ArticleMolecular ecology resources2023
Plastid Genome Assembly Using Long-read data.
Article in Molecular ecology resources, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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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
42 citing papers in PubMed, 58 citations in OpenAlex.
- Towards whole plastome phylogeography: resolving small genetic distances among European Arnica montana L. with the PlastidPipeline.Scientific reports · 2026Article
- Complete organellar genomes of Cystophora brownii: Insights into mitochondrial and plastid structure and evolution in brown algae.Journal of phycology · 2026Article
- Herbariomic approach solved identity crisis of the putatively extinct Armeria arcuata Welw. ex Boiss. & Reut. (Plumbaginaceae).Annals of botany · 2026Article
- Assembly and comparative analysis of the complete mitochondrial genome of the endangered plant Fraxinus mandshurica.BMC plant biology · 2026Article
- Chloroplast Genome Insights ofEcology and evolution · 2026Article
- Article
- Multipartite mitochondrial genome evolution in Halophila seagrasses: repeat-driven structural plasticity and selection signatures of marine adaptation.BMC plant biology · 2026Article
- Cookbook for plant genome sequences.BMC genomics · 2026Review
- Assembly and comparative analysis of the complete mitochondrial genome of the Maclura tricuspidata.BMC genomics · 2026Article
- Complex plastome structural variation caused by intermolecular and intramolecular recombination accounts for leaf variegation inPlant diversity · 2026Article
- Organelle genome architecture ofFrontiers in plant science · 2026Article
- Chloroplast genome sequence characteristics and phylogenetic analysis ofMitochondrial DNA. Part B, Resources · 2026Article
- The complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2026Article
- Plastid genome variation in the green algal genusFrontiers in plant science · 2026Article
- Assembly and comparative analysis of the complete mitochondrial and chloroplast genomes of the medicinal plant Vincetoxicum Pycnostelma.BMC genomics · 2025Article
- High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination.The plant genome · 2025Article
- Three Novel Genomes Broaden the Wild Side of thePlant direct · 2025Article
- Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae.bioRxiv : the preprint server for biology · 2025Article
- Chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.).Scientific data · 2025Article
- Beyond conservation: the landscape of chloroplast genome rearrangements in angiosperms.The New phytologist · 2025Review
Corrections and comments
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Authors and funding
9 authors at 5 institutions in 3 countries.
Funding
Abstract
Although plastid genome (plastome) structure is highly conserved across most seed plants, investigations during the past two decades have revealed several disparately related lineages that experienced substantial rearrangements. Most plastomes contain a large inverted repeat and two single-copy regions, and a few dispersed repeats; however, the plastomes of some taxa harbour long repeat sequences (>300 bp). These long repeats make it challenging to assemble complete plastomes using short-read data, leading to misassemblies and consensus sequences with spurious rearrangements. Single-molecule, long-read sequencing has the potential to overcome these challenges, yet there is no consensus on the most effective method for accurately assembling plastomes using long-read data. We generated a pipeline, plastid Genome Assembly Using Long-read data (ptGAUL), to address the problem of plastome assembly using long-read data from Oxford Nanopore Technologies (ONT) or Pacific Biosciences platforms. We demonstrated the efficacy of the ptGAUL pipeline using 16 published long-read data sets. We showed that ptGAUL quickly produces accurate and unbiased assemblies using only ~50× coverage of plastome data. Additionally, we deployed ptGAUL to assemble four new Juncus (Juncaceae) plastomes using ONT long reads. Our results revealed many long repeats and rearrangements in Juncus plastomes compared with basal lineages of Poales. The ptGAUL pipeline is available on GitHub: https://github.com/Bean061/ptgaul.
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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 Socratic graph.