ArticleBMC genomics2017
Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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49 citing papers in PubMed, 88 citations in OpenAlex.
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- The complete mitogenome of Amazonian Brachyplatystoma filamentosum and the evolutionary history of body size in the order Siluriformes.Scientific reports · 2025Article
- TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data.Molecular biology and evolution · 2025Article
- Complete genome of the Medicago anthracnose fungus,Microbial genomics · 2024Article
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- Aphid resistance segregates independently of cardiac glycoside and glucosinolate content in anbioRxiv : the preprint server for biology · 2024Article
- Comparative plastome assembly of the yellow ironweed (Frontiers in plant science · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Two long read-based genome assembly and annotation of polyploidy woody plants, Hibiscus syriacus L. using PacBio and Nanopore platforms.Scientific data · 2023Article
- Plastid Genome Assembly Using Long-read data.Molecular ecology resources · 2023Article
- Poaceae Chloroplast Genome Sequencing: Great Leap Forward in Recent Ten Years.Current genomics · 2023Review
- Genomic Approaches for the Study of Flower Development in Floriculture Crops.Methods in molecular biology (Clifton, N.J.) · 2023Article
- PolyploidFrontiers in plant science · 2023Article
- Mitochondrial genome of Garcinia mangostana L. variety Mesta.Scientific reports · 2022Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present.
resultsWe present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae).
conclusionOrganelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA .
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