De novo assembly of human genomes with massively parallel short read sequencing

Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue; Qian, Wubin; Fang, Xiaodong; Shi, Zhang; Li, Yingrui; Li, Shengting; Gao, Shan; Kristiansen, Karsten; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

doi:10.1101/gr.097261.109

Cited by 2,602 publications

(2,107 citation statements)

References 31 publications

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“…The assembly used default parameters with the exception of using a ploidy setting of 2 (PLOIDY = 2), as recommended for a diploid organism, in the data preparation stage, and a minimum contig size set to 200 bp (MIN_CONTIG = 200) in the running stage (running the RunAllPathsLG command). Gaps within the scaffolds were filled based on the short insert size libraries, using the GapCloser in the SOAPdenovo package 42 . Assembled scaffolds were assigned to chromosomes by the order and orientation of a linkage map combined with a synteny analysis between S. litura and B. mori.…”

Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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The tobacco cutworm, Spodoptera litura, is among the most widespread and destructive agricultural pests, feeding on over 100 crops throughout tropical and subtropical Asia. By genome sequencing, physical mapping and transcriptome analysis, we found that the gene families encoding receptors for bitter or toxic substances and detoxification enzymes, such as cytochrome P450, carboxylesterase and glutathione-S-transferase, were massively expanded in this polyphagous species, enabling its extraordinary ability to detect and detoxify many plant secondary compounds. Larval exposure to insecticidal toxins induced expression of detoxification genes, and knockdown of representative genes using short interfering RNA (siRNA) reduced larval survival, consistent with their contribution to the insect’s natural pesticide tolerance. A population genetics study indicated that this species expanded throughout southeast Asia by migrating along a South India–South China–Japan axis, adapting to wide-ranging ecological conditions with diverse host plants and insecticides, surviving and adapting with the aid of its expanded detoxification systems. The findings of this study will enable the development of new pest management strategies for the control of major agricultural pests such as S. litura.

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Section: Methodsmentioning

confidence: 99%

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

et al. 2017

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“…We carried out the whole-genome assembly using SOAPdenovo for the remaining reads after the above filtering and correction steps 9,10 . The contigs after SOAPdenovo corrections were formed without any gap.…”

Section: Methodsmentioning

confidence: 99%

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

et al. 2011

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Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sangerbased bacterial artificial chromosome end sequences and a genetic map, we assembled into scaffolds representing 72.7% (605.78 Mb) of the 833.07 Mb pigeonpea genome. Genome analysis predicted 48,680 genes for pigeonpea and also showed the potential role that certain gene families, for example, drought tolerance-related genes, have played throughout the domestication of pigeonpea and the evolution of its ancestors. Although we found a few segmental duplication events, we did not observe the recent genome-wide duplication events observed in soybean. This reference genome sequence will facilitate the identification of the genetic basis of agronomically important traits, and accelerate the development of improved pigeonpea varieties that could improve food security in many developing countries.

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“…1). These sequences were assembled de novo using SOAPdenovo (version 1.03) software 15 , resulting in 542,145 contigs and 285,383 scaffolds longer than 100 bp. The contig N50 size was 18.7 kb, which represents the size above which half of the total length of the sequence set can be found.…”

Section: Short-read De Novo Sequencing and Assemblymentioning

confidence: 99%

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

et al. 2012

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De novo assembly of human genomes with massively parallel short read sequencing

Cited by 2,602 publications

References 31 publications

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

Genomic adaptation to polyphagy and insecticides in a major East Asian noctuid pest

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus)

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