ArticleInternational journal of molecular sciences2022
Chloroplast Genome Annotation Tools: Prolegomena to the Identification of Inverted Repeats.
Article in International journal of molecular sciences, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The Complete Chloroplast Genome of Tree Fern Cyathea delgadii and Its Comparison to Other Cyatheales.Biochemical genetics · 2026Article
- Unraveling the Chloroplast Genome of Stellaria media: Comprehensive Analysis, Taxonomic Implications, and Evolutionary Perspectives.Biochemical genetics · 2026Article
- Comprehensive analysis of chloroplast genome evolution in Poaceae: codon usage patterns, selection pressures, and phylogenomic relationships.BMC genomics · 2026Article
- The impact of awn length on seed yield and drought resistance in Elymus sibiricus L. and the molecular mechanism underlying awn length regulation.BMC plant biology · 2025Article
- PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics.Plant diversity · 2025Article
- Exploring Structural Plastome Evolution in Asterales: Insights from Off-Target Hybrid Enrichment Data on the Small Single-Copy Region.Journal of molecular evolution · 2025Article
- Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae).BMC plant biology · 2023Article
- Analysis of the Chloroplast Genome ofCurrent issues in molecular biology · 2023Article
- Variation in Chloroplast Genome Size: Biological Phenomena and Technological Artifacts.Plants (Basel, Switzerland) · 2023Article
- Progress, challenge and prospect of plant plastome annotation.Frontiers in plant science · 2023Review
- Article
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Authors and funding
6 authors.
Funding
Abstract
The development of next-generation sequencing technology and the increasing amount of sequencing data have brought the bioinformatic tools used in genome assembly into focus. The final step of the process is genome annotation, which works on assembled genome sequences to identify the location of genome features. In the case of organelle genomes, specialized annotation tools are used to identify organelle genes and structural features. Numerous annotation tools target chloroplast sequences. Most chloroplast DNA genomes have a quadripartite structure caused by two copies of a large inverted repeat. We investigated the strategies of six annotation tools (Chloë, Chloroplot, GeSeq, ORG.Annotate, PGA, Plann) for identifying inverted repeats and analyzed their success using publicly available complete chloroplast sequences of taxa belonging to the asterid and rosid clades. The annotation tools use two different approaches to identify inverted repeats, using existing general search tools or implementing stand-alone solutions. The chloroplast sequences studied show that there are different types of imperfections in the assembled data and that each tool performs better on some sequences than the others.
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