ArticleScientific reports2018
Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq.
Article in Scientific reports, 2018. 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, 23 citations in OpenAlex.
- Complete chloroplast genome of the federally endangered Menzies' wallflowerMicrobiology resource announcements · 2026Article
- Chloroplast genome sequencing in winged bean (Psophocarpus tetragonolobus L.) and comparative analysis with other legumes.BMC plant biology · 2026Article
- Article
- Comparative and phylogenetic analyses based on the complete chloroplast genome ofFrontiers in plant science · 2024Article
- The Chloroplast Genome of Endive (Genes · 2023Article
- Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.Current genomics · 2023Review
- Transcriptional Basis for Haustorium Formation and Host Establishment in HemiparasiticFrontiers in genetics · 2022Article
- Chloroplast genome sequence of Chongming lima bean (Phaseolus lunatus L.) and comparative analyses with other legume chloroplast genomes.BMC genomics · 2021Article
- Disentangling Sources of Gene Tree Discordance in Phylogenomic Data Sets: Testing Ancient Hybridizations in Amaranthaceae s.l.Systematic biology · 2021Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2021Article
- Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul.BMC genomics · 2019Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Seq instead of genomic DNA libraries remains to be thoroughly verified. In this study, we assembled chloroplast genomes for three Erysimum (Brassicaceae) species from three RNA-Seq replicas and from one genomic library of each species, using a streamlined bioinformatics protocol. We compared these assembled genomes, confirming that assembled cp genomes from RNA-Seq data were highly similar to each other and to those from genomic libraries in terms of overall structure, size, and composition. Although post-transcriptional modifications, such as RNA-editing, may introduce variations in the RNA-seq data, the assembly of cp genomes from RNA-seq appeared to be reliable. Moreover, RNA-Seq assembly was less sensitive to sources of error such as the recovery of nuclear plastid DNAs (NUPTs). Although some precautions should be taken when producing reference genomes in non-model plants, we conclude that assembling cp genomes from RNA-Seq data is a fast, accurate, and reliable strategy.
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