ArticleGenome biology2020
A systematic comparison of chloroplast genome assembly tools.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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56 citing papers in PubMed, 94 citations in OpenAlex.
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- Complete mitogenomes of the endangered Galapagos fur seal (Arctocephalus galapagoensis): new insights on its evolutionary history.Genetica · 2026Article
- Ongoing structural changes highlight the dynamic nature of chloroplast genomes.Nucleic acids research · 2026Article
- Complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2026Article
- New mitogenomic evidence for the phylogeny of Siphonaptera: insights fromFrontiers in veterinary science · 2026Article
- Advance in the assembly of the plant mitochondrial genomes using high-throughput DNA sequencing data of total cellular DNAs.Plant biotechnology journal · 2025Review
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- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Scientific reports · 2025Article
- Variation of and associations with the depth and evenness of sequencing coverage in archived plastid genomes.Research square · 2025Article
- Comprehensive analysis of 385 chloroplast genomes unveils phylogenetic relationships and evolutionary history in cassava.BMC plant biology · 2025Article
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- Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region.Journal of molecular evolution · 2025Article
- A Snakemake Toolkit for the Batch Assembly, Annotation and Phylogenetic Analysis of Mitochondrial Genomes and Ribosomal Genes From Genome Skims of Museum Collections.Molecular ecology resources · 2025Article
- Article
- Exploring the plastome diversity of fifteen centuries-old olive trees (Frontiers in plant science · 2025Article
- The complete chloroplast genomes and comparative study of the two tung trees of Vernicia (Euphorbiaceae).BMC genomics · 2024Article
- Complete mitochondrial genome of Melia azedarach L., reveals two conformations generated by the repeat sequence mediated recombination.BMC plant biology · 2024Article
- Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChloroplasts are intracellular organelles that enable plants to conduct photosynthesis. They arose through the symbiotic integration of a prokaryotic cell into an eukaryotic host cell and still contain their own genomes with distinct genomic information. Plastid genomes accommodate essential genes and are regularly utilized in biotechnology or phylogenetics. Different assemblers that are able to assess the plastid genome have been developed. These assemblers often use data of whole genome sequencing experiments, which usually contain reads from the complete chloroplast genome.
resultsThe performance of different assembly tools has never been systematically compared. Here, we present a benchmark of seven chloroplast assembly tools, capable of succeeding in more than 60% of known real data sets. Our results show significant differences between the tested assemblers in terms of generating whole chloroplast genome sequences and computational requirements. The examination of 105 data sets from species with unknown plastid genomes leads to the assembly of 20 novel chloroplast genomes.
conclusionsWe create docker images for each tested tool that are freely available for the scientific community and ensure reproducibility of the analyses. These containers allow the analysis and screening of data sets for chloroplast genomes using standard computational infrastructure. Thus, large scale screening for chloroplasts within genomic sequencing data is feasible.
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