can generate unprecedented amounts of
data, greatly facilitating research in genomics and
X. Xiang
Institute of Biotechnology and Nuclear Technology,
Sichuan Academy of Agricultural Sciences,
Chengdu, China
C. Li (&)
Institute of Plant Physiology & Ecology, Shanghai
Institutes for Biological Sciences, Chinese Academy
of Sciences, Beijing, China
e-mail: lcslyh@yahoo.com
© 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_6
67