ArticleGigaScience2019
A critical comparison of technologies for a plant genome sequencing project.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 61 citations in OpenAlex.
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- Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences.Database : the journal of biological databases and curation · 2023Review
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- Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid,International journal of molecular sciences · 2023Article
- Chloroplast genome draft assembly of Falcataria moluccana using hybrid sequencing technology.BMC research notes · 2023Article
- A first draft genome of holm oak (Frontiers in molecular biosciences · 2023Article
- Assembly of complete diploid-phased chromosomes from draft genome sequences.G3 (Bethesda, Md.) · 2022Article
- De Novo Reference Assembly of the Upriver Orange Mangrove (Bruguiera sexangula) Genome.Genome biology and evolution · 2022Article
- Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids.Plants (Basel, Switzerland) · 2022Review
- Recognition of Pep-13/25 MAMPs ofFrontiers in plant science · 2022Article
- Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions.Quantitative plant biology · 2022Review
- Hairy CRISPR: Genome Editing in Plants Using Hairy Root Transformation.Plants (Basel, Switzerland) · 2021Review
- De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa.Molecular biology and evolution · 2021Article
- Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise.Molecular ecology resources · 2021Article
- Article
- Genomic interventions for sustainable agriculture.Plant biotechnology journal · 2020Review
- Twelve quick steps for genome assembly and annotation in the classroom.PLoS computational biology · 2020Article
- Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight.G3 (Bethesda, Md.) · 2020Article
- Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundA high-quality genome sequence of any model organism is an essential starting point for genetic and other studies. Older clone-based methods are slow and expensive, whereas faster, cheaper short-read-only assemblies can be incomplete and highly fragmented, which minimizes their usefulness. The last few years have seen the introduction of many new technologies for genome assembly. These new technologies and associated new algorithms are typically benchmarked on microbial genomes or, if they scale appropriately, on larger (e.g., human) genomes. However, plant genomes can be much more repetitive and larger than the human genome, and plant biochemistry often makes obtaining high-quality DNA that is free from contaminants difficult. Reflecting their challenging nature, we observe that plant genome assembly statistics are typically poorer than for vertebrates.
resultsHere, we compare Illumina short read, Pacific Biosciences long read, 10x Genomics linked reads, Dovetail Hi-C, and BioNano Genomics optical maps, singly and combined, in producing high-quality long-range genome assemblies of the potato species Solanum verrucosum. We benchmark the assemblies for completeness and accuracy, as well as DNA compute requirements and sequencing costs.
conclusionsThe field of genome sequencing and assembly is reaching maturity, and the differences we observe between assemblies are surprisingly small. We expect that our results will be helpful to other genome projects, and that these datasets will be used in benchmarking by assembly algorithm developers.
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Registered trials
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.