scholarly journals Construction and Characterization of a Bacterial Artificial Chromosome Library for the A-Genome of Cotton (G.arboreumL.)

2011 ◽  
Vol 2011 ◽  
pp. 1-5 ◽  
Author(s):  
Yan Hu ◽  
Yamin Lu ◽  
Dan Ma ◽  
Wangzhen Guo ◽  
Tianzhen Zhang
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Gene Isolation ◽  
Comparative Genome Analysis ◽  
Bac Clones ◽  
A Genome ◽  
Reference Map ◽  
Insert Length

A bacterial artificial chromosome (BAC) library for the A-genome of cotton has been constructed from the leaves ofG. arboreumL cv. Jianglinzhongmian. It is used as elite A-genome germplasm resources in the present cotton breeding program and has been used to build a genetic reference map of cotton. The BAC library consists of 123,648 clones stored in 322 384-well plates. Statistical analysis of a set of 103 randomly selected BAC clones indicated that each clone has an average insert length of 100.2 kb per plasmid, with a range of 30 to 190 kb. Theoretically, this represents 7.2 haploid genome equivalents based on an A-genome size of 1697 Mb. The BAC library has been arranged in column pools and superpools allowing screening with various PCR-based markers. In the future, the A-genome cotton BAC library will serve as both a giant gene resource and a valuable tool for map-based gene isolation, physical mapping and comparative genome analysis.

Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 239-245 ◽  
Author(s):  
Yaping Qian ◽  
Li Jin ◽  
Bing Su
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Large Scale ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Spider Monkey ◽  
Ateles Geoffroyi ◽  
Comparative Genomic ◽  
Average Insert Size ◽  
Bac Clones ◽  
Genomic Study

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey (Ateles geoffroyi). A total of 193 152 BAC clones were generated in this library. The average insert size of the BAC clones was estimated to be 184.6 kb with the small inserts (50-100 kb) accounting for less than 3% and the non-recombinant clones only 1.2%. Assuming a similar genome size with humans, the spider monkey BAC library has about 11× genome coverage. In addition, by end sequencing of randomly selected BAC clones, we generated 367 sequence tags for the library. When blasted against human genome, they showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the library. This black-handed spider monkey BAC library would serve as a valuable resource in comparative genomic study and large-scale genome sequencing of nonhuman primates.Key words: black-handed spider monkeys, Ateles geoffroyi, BAC library.

scholarly journals Use of a Mycobacterium tuberculosisH37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics

1998 ◽  
Vol 66 (5) ◽  
pp. 2221-2229 ◽  
Author(s):  
Roland Brosch ◽  
Stephen V. Gordon ◽  
Alain Billault ◽  
Thierry Garnier ◽  
Karin Eiglmeier ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Bacterial Artificial Chromosome ◽  
Genome Mapping ◽  
Sequence Data ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Excellent Correlation ◽  
Sequencing Project ◽  
Polysaccharide Biosynthesis ◽  
Bac Clones

ABSTRACT The bacterial artificial chromosome (BAC) cloning system is capable of stably propagating large, complex DNA inserts in Escherichia coli. As part of the Mycobacterium tuberculosis H37Rv genome sequencing project, a BAC library was constructed in the pBeloBAC11 vector and used for genome mapping, confirmation of sequence assembly, and sequencing. The library contains about 5,000 BAC clones, with inserts ranging in size from 25 to 104 kb, representing theoretically a 70-fold coverage of the M. tuberculosisgenome (4.4 Mb). A total of 840 sequences from the T7 and SP6 termini of 420 BACs were determined and compared to those of a partial genomic database. These sequences showed excellent correlation between the estimated sizes and positions of the BAC clones and the sizes and positions of previously sequenced cosmids and the resulting contigs. Many BAC clones represent linking clones between sequenced cosmids, allowing full coverage of the H37Rv chromosome, and they are now being shotgun sequenced in the framework of the H37Rv sequencing project. Also, no chimeric, deleted, or rearranged BAC clones were detected, which was of major importance for the correct mapping and assembly of the H37Rv sequence. The minimal overlapping set contains 68 unique BAC clones and spans the whole H37Rv chromosome with the exception of a single gap of ∼150 kb. As a postgenomic application, the canonical BAC set was used in a comparative study to reveal chromosomal polymorphisms between M. tuberculosis, M. bovis, and M. bovis BCG Pasteur, and a novel 12.7-kb segment present in M. tuberculosis but absent from M. bovis and M. bovis BCG was characterized. This region contains a set of genes whose products show low similarity to proteins involved in polysaccharide biosynthesis. The H37Rv BAC library therefore provides us with a powerful tool both for the generation and confirmation of sequence data as well as for comparative genomics and other postgenomic applications. It represents a major resource for present and future M. tuberculosis research projects.

