ArticleNature communications2020
Effect of sequence depth and length in long-read assembly of the maize inbred NC358.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Near-complete genome assembly of a transformation-efficient elite inbred line LH244 and its comparison with B73.Journal of integrative plant biology · 2026Article
- Decades' progress and prospects on maize functional genomics and molecular breeding.Science China. Life sciences · 2025Review
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Article
- Contrasting new and available reference genomes to highlight uncertainties in assemblies and areas for future improvement: an example with monodontid species.BMC genomics · 2023Article
- Mabs, a suite of tools for gene-informed genome assembly.BMC bioinformatics · 2023Article
- Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications.Communications biology · 2023Article
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- A large-scale assessment of the quality of plant genome assemblies using the LTR assembly index.AoB PLANTS · 2023Article
- Highly accurate long reads are crucial for realizing the potential of biodiversity genomics.BMC genomics · 2023Article
- Accelerating the alignment processing speed of the comprehensive end-to-end whole-genome bisulfite sequencing pipeline, wg-blimp.Biology methods & protocols · 2023Article
- Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes.Nucleic acids research · 2022Article
- BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.Genetics · 2022Article
- LIFE-Seq: a universal Large Integrated DNA Fragment Enrichment Sequencing strategy for deciphering the transgene integration of genetically modified organisms.Plant biotechnology journal · 2022Article
- Transposable element variants and their potential adaptive impact in urban populations of the malaria vectorGenome research · 2022Article
- A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean.Nature communications · 2021Article
- Genomic variation within the maize stiff-stalk heterotic germplasm pool.The plant genome · 2021Article
- LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology.Genome biology · 2021Article
- De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science (New York, N.Y.) · 2021Article
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24 authors.
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Abstract
Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11-21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature.
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