ArticleNucleic acids research2008
Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers, 1 of them a synthesis that pooled it.
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Who cites it
191 citing papers in PubMed, 1 synthesis or guideline pooled it, 557 citations in OpenAlex.
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- Extraction and analysis of high-quality chloroplast DNA with reduced nuclear DNA for medicinal plants.BMC biotechnology · 2024Article
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- Comparative and phylogenetic analyses based on the complete chloroplast genome ofFrontiers in plant science · 2024Article
- Complete chloroplast genome sequence ofMitochondrial DNA. Part B, Resources · 2024Article
- The first complete chloroplast genome ofFrontiers in plant science · 2024Article
- Retrieval of long DNA reads from herbarium specimens.AoB PLANTS · 2023Review
- Characterization and Comparative Analysis of Chloroplast Genomes of Medicinal HerbInternational journal of molecular sciences · 2023Article
- Characteristics, Comparative Analysis, and Phylogenetic Relationships of Chloroplast Genomes of Cultivars and Wild Relatives of Eggplant (Current issues in molecular biology · 2023Article
- Genome Evolution and the Future of Phylogenomics of Non-Avian Reptiles.Animals : an open access journal from MDPI · 2023Review
- Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae.BMC plant biology · 2023Article
- Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections.Biodiversity data journal · 2023Article
131 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organellar DNA sequences are widely used in evolutionary and population genetic studies, however, the conservative nature of chloroplast gene and genome evolution often limits phylogenetic resolution and statistical power. To gain maximal access to the historical record contained within chloroplast genomes, we have adapted multiplex sequencing-by-synthesis (MSBS) to simultaneously sequence multiple genomes using the Illumina Genome Analyzer. We PCR-amplified approximately 120 kb plastomes from eight species (seven Pinus, one Picea) in 35 reactions. Pooled products were ligated to modified adapters that included 3 bp indexing tags and samples were multiplexed at four genomes per lane. Tagged microreads were assembled by de novo and reference-guided assembly methods, using previously published Pinus plastomes as surrogate references. Assemblies for these eight genomes are estimated at 88-94% complete, with an average sequence depth of 55x to 186x. Mononucleotide repeats interrupt contig assembly with increasing repeat length, and we estimate that the limit for their assembly is 16 bp. Comparisons to 37 kb of Sanger sequence show a validated error rate of 0.056%, and conspicuous errors are evident from the assembly process. This efficient sequencing approach yields high-quality draft genomes and should have immediate applicability to genomes with comparable complexity.
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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 OpenQuestion graph.