scholarly journals Genotypic characterization of two bacterial artificial chromosome clones derived from a single DNA source of the very virulent gallid herpesvirus-2 strain C12/130

2011 ◽  
Vol 92 (7) ◽  
pp. 1500-1507 ◽  
Author(s):  
Stephen J. Spatz ◽  
Lorraine P. Smith ◽  
Susan J. Baigent ◽  
Lawrence Petherbridge ◽  
Venugopal Nair
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Artificial Chromosome ◽  
Genetic Changes ◽  
Mixed Genotype ◽  
Bac Clones ◽  
Gallid Herpesvirus 2 ◽  
The Individual

The identification of specific genetic changes associated with differences in the pathogenicity of Marek's disease virus strains (GaHV-2) has been a formidable task due to the large number of mutations in mixed-genotype populations within DNA preparations. Very virulent UK isolate C12/130 induces extensive lymphoid atrophy, neurological manifestations and early mortality in young birds. We have recently reported the construction of several independent full-length bacterial artificial chromosome (BAC) clones of C12/130 capable of generating fully infectious viruses with significant differences in their pathogenicity profiles. Two of these clones (vC12/130-10 and vC12/130-15), which showed differences in virulence relative to each other and to the parental strain, had similar replication kinetics both in vitro and in vivo in spite of the fact that vC12/130-15 was attenuated. To investigate the possible reasons for this, the nucleotide sequences of both clones were determined. Sequence analysis of the two genomes identified mutations within eight genes. A single 494 bp insertion was identified within the genome of the virulent vC12/130-10 clone. Seven non-synonymous substitutions distinguished virulent vC12/130-10 from that of attenuated vC12/130-15. By sequencing regions of parental DNA that differed between the two BAC clones, we confirmed that C12/130 does contain these mutations in varying proportions. Since the individual reconstituted BAC clones were functionally attenuated in vivo and derived from a single DNA source of phenotypically very virulent C12/130, this suggests that the C12/130 virus population exists as a collection of mixed genotypes.

scholarly journals DECONVOLUTING BAC–GENE RELATIONSHIPS USING A PHYSICAL MAP

2008 ◽  
Vol 06 (03) ◽  
pp. 603-622
Author(s):  
YONGHUI WU ◽  
LAN LIU ◽  
TIMOTHY J. CLOSE ◽  
STEFANO LONARDI
Keyword(s):  
Physical Map ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Hybridization Experiment ◽  
Pooling Design ◽  
Bac Clones ◽  
Hybridization Data ◽  
A Genome ◽  
The Right ◽  
Combinatorial Pooling

Deconvolution of relationships between bacterial artificial chromosome (BAC) clones and genes is a crucial step in the selective sequencing of regions of interest in a genome. It often includes combinatorial pooling of unique probes obtained from the genes (unigenes), and screening of the BAC library using the pools in a hybridization experiment. Since several probes can hybridize to the same BAC, in order for the deconvolution to be achievable the pooling design has to be able to handle a large number of positives. As a consequence, smaller pools need to be designed, which in turn increases the number of hybridization experiments, possibly making the entire protocol unfeasible. We propose a new algorithm that is capable of producing high-accuracy deconvolution even in the presence of a weak pooling design, i.e. when pools are rather large. The algorithm compensates for the decrease of information in the hybridization data by taking advantage of a physical map of the BAC clones. We show that the right combination of combinatorial pooling and our algorithm not only dramatically reduces the number of pools required, but also successfully deconvolutes the BAC–gene relationships with almost perfect accuracy. Software is available on request from the first author.

