SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Luo, Ruibang; Liu, Binghang; Xie, Yinlong; Li, Zhenyu; Huang, Weihua; Yuan, Jianying; He, Guangzhu; Chen, Yanxiang; Pan, Qi; Liu, Yunjie; Tang, Jingbo; Wu, Gengxiong; Zhang, Hao; Shi, Yujian; Liu, Yong; Yu, Chang; Wang, Bo; Lu, Yao; Han, Changlei; Cheung, David W.; Yiu, Siu-Ming; Peng, Shaoliang; Zhu, Xinhua; Liu, Guangming; Liao, Xiangke; Li, Yingrui; Yang, Huanming; Wang, Jian; Lam, Tak Wah; Wang, Jun

doi:10.1186/2047-217x-1-18

Cited by 4,354 publications

(3,425 citation statements)

References 11 publications

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“…Gap closing was performed using 670 million Illumina paired-end reads generated from two PCR-amplified libraries with insert sizes 600 nt and 250 nt, and from five PCR-free libraries with insert sizes 200-700 nt as input for GapCloser 20 (v1.12-r6, default parameters and -p set to 31). Fig.…”

Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

515

534

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Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n 5 18 chromosomes, has an estimated genome size of 714-758 megabases 1 and shares an ancient genome triplication with other eudicot plants 2 . Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet 3 . Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated 4 to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.During the last 200 years of sugar beet breeding, the sugar content has increased from 8% to 18% in today's cultivars. Breeding has also actively selected for traits like resistance to viral and fungal diseases, improved taproot yield, monogermy of the seed and bolting resistance.

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Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

515

534

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“…The RefSeq reference genome of the Chinese hamster is based on the SOAPdenovo2 [Luo et al, 2012] assembly [Lewis et al, 2013]. The different paired-end and mate-pair Illumina libraries were assembled using SOAPdenovo2 [Luo et al, 2012].…”

Section: Methodsmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

112

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Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

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“…To assemble w Spc, we initially cleaned, trimmed, and assembled reads for the Wolbachia ‐infected D. subpulchrella using Sickle (https://github.com/najoshi/sickle) and SOAPdenovo v. 2.04 (Luo et al., 2012). For the assembly, K values of 31, 41, …, 101 were tried, and the best assembly (fewest contigs and largest N50) was kept.…”

Section: Methodsmentioning

confidence: 99%

“…The D. suzukii and D. subpulchrella reads were aligned to the w Spc assembly with bwa 0.7.12 (Li & Durbin, 2009). For both contigs that contain part of the WRi_006720 gene, reads mapping to the ISWpi7 transposable element plus the neighboring 500 bp were extracted and assembled with SOAPdenovo v. 2.04 (Luo et al., 2012), using a K value of 55. Both the D. suzukii and D. subpulchrella reads assembled into a single contig containing the two pieces of WRi_006720 interrupted by a single copy of ISWpi7.…”

Section: Methodsmentioning

confidence: 99%

Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

Conner

Blaxter

Anfora

et al. 2017

Ecology and Evolution

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Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D. simulans, but CI has not been detected in D. suzukii or D. subpulchrella. Our draft genomes of wSuz and wSpc contain full‐length copies of 703 of the 734 single‐copy genes found in wRi. Over these coding sequences, wSuz and wSpc differ by only 0.004% (i.e., 28 of 704,883 bp); they are sisters relative to wRi, from which each differs by 0.014%–0.015%. Using published data from D. melanogaster, Nasonia wasps and Nomada bees to calibrate relative rates of Wolbachia versus host nuclear divergence, we conclude that wSuz and wSpc are too similar—by at least a factor of 100—to be plausible candidates for cladogenic transmission. These three wRi‐like Wolbachia, which differ in CI phenotype in their native hosts, have different numbers of orthologs of genes postulated to contribute to CI; and the CI loci differ at several nucleotides that may account for the CI difference. We discuss the general problem of distinguishing alternative modes of Wolbachia acquisition, focusing on the difficulties posed by limited knowledge of variation in absolute and relative rates of molecular evolution for host nuclear genomes, mitochondria, and Wolbachia.

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SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Cited by 4,354 publications

References 11 publications

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Genome comparisons indicate recent transfer of wRi‐like Wolbachia between sister species Drosophila suzukii and D. subpulchrella

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