Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing

Alonge, Michael; Lebeigle, Ludivine; Kirsche, Melanie; Aganezov, Sergey; Wang, Xingang; Lippman, Zachary B.; Schatz, Michael C.; Soyk, Sebastian

doi:10.1101/2021.11.18.469135

Cited by 97 publications

(102 citation statements)

References 56 publications

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“…K-mer completeness estimated by Merqury (36) as a function of input coverage (e) and median read length (j) . QV and completeness were computed after reference-based scaffolding with RagTag (40).…”

Section: Resultsmentioning

confidence: 99%

“…After scaffolding, this time with RagTag (40), a reference-based scaffolding tool, we evaluated accuracy and completeness as described before. For all assemblers, QV scores were largely unaffected by coverage (Figure 2d), with HiFi-Hifiasm leading and HiFi-HiCanu coming in second.…”

Section: Resultsmentioning

confidence: 99%

“… (a) Contiguity plot comparing the CLR-Canu and HiFi-Hifiasm assemblies alone, combined with RagTag “patch” (40) or as hybrid scaffolds with Bionano optical maps. For each assembly, the cumulative contig – or scaffold – length (ordered from largest to shortest) is plotted over the estimated genome size of A. thaliana accession Ey15-2 (∼140 Mb).…”

Section: Resultsmentioning

confidence: 99%

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Pushing the limits of HiFi assemblies reveals centromere diversity between twoArabidopsis thalianagenomes

Rabanal

Gräff

Lanz

et al. 2022

Preprint

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Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two A. thaliana accessions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Pushing the limits of HiFi assemblies reveals centromere diversity between twoArabidopsis thalianagenomes

Rabanal

Gräff

Lanz

et al. 2022

Preprint

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“…Contigs were scaffolded into chromosomes by the reference-guided approach of RagTag (Alonge et al, 2021) (v2.0.1) to ARS-UCD1.2, using the additional parameters “--mm2-params “-cx asm5” -r -m 1000000”.…”

Section: Methodsmentioning

confidence: 99%

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Leonard

Crysnanto

Fang

et al. 2021

Preprint

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Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Ten haplotype-resolved assemblies of three bovine trios representing increasing levels of heterozygosity were generated that each demonstrate a substantial improvement in contiguity and accuracy over the current Bos taurus reference genome, with more telomere and centromere content and an average 2.5x increase in NG50 and 11x decrease in base errors. Downsampling analysis demonstrated that diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. The assemblies were integrated into structural variant-based pangenomes that demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified approximately 900 structural variants overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46 and GC that have potential to affect phenotype.

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“…The draft genome of strain ZZQ-130 has a size of 6,677,513 bp, derived from 351 contigs, with an N 50 value of 119,425 bp and a GC content of 34.72%. Whole-genome alignment and assembly improvement were conducted using RagTag ( 7 ), with B. thuringiensis YBT-1520 ( 8 ) as the reference genome. The command line and parameters are “ragtag.py scaffold -f 1200 -t 10 ref/YBT-1520.fasta output_dir/ZZQ-130.fasta.” The scaffolded genome of ZZQ-130 harbors a chromosome with a size of 5,383,145 bp, and eight plasmids, including pB130-1 (305,619 bp), pB130-2 (42,407 bp), pB130-3 (39,632 bp), pB130-4 (32,648 bp), pB130-5 (28,563 bp), pB130-6 (14,861 bp), pB130-7 (8,352 bp), and pB130-8 (8,091 bp).…”

Section: Announcementmentioning

confidence: 99%

Draft Genome Sequence of Bacillus thuringiensis ZZQ-130 with Multiple Pesticidal Genes, Isolated from Caka Salt Lake, China

Zheng

Lan

Wang

et al. 2022

Microbiol Resour Announc

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Bacillus thuringiensis is a typical pesticide, with global application for over 40 years. Here, we report the draft genome sequence of B. thuringiensis ZZQ-130 from a salt lake; this strain has 31 pesticidal genes, including five cry genes, one vip gene, two vpa genes, and two vpb genes.

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Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing

Cited by 97 publications

References 56 publications

Pushing the limits of HiFi assemblies reveals centromere diversity between twoArabidopsis thalianagenomes

Pushing the limits of HiFi assemblies reveals centromere diversity between twoArabidopsis thalianagenomes

Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies

Draft Genome Sequence of Bacillus thuringiensis ZZQ-130 with Multiple Pesticidal Genes, Isolated from Caka Salt Lake, China

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