5.5 Second Generation Alone
As confidence in NGS techniques increased, more genomes were assembled solely
from second-generation reads. Different insert size libraries and mate-pair sequencing were essential in assembly of these genomes. Examples of genome assembled
using second-generation sequencing alone include saltwater cress (Dassanayake
et al. 2011), brown mustard (Yang et al. 2016), Hall’s panicgrass, pepper,
A-genome cotton, narrow-leaved lupin (Yang et al. 2013; Hane et al. 2017), sesame
(Wang et al. 2014a), cut-grass, sweet orange (Xu et al. 2013), mung bean (Kang et al.
2014), asparagus, field mustard (Wang et al. 2011), Oryza punctate,
O. longistaminata (Zhang et al. 2015b), O. glumipatula, O. brachyantha (Chen
et al. 2013a), O. meridionalis, rapeseed, adzuki bean (Yang et al. 2015), black
mustard, Indian wild rice, chickpea (Varshney et al. 2013), common jujube (Liu
et al. 2014), false flax (Kagale et al. 2014), Japanese apricot (Zhang et al. 2012), wild
strawberry (Shulaev et al. 2011), cassava, A- and B-genome peanuts (Bertioli et al.
2016), Guinea yam, African wild rice, pearl millet (Varshney et al. 2017), and red
clover (Ištvánek et al. 2014). Although the preceding genomes have high enough
quality to make the list in Table 3, the use of only second-generation sequencing, in
general, greatly hobbled the quality of genome assemblies. In brief, the genes and
unique regions of genomes could often be assembled fairly easily. However, the
short-read lengths prevented assembly of many repetitive regions. Of note, Illumina
sequencing of wild emmer wheat was greatly enhanced by the addition of Hi-C
chromatin configuration sequencing/analysis (Avni et al. 2017).
5.6 Third- + Second-Generation Sequencing
Third-generation sequencing, while still lacking the accuracy and output of Illumina
sequencers, provides relatively long-read lengths that can be used to help link
contigs into scaffolds. Alternatively, contigs/scaffolds generated using thirdgeneration reads can be “polished” using Illumina reads to correct mistakes and
fill in gaps. Genomes that have been sequenced and assembled using a combination
of second- and third-generation platforms include pummelo (Wang et al. 2017),
sunflower (Badouin et al. 2017), pineapple (Ming et al. 2015), and coyote tobacco.
Moreover, several published genomes assembled using first- and second-generation
technologies have later been improved by incorporating third-generation long-read
sequencing data (e.g., Jiao et al. 2017; Zimin et al. 2017).
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As confidence in NGS techniques increased, more genomes were assembled solely
from second-generation reads. Different insert size libraries and mate-pair sequencing were essential in assembly of these genomes. Examples of genome assembled
using second-generation sequencing alone include saltwater cress (Dassanayake
et al. 2011), brown mustard (Yang et al. 2016), Hall’s panicgrass, pepper,
A-genome cotton, narrow-leaved lupin (Yang et al. 2013; Hane et al. 2017), sesame
(Wang et al. 2014a), cut-grass, sweet orange (Xu et al. 2013), mung bean (Kang et al.
2014), asparagus, field mustard (Wang et al. 2011), Oryza punctate,
O. longistaminata (Zhang et al. 2015b), O. glumipatula, O. brachyantha (Chen
et al. 2013a), O. meridionalis, rapeseed, adzuki bean (Yang et al. 2015), black
mustard, Indian wild rice, chickpea (Varshney et al. 2013), common jujube (Liu
et al. 2014), false flax (Kagale et al. 2014), Japanese apricot (Zhang et al. 2012), wild
strawberry (Shulaev et al. 2011), cassava, A- and B-genome peanuts (Bertioli et al.
2016), Guinea yam, African wild rice, pearl millet (Varshney et al. 2017), and red
clover (Ištvánek et al. 2014). Although the preceding genomes have high enough
quality to make the list in Table 3, the use of only second-generation sequencing, in
general, greatly hobbled the quality of genome assemblies. In brief, the genes and
unique regions of genomes could often be assembled fairly easily. However, the
short-read lengths prevented assembly of many repetitive regions. Of note, Illumina
sequencing of wild emmer wheat was greatly enhanced by the addition of Hi-C
chromatin configuration sequencing/analysis (Avni et al. 2017).
5.6 Third- + Second-Generation Sequencing
Third-generation sequencing, while still lacking the accuracy and output of Illumina
sequencers, provides relatively long-read lengths that can be used to help link
contigs into scaffolds. Alternatively, contigs/scaffolds generated using thirdgeneration reads can be “polished” using Illumina reads to correct mistakes and
fill in gaps. Genomes that have been sequenced and assembled using a combination
of second- and third-generation platforms include pummelo (Wang et al. 2017),
sunflower (Badouin et al. 2017), pineapple (Ming et al. 2015), and coyote tobacco.
Moreover, several published genomes assembled using first- and second-generation
technologies have later been improved by incorporating third-generation long-read
sequencing data (e.g., Jiao et al. 2017; Zimin et al. 2017).
164
D. G. Peterson and M. Arick