ArticleGigaScience2020
Comparison of long-read methods for sequencing and assembly of a plant genome.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers.
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Who cites it
61 citing papers in PubMed.
- Chromosome-scale assembly of wheat cultivar Sumai 3, a major germplasm source for Fusarium head blight resistance.The plant genome · 2026Article
- Structural Variation and Its Roles in Plant Genomes.Plants (Basel, Switzerland) · 2026Review
- Chromosome-level genome assemblies of Brownlowia tersa and Brownlowia argentata (Brownlowioideae: Malvaceae).Scientific data · 2026Article
- Draft Genome Assembly and Differential Expression ofPlants (Basel, Switzerland) · 2026Article
- Whole-genome sequences of the dwarf honey bee subgenus Micrapis: Apis andreniformis and Apis florea.G3 (Bethesda, Md.) · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data:Journal of fungi (Basel, Switzerland) · 2025Article
- Nuclear and organelle genome assemblies of 5 Cucumis melo L. accessions, Ananas, Canton, PI 414723, Vedrantais, and Zhimali, belonging to diverse botanical groups.G3 (Bethesda, Md.) · 2025Article
- Recent duplications and rare structural variations revealed by comparative sequence analysis of low molecular weight glutenin subunits (LMW-GS) genes re-identified using LMWgsFinder in 26 genomes of the grass family.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- A High-Resolution Genomic Study of the Pama-Nyungan Speaking Yolngu People of Northeast Arnhem Land, Australia.American journal of biological anthropology · 2025Article
- Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia.Scientific reports · 2025Article
- Insights into the nuclear-organelle DNA integration in Cicuta virosa (Apiaceae) provided by complete plastid and mitochondrial genomes.BMC genomics · 2025Article
- Re-calibration of flow cytometry standards for plant genome size estimation.Frontiers in plant science · 2025Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.ACS synthetic biology · 2024Article
- The Bioinformatic Applications of Hi-C and Linked Reads.Genomics, proteomics & bioinformatics · 2024Review
- Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes.Nature communications · 2024Article
- Sequencing Strategy to Ensure Accurate Plasmid Assembly.bioRxiv : the preprint server for biology · 2024Article
- Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities.Microbiology (Reading, England) · 2024Article
- PlasCAT: Plasmid Cloud Assembly Tool.Bioinformatics (Oxford, England) · 2024Article
1 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSequencing technologies have advanced to the point where it is possible to generate high-accuracy, haplotype-resolved, chromosome-scale assemblies. Several long-read sequencing technologies are available, and a growing number of algorithms have been developed to assemble the reads generated by those technologies. When starting a new genome project, it is therefore challenging to select the most cost-effective sequencing technology, as well as the most appropriate software for assembly and polishing. It is thus important to benchmark different approaches applied to the same sample.
resultsHere, we report a comparison of 3 long-read sequencing technologies applied to the de novo assembly of a plant genome, Macadamia jansenii. We have generated sequencing data using Pacific Biosciences (Sequel I), Oxford Nanopore Technologies (PromethION), and BGI (single-tube Long Fragment Read) technologies for the same sample. Several assemblers were benchmarked in the assembly of Pacific Biosciences and Nanopore reads. Results obtained from combining long-read technologies or short-read and long-read technologies are also presented. The assemblies were compared for contiguity, base accuracy, and completeness, as well as sequencing costs and DNA material requirements.
conclusionsThe 3 long-read technologies produced highly contiguous and complete genome assemblies of M. jansenii. At the time of sequencing, the cost associated with each method was significantly different, but continuous improvements in technologies have resulted in greater accuracy, increased throughput, and reduced costs. We propose updating this comparison regularly with reports on significant iterations of the sequencing technologies.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.