Efficient assembly of nanopore reads via highly accurate and intact error correction

Chen, Ying; Nie, Fan; Xie, Shuang; Zheng, Yingfeng; Dai, Qi; Bray, T. A.; Wang, Yao-Xin; Xing, Jian-Feng; Huang, Zhijian; Wang, Depeng; He, Li; Luo, Feng; Wang, Jianxin; Liu, Yizhi; Xiao, Chuan-Le

doi:10.1038/s41467-020-20236-7

Cited by 259 publications

(212 citation statements)

References 34 publications

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“…To construct chromosomal assemblies for the two type-B individuals, we employed the strategy shown in supplementary figure 1 A , Supplementary Material online. First, for each specimen, we built contigs from long Nanopore reads with the NECAT assembler ( Chen et al 2021 ) and polished obtained contigs with Illumina reads using the Nextpolish software ( Hu et al 2020 ). The total lengths of the contigs greatly exceeded the estimated genome size.…”

Section: Resultsmentioning

confidence: 99%

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Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Satou

Sato

Yasuo

et al. 2021

Genome Biology and Evolution

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Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. While these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. While the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.

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Section: Resultsmentioning

confidence: 99%

“…Contig assembly was performed using the NECAT program with default parameters ( Chen et al 2021 ). Then contigs were polished using Nextpolish ( Hu et al 2020 ) with Illumina reads obtained from the same specimens.…”

Section: Methodsmentioning

confidence: 99%

Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Satou

Sato

Yasuo

et al. 2021

Genome Biology and Evolution

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“…Notably, we did not find any multicopy, rearrangements, the presence of backbone sequences, or truncations in the maize genome. Although the nanopore-based sequencing technology help us acquire long sequencing reads, the error rate of nanopore reads is about 5–15% (Chen et al, 2021 ), which remains a formidable challenge for bioinformatics and for accurately determining the insertion position. However, when coupled to a linkage analysis, this may help us reliably infer the region of a given insertion position, by eliminating interference from other regions of the genome.…”

Section: Discussionmentioning

confidence: 99%

Using Combined Methods of Genetic Mapping and Nanopore-Based Sequencing Technology to Analyze the Insertion Positions of G10evo-EPSPS and Cry1Ab/Cry2Aj Transgenes in Maize

et al. 2021

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The insertion position of the exogenous fragment sequence in a genetically modified organism (GMO) is important for the safety assessment and labeling of GMOs. SK12-5 is a newly developed transgenic maize line transformed with two trait genes [i.e., G10evo-5-enolpyrul-shikimate-3-phosphate synthase (EPSPS) and Cry1Ab/Cry2Aj] that was recently approved for commercial use in China. In this study, we tried to determine the insertion position of the exogenous fragment for SK12-5. The transgene–host left border and right border integration junctions were obtained from SK12-5 genomic DNA by using the thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) and next-generation Illumina sequencing technology. However, a Basic Local Alignment Search Tool (BLAST) analysis revealed that the flanking sequences in the maize genome are unspecific and that the insertion position is located in a repetitive sequence area in the maize genome. To locate the fine-scale insertion position in SK12-5, we combined the methods of genetic mapping and nanopore-based sequencing technology. From a classical bulked-segregant analysis (BSA), the insertion position in SK12-5 was mapped onto Bin9.03 of chromosome 9 between the simple sequence repeat (SSR) markers umc2337 and umc1743 (26,822,048–100,724,531 bp). The nanopore sequencing results uncovered 10 reads for which one end was mapped onto the vector and the other end was mapped onto the maize genome. These observations indicated that the exogenous T-DNA fragments were putatively integrated at the position from 82,329,568 to 82,379,296 bp of chromosome 9 in the transgenic maize SK12-5. This study is helpful for the safety assessment of the novel transgenic maize SK12-5 and shows that the combined method of genetic mapping and the nanopore-based sequencing technology will be a useful approach for identifying the insertion positions of transgenic sequences in other GM plants with relatively large and complex genomes.

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“…The first stage of our assembly approach involved comparing three long-read assemblers using the ONT data as input: NECAT v0.01 [24], Flye (Flye, RRID:SCR_017016) v2.6 [25] and Canu (Canu, RRID:SCR_015880) v1.9 [26]. The genome size parameter used for the assemblers was 1134 Mb, as previously reported for Telopea truncata [27].…”

Section: Draft Long-read and 10x Assembliesmentioning

confidence: 99%

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

Rossetto

et al. 2021

Preprint

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Background: Telopea speciosissima, the New South Wales waratah, is Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Findings: Here, we report the first chromosome-level reference genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 91.2 % of Embryophyta BUSCOs complete. We introduce a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering assembly scaffolds. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and find that the assembly is 93.9 % of the estimated genome size. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. Our results indicate that the waratah genome is highly repetitive, with a repeat content of 62.3 %. Conclusions: The T. speciosissima genome (Tspe_v1) will accelerate waratah evolutionary genomics and facilitate marker assisted approaches for breeding. Broadly, it represents an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

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Efficient assembly of nanopore reads via highly accurate and intact error correction

Cited by 259 publications

References 34 publications

Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages

Using Combined Methods of Genetic Mapping and Nanopore-Based Sequencing Technology to Analyze the Insertion Positions of G10evo-EPSPS and Cry1Ab/Cry2Aj Transgenes in Maize

Chromosome-levelde novogenome assembly ofTelopea speciosissima(New South Wales waratah) using long-reads, linked-reads and Hi-C

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