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sequencing and assembly by long reads in plants.
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novo assembly for noisy long sequences. Bioinformatics 32:2103–2110
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et al (2017) Comprehensive definition of genome
features in Spirodela polyrhiza by high-depth physical
mapping and short-read DNA sequencing strategies.
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the future of crop genomes. Curr Opin Plant Biol
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(2008) The draft genome of the transgenic tropical
fruit tree papaya (Carica papaya Linnaeus). Nature
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et al (2000) A whole-genome assembly of Drosophila.
Science 287:2196–2204
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amongst noisy long reads. In: International workshop
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high-quality long reads. Pacific Biosciences
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cost-effective access to SMRT Sequencing
Phillippy AM (2017) New advances in sequence assembly. Genome Res 27:xi–xiii
Schadt EE, Turner S, Kasarskis A (2010) A window into
third-generation sequencing. Hum Mol Genet 19:
R227–240
Shibata TF, Maeda T, Nikoh N, Yamaguchi K, Oshima K
et al (2013) Complete Genome Sequence of
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of the Bean Bug Riptortus pedestris. Genome
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Chin J (2016) Falcon Genome Assembly Tool Kit Manual
Denisov G, Walenz B, Halpern AL, Miller J, Axelrod N
et al (2008) Consensus generation and variant detection by Celera Assembler. Bioinformatics 24:1035–
1040
Deschamps S, Zhang Y, Llaca V, Ye L, May G et al
(2018) A chromosome-scale assembly of the sorghum
genome using nanopore sequencing and optical mapping. bioRxiv: 327817
Ernst E (2016) Status of the Lemna gibba 7742a and
Lemna minor 8627 genomes, pp. 9–10. 3
Gnerre S, Maccallum I, Przybylski D, Ribeiro FJ, Burton JN et al (2011) High-quality draft assemblies of
mammalian genomes from massively parallel
sequence data. Proc Natl Acad Sci U S A 108:1513–
1518
Guo L, Winzer T, Yang X, Li Y, Ning Z et al (2018) The
opium poppy genome and morphinan production.
Science
Guo S, Zhang J, Sun H, Salse J, Lucas WJ et al (2013)
The draft genome of watermelon (Citrullus lanatus)
and resequencing of 20 diverse accessions. Nat Genet
45:51–58
Henson J, Tischler G, Ning Z (2012) Next-generation
sequencing and large genome assemblies. Pharmacogenomics 13:901–915
Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ,
Soifer I et al (2016) Draft assembly of elite Inbred
Line PH207 provides insights into genomic and
transcriptome diversity in maize. Plant Cell
28:2700–2714
Huang S, Li R, Zhang Z, Li L, Gu X et al (2009) The
genome of the cucumber, Cucumis sativus L. Nat
Genet 41:1275–1281
Jain M, Koren S, Miga KH, Quick J, Rand AC et al
(2018) Nanopore sequencing and assembly of a
human genome with ultra-long reads. Nat Biotechnol
36:338–345
Jarvis DE, Ho YS, Lightfoot DJ, Schmöckel SM, Li B
et al (2017) The genome of Chenopodium quinoa.
Nature: 1–20
Jiao W-B, Accinelli GG, Hartwig B, Kiefer C, Baker D
et al (2017a) Improving and correcting the contiguity
of long-read genome assemblies of three plant species
using optical mapping and chromosome conformation
capture data. Genome research
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC et al (2017b)
Improved
maize
reference
genome
with
single-molecule technologies. Nature 546:524–527
Kang C, Darwish O, Geretz A, Shahan R, Alkharouf N
et al (2013) Genome-scale transcriptomic insights into
early-stage fruit development in woodland strawberry
Fragaria vesca. Plant Cell 25:1960–1978
Koren S, Phillippy AM (2015) One chromosome, one
contig: complete microbial genomes from long-read
sequencing and assembly. Curr Opin Microbiol
23:110–120
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT
et al (2012) Hybrid error correction and de novo
assembly of single-molecule sequencing reads. Nat
Biotechnol 30:693–700
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH
et al (2017) Canu: scalable and accurate long-read
assembly via adaptive k-mer weighting and repeat
separation. Genome Res 27:722–736
Kumar A, Bennetzen JL (1999) Plant retrotransposons.
Annu Rev Genet 33:479–532
Lan T, Renner T, Ibarra-Laclette E, Farr KM, Chang T-H
et al (2017) Long-read sequencing uncovers the
adaptive topography of a carnivorous plant genome.
Proc Natl Acad Sci 114:E4435–E4441
Li C, Lin F, An D, Wang W, Huang R (2018) Genome
sequencing and assembly by long reads in plants.
Genes 9:6
Li H (2016) Minimap and miniasm: fast mapping and de
novo assembly for noisy long sequences. Bioinformatics 32:2103–2110
Luo R, Liu B, Xie Y, Li Z, Huang W et al (2012) SOAP
denovo2: an empirically improved memory-efficient
short-read de novo assembler. Gigascience 1:18
Mascher M, Gundlach H, Himmelbach A, Beier S,
Twardziok SO et al (2017) A chromosome conformation capture ordered sequence of the barley genome.
Nature 544:427–433
Michael TP, Bryant D, Gutierrez R, Borisjuk N, Chu P
et al (2017) Comprehensive definition of genome
features in Spirodela polyrhiza by high-depth physical
mapping and short-read DNA sequencing strategies.
Plant J 89:617–635
Michael TP, VanBuren R (2015) Progress, challenges and
the future of crop genomes. Curr Opin Plant Biol
24:71–81
Ming R, Hou S, Feng Y, Yu Q, Dionne-Laporte A et al
(2008) The draft genome of the transgenic tropical
fruit tree papaya (Carica papaya Linnaeus). Nature
452:991–996
Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP
et al (2000) A whole-genome assembly of Drosophila.
Science 287:2196–2204
Myers G (2014) Efficient local alignment discovery
amongst noisy long reads. In: International workshop
on algorithms in bioinformatics. Springer, pp 52–67
Pacific B (2018a) Produce exceptional results with
high-quality long reads. Pacific Biosciences
Pacific B (2018b) Sequel System: high-throughput,
cost-effective access to SMRT Sequencing
Phillippy AM (2017) New advances in sequence assembly. Genome Res 27:xi–xiii
Schadt EE, Turner S, Kasarskis A (2010) A window into
third-generation sequencing. Hum Mol Genet 19:
R227–240
Shibata TF, Maeda T, Nikoh N, Yamaguchi K, Oshima K
et al (2013) Complete Genome Sequence of
Burkholderia sp. Strain RPE64, Bacterial Symbiont
of the Bean Bug Riptortus pedestris. Genome
Announc 1
74
X. Xiang and C. Li