or Fosmid to improve assembly results. With the
development of sequencing technology, some of
the high-throughput physical mapping technologies have emerged, such as Bionano, chromosome conformation capture (Hi-C), and 10X
Genomics, which compensate the shortcomings
of traditional genetic and physical mapping
techniques (Li et al. 2018).
Different from the method of BAC physical
maps, Bionano technology labels long DNA
molecules at a specific recognition site that is
widely distributed in the genome, then linearizes
and images labeled DNA molecules by Saphyr
instrument to construct the physical maps. The
Bionano optical map can improve the contiguity
of genome assemblies by ordering and orienting
contigs, but also can correct potential chimeric
contigs in genome assemblies and estimate the
gap size between adjacent contigs. A certain
plant genome assembly has been improved by
Bionano in terms of their accuracy and contiguity
without the laborious and expensive construction
of BAC physical maps, such as wheat sequenced
by Illumina and PacBio reads (Zimin et al. 2017),
sorghum using Nanopore reads (Deschamps
et al. 2018), and maize using PacBio reads (Jiao
et al. 2017b). The scaffold N50 of Spirodela
polyrhiza 9509 was improved to 7.7 Mb with the
integration of Bionano optical map, almost twofold of the MP version (4.3 Mb), and reached the
assembly level of Spirodela polyrhiza 7498 with
the scaffolds N50 was 7.6 Mb (Wang et al.
2014).
10X Genomics technology barcodes each
DNA molecule (>50 kb) with the Linked-Reads
(Phillippy 2017) and combines the Illumina
sequencing to extend scaffolds. It is another
long-range scaffolding technology with less cost
but high throughput compared to the traditional
BAC fingerprint technologies. For instance, the
scaffold N50 sizes were significantly increased
from 359.12 Kb to 1.217 Mb for P. equestris
and from 391.46 Kb to 1.055 Mb for D. catenatum with the addition of 10Â Genomics
Linked-Reads (Zhang et al. 2017). There are
currently no duckweed genomes using 10Â
Genomics technology for the scaffold extension.
The technique of Hi-C is able to capture the
genome conformation based on the chromosomal
interaction
rules
to
reconstruct
chromosome-scale genomes (Burton et al. 2013).
Hi-C technique avoids complicated experiments
in genetic and BAC-based physical maps,
resulting in its extensive applications in the following fields:
1. Improvement of draft genome. The initial
genome assembly can be further improved to
the chromosome level by Hi-C information.
By using chromosome conformation capture
data, 6347 super scaffolds of the barley genome were ordered, and 4.54 Gb (*90%) of
the genomic sequence were mapped to the
precise chromosomal location in the Hi-C
map (Mascher et al. 2017).
2. Improvement of the highly heterozygous
plant genome. Because each chromosome
occupies a unique territory, even for homologous chromosomes, it has an important role
in distinguishing heterozygous chromosomes.
For example, durian is a highly heterozygous
genome. With the contact maps of CHiCAGO
(in vitro chromatin reconstitution of highmolecular-weight DNA) and Hi-C (in vivo
fixation of chromosomes), the final reference
assembly reached 30 chromosome-scale
pseudomolecules longer than 10 Mb and
covered 95% of the 712 Mb assembly (Teh
et al. 2017).
3. Improvement of the polyploid genome. Using
single-molecule real-time (SMRT) sequencing technology from PacBio and optical maps
from Bionano, the initial assembly of Chenopodium quinoa (polyploid species) contains 4014 scaffolds, with a scaffold N50 of
2.45 Mb. After using chromosome-intact data
from Dovetail Genomics, the number of
scaffolds was reducing to 3486, with a scaffold N50 of 3.84 Mb. There were 439 scaffolds that covered 90% of the assembled
genome (Jarvis et al. 2017).
The chromosomally integrated genome of
Spirodela polyrhiza was constructed by using
70
X. Xiang and C. Li
development of sequencing technology, some of
the high-throughput physical mapping technologies have emerged, such as Bionano, chromosome conformation capture (Hi-C), and 10X
Genomics, which compensate the shortcomings
of traditional genetic and physical mapping
techniques (Li et al. 2018).
Different from the method of BAC physical
maps, Bionano technology labels long DNA
molecules at a specific recognition site that is
widely distributed in the genome, then linearizes
and images labeled DNA molecules by Saphyr
instrument to construct the physical maps. The
Bionano optical map can improve the contiguity
of genome assemblies by ordering and orienting
contigs, but also can correct potential chimeric
contigs in genome assemblies and estimate the
gap size between adjacent contigs. A certain
plant genome assembly has been improved by
Bionano in terms of their accuracy and contiguity
without the laborious and expensive construction
of BAC physical maps, such as wheat sequenced
by Illumina and PacBio reads (Zimin et al. 2017),
sorghum using Nanopore reads (Deschamps
et al. 2018), and maize using PacBio reads (Jiao
et al. 2017b). The scaffold N50 of Spirodela
polyrhiza 9509 was improved to 7.7 Mb with the
integration of Bionano optical map, almost twofold of the MP version (4.3 Mb), and reached the
assembly level of Spirodela polyrhiza 7498 with
the scaffolds N50 was 7.6 Mb (Wang et al.
2014).
10X Genomics technology barcodes each
DNA molecule (>50 kb) with the Linked-Reads
(Phillippy 2017) and combines the Illumina
sequencing to extend scaffolds. It is another
long-range scaffolding technology with less cost
but high throughput compared to the traditional
BAC fingerprint technologies. For instance, the
scaffold N50 sizes were significantly increased
from 359.12 Kb to 1.217 Mb for P. equestris
and from 391.46 Kb to 1.055 Mb for D. catenatum with the addition of 10Â Genomics
Linked-Reads (Zhang et al. 2017). There are
currently no duckweed genomes using 10Â
Genomics technology for the scaffold extension.
The technique of Hi-C is able to capture the
genome conformation based on the chromosomal
interaction
rules
to
reconstruct
chromosome-scale genomes (Burton et al. 2013).
Hi-C technique avoids complicated experiments
in genetic and BAC-based physical maps,
resulting in its extensive applications in the following fields:
1. Improvement of draft genome. The initial
genome assembly can be further improved to
the chromosome level by Hi-C information.
By using chromosome conformation capture
data, 6347 super scaffolds of the barley genome were ordered, and 4.54 Gb (*90%) of
the genomic sequence were mapped to the
precise chromosomal location in the Hi-C
map (Mascher et al. 2017).
2. Improvement of the highly heterozygous
plant genome. Because each chromosome
occupies a unique territory, even for homologous chromosomes, it has an important role
in distinguishing heterozygous chromosomes.
For example, durian is a highly heterozygous
genome. With the contact maps of CHiCAGO
(in vitro chromatin reconstitution of highmolecular-weight DNA) and Hi-C (in vivo
fixation of chromosomes), the final reference
assembly reached 30 chromosome-scale
pseudomolecules longer than 10 Mb and
covered 95% of the 712 Mb assembly (Teh
et al. 2017).
3. Improvement of the polyploid genome. Using
single-molecule real-time (SMRT) sequencing technology from PacBio and optical maps
from Bionano, the initial assembly of Chenopodium quinoa (polyploid species) contains 4014 scaffolds, with a scaffold N50 of
2.45 Mb. After using chromosome-intact data
from Dovetail Genomics, the number of
scaffolds was reducing to 3486, with a scaffold N50 of 3.84 Mb. There were 439 scaffolds that covered 90% of the assembled
genome (Jarvis et al. 2017).
The chromosomally integrated genome of
Spirodela polyrhiza was constructed by using
70
X. Xiang and C. Li