ArticleNucleic acids research2017
pBACode: a random-barcode-based high-throughput approach for BAC paired-end sequencing and physical clone mapping.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 19 citations in OpenAlex.
- Investigating the effects of Carpesii fructus extract on the liver transcriptome of olive flounder (Paralichthys olivaceus) as a potential antiparasitic agent.Genetics and molecular biology · 2024Article
- High-quality Japanese flounder genome aids in identifying stress-related genes using gene coexpression network.Scientific data · 2022Article
- Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline.BMC genomic data · 2021Article
- Genome reconstruction and haplotype phasing using chromosome conformation capture methodologies.Briefings in functional genomics · 2020Article
- A high-throughput BAC end analysis protocol (BAC-anchor) for profiling genome assembly and physical mapping.Plant biotechnology journal · 2020Article
- High-throughput long paired-end sequencing of a Fosmid library by PacBio.Plant methods · 2019Article
- Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni.Nucleic acids research · 2018Article
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Authors and funding
13 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Applications that use Bacterial Artificial Chromosome (BAC) libraries often require paired-end sequences and knowledge of the physical location of each clone in plates. To facilitate obtaining this information in high-throughput, we generated pBACode vectors: a pool of BAC cloning vectors, each with a pair of random barcodes flanking its cloning site. In a pBACode BAC library, the BAC ends and their linked barcodes can be sequenced in bulk. Barcode pairs are determined by sequencing the empty pBACode vectors, which allows BAC ends to be paired according to their barcodes. For physical clone mapping, the barcodes are used as unique markers for their linked genomic sequence. After multi-dimensional pooling of BAC clones, the barcodes are sequenced and deconvoluted to locate each clone. We generated a pBACode library of 94,464 clones for the flounder Paralichthys olivaceus and obtained paired-end sequence from 95.4% of the clones. Incorporating BAC paired-ends into the genome preassembly improved its continuity by over 10-fold. Furthermore, we were able to use the barcodes to map the physical locations of each clone in just 50 pools, with up to 11 808 clones per pool. Our physical clone mapping located 90.2% of BAC clones, enabling targeted characterization of chromosomal rearrangements.
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