scholarly journals Construction and Characterization of a Bacterial Artificial Chromosome Library for the Hexaploid Wheat Line 92R137

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Qingdong Zeng ◽  
Fengping Yuan ◽  
Xin Xu ◽  
Xue Shi ◽  
Xiaojun Nie ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Hexaploid Wheat ◽  
Positional Cloning ◽  
Bac Library ◽  
Restriction Enzymes ◽  
Artificial Chromosome ◽  
Stripe Rust Resistance ◽  
Wheat Line ◽  
Genomic Resource

For map-based cloning of genes conferring important traits in the hexaploid wheat line 92R137, a bacterial artificial chromosome (BAC) library, including two sublibraries, was constructed using the genomic DNA of 92R137 digested with restriction enzymesHindIII andBamHI. The BAC library was composed of total 765,696 clones, of which 390,144 were from theHindIII digestion and 375,552 from theBamHI digestion. Through pulsed-field gel electrophoresis (PFGE) analysis of 453 clones randomly selected from theHindIII sublibrary and 573 clones from theBamHI sublibrary, the average insert sizes were estimated as 129 and 113 kb, respectively. Thus, theHindIII sublibrary was estimated to have a 3.01-fold coverage and theBamHI sublibrary a 2.53-fold coverage based on the estimated hexaploid wheat genome size of 16,700 Mb. The 765,696 clones were arrayed in 1,994 384-well plates. All clones were also arranged into plate pools and further arranged into 5-dimensional (5D) pools. The probability of identifying a clone corresponding to any wheat DNA sequence (such as geneYr26for stripe rust resistance) from the library was estimated to be more than 99.6%. Through polymerase chain reaction screening the 5D pools withXwe173, a marker tightly linked toYr26, six BAC clones were successfully obtained. These results demonstrate that the BAC library is a valuable genomic resource for positional cloning ofYr26and other genes of interest.

scholarly journals Construction and Characterization of a Bacterial Artificial Chromosome (BAC) Library from the Japanese Malting Barley variety ‘Haruna Nijo’

2007 ◽  
Vol 57 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Daisuke Saisho ◽  
Eriko Myoraku ◽  
Shinji Kawasaki ◽  
Kazuhiro Sato ◽  
Kazuyoshi Takeda
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Barley Variety ◽  
Malting Barley

Construction of a Coix BAC library and isolation of the 22 kDa α-coixin gene cluster

Genome ◽  
2010 ◽  
Vol 53 (9) ◽  
pp. 667-674 ◽  
Author(s):  
Xiangzong Meng ◽  
Binbin Huang ◽  
Liangliang Zhou ◽  
Yunxia He ◽  
Qi Chen ◽  
...  
Keyword(s):  
Genetic Resource ◽  
Crop Improvement ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Gene Isolation ◽  
Close Relative ◽  
Average Insert Size ◽  
Insert Size ◽  
Bac Clones ◽  
Organellar Dna

Coix lacryma-jobi L. (Coix) is a close relative of maize and is considered a valuable genetic resource for crop improvement. Here we report the construction of the first Coix bacterial artificial chromosome (BAC) library using accession PI 324059. This BAC library contains about 230 400 clones with an average insert size of 113 kb, has low organellar DNA contamination, and provides 16.3-fold coverage of the genome. The library was stored in 12 × 96 pools that could be screened with a PCR protocol. Library screening was performed for the 22 kDa α-coixin gene family. A total of 57 positive pools were identified, and single clones were isolated from 19 of these pools. Based on DNA fingerprinting and Southern blot analysis, these 19 BAC clones form a single contig of about 340 kb in length, indicating that the 22 kDa α-coixin genes occur in a cluster. These results demonstrated the suitability of this BAC library for gene isolation and comparative genomics studies of the Coix genome.

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