scholarly journals A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes v1 (protocols.io.qpndvme)

protocols.io ◽  
2018 ◽  
Author(s):  
Kae Koganebuchi
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Artificial Chromosome ◽  
Capture Method ◽  
Bac Libraries ◽  
Targeted Capture ◽  
Large Genes

scholarly journals A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

PLoS ONE ◽  
2018 ◽  
Vol 13 (7) ◽  
pp. e0200170
Author(s):  
Kae Koganebuchi ◽  
Takashi Gakuhari ◽  
Hirohiko Takeshima ◽  
Kimitoshi Sato ◽  
Kiyotaka Fujii ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Artificial Chromosome ◽  
Capture Method ◽  
Bac Libraries ◽  
Targeted Capture ◽  
Large Genes

scholarly journals A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes

2018 ◽  
Author(s):  
Kae Koganebuchi ◽  
Takashi Gakuhari ◽  
Hirohiko Takeshima ◽  
Kimitoshi Sato ◽  
Kiyotaka Fujii ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Data Quality ◽  
Susceptibility Gene ◽  
Artificial Chromosome ◽  
Individual Genome ◽  
Genome Region ◽  
Capture Method ◽  
Bac Libraries ◽  
Targeted Capture ◽  
Commercial Kit

AbstractTo analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome region with substantial length.

scholarly journals Use of Recombination-Mediated Genetic Engineering for Construction of Rescue Human Cytomegalovirus Bacterial Artificial Chromosome Clones

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kalpana Dulal ◽  
Benjamin Silver ◽  
Hua Zhu
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Homologous Recombination ◽  
Human Cytomegalovirus ◽  
Artificial Chromosome ◽  
Bac Clone ◽  
Dna Viruses ◽  
E Coli ◽  
Recombination System ◽  
Capture Method

Bacterial artificial chromosome (BAC) technology has contributed immensely to manipulation of larger genomes in many organisms including large DNA viruses like human cytomegalovirus (HCMV). The HCMV BAC clone propagated and maintained insideE. coliallows for accurate recombinant virus generation. Using this system, we have generated a panel of HCMV deletion mutants and their rescue clones. In this paper, we describe the construction of HCMV BAC mutants using a homologous recombination system. A gene capture method, or gap repair cloning, to seize large fragments of DNA from the virus BAC in order to generate rescue viruses, is described in detail. Construction of rescue clones using gap repair cloning is highly efficient and provides a novel use of the homologous recombination-based method inE. colifor molecular cloning, known colloquially as recombineering, when rescuing large BAC deletions. This method of excising large fragments of DNA provides important prospects forin vitrohomologous recombination for genetic cloning.

Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2)

Genome ◽  
2001 ◽  
Vol 44 (2) ◽  
pp. 154-162 ◽  
Author(s):  
Meizhong Luo ◽  
Yi-Hong Wang ◽  
David Frisch ◽  
Tarek Joobeur ◽  
Rod A Wing ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Fusarium Wilt ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Microtiter Plates ◽  
Bac Libraries ◽  
Average Size ◽  
Improved Methods

Utilizing improved methods, two bacterial artificial chromosome (BAC) libraries were constructed for the multidisease-resistant line of melon MR-1. The HindIII library consists of 177 microtiter plates in a 384-well format, while the EcoRI library consists of 222 microtiter plates. Approximately 95.6% of the HindIII library clones contain nuclear DNA inserts with an average size of 118 kb, providing a coverage of 15.4 genome equivalents. Similarly, 96% of the EcoRI library clones contain nuclear DNA inserts with an average size of 114 kb, providing a coverage of 18.7 genome equivalents. Both libraries were evaluated for contamination with high-copy vector, empty pIndigoBac536 vector, and organellar DNA sequences. High-density filters were screened with two genetic markers FM and AM that co-segregate with Fom-2, a gene conferring resistance to races 0 and 1 of Fusarium wilt. Fourteen and 18 candidate BAC clones were identified for the FM and AM probes, respectively, from the HindIII library, while 34 were identified for the AM probe from filters A, B, and C of the EcoRI library.Key words: bacterial artificial chromosome (BAC) library, Fusarium wilt, melon, pCUGIBAC1, resistant gene.

scholarly journals Construction of bacterial artificial chromosome (BAC) libraries of banana (Musa acuminataandMusa balbisiana)

Fruits ◽  
2008 ◽  
Vol 63 (6) ◽  
pp. 375-379 ◽  
Author(s):  
Pietro Piffanelli ◽  
Alberto D. Vilarinhos ◽  
Jan Safar ◽  
Xavier Sabau ◽  
Jaroslav Dolezel
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Artificial Chromosome ◽  
Bac Libraries

Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes

Genome ◽  
2007 ◽  
Vol 50 (9) ◽  
pp. 871-875 ◽  
Author(s):  
C.J. Coyne ◽  
M.T. McClendon ◽  
J.G. Walling ◽  
G.M. Timmerman-Vaughan ◽  
S. Murray ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Bacterial Artificial Chromosome ◽  
Pisum Sativum ◽  
Plant Disease Resistance ◽  
Copy Number ◽  
Artificial Chromosome ◽  
Pisum Sativum L ◽  
A Genome ◽  
Low Copy Number ◽  
Bac Libraries

Pea ( Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2–0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.

Phylogenetic Screening of Ribosomal RNA Gene-Containing Clones in Bacterial Artificial Chromosome (BAC) Libraries from Different Depths in Monterey Bay

2004 ◽  
Vol 48 (4) ◽  
pp. 473-488 ◽  
Author(s):  
M.T. Suzuki ◽  
C.M. Preston ◽  
O. B�j� ◽  
J.R. de la Torre ◽  
G.F. Steward ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Ribosomal Rna ◽  
Artificial Chromosome ◽  
Monterey Bay ◽  
Ribosomal Rna Gene ◽  
Bac Libraries ◽  
Different Depths
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