A 5× genome coverage bovine BAC library: production, characterization, and distribution

1999 ◽  
Vol 10 (7) ◽  
pp. 706-709 ◽  
Author(s):  
Baoli Zhu ◽  
Judith A. Smith ◽  
Simon M. Tracey ◽  
Bernard A. Konfortov ◽  
Katrin Welzel ◽  
...  
Keyword(s):  
Bac Library ◽  
Genome Coverage

scholarly journals A porcine BAC library with tenfold genome coverage: a resource for physical and genetic map integration

2001 ◽  
Vol 12 (6) ◽  
pp. 472-474 ◽  
Author(s):  
Scott C. Fahrenkrug ◽  
Gary A. Rohrer ◽  
Brad A. Freking ◽  
Timothy P.L. Smith ◽  
Kazutoyo Osoegawa ◽  
...  
Keyword(s):  
Genetic Map ◽  
Bac Library ◽  
Genome Coverage ◽  
Physical And Genetic Map ◽  
Map Integration

scholarly journals A Bacterial Artificial Chromosome Library of Lotus japonicus Constructed in an Agrobacterium tumefaciens-Transformable Vector

2001 ◽  
Vol 14 (3) ◽  
pp. 422-425 ◽  
Author(s):  
Artem E. Men ◽  
Khalid Meksem ◽  
My Abdelmajid Kassem ◽  
Dasharath Lohar ◽  
Jiri Stiller ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Agrobacterium Tumefaciens ◽  
Plant Transformation ◽  
Lotus Japonicus ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Average Insert Size ◽  
Insert Size ◽  
Model Legume ◽  
Genome Coverage

We constructed a BAC library of the model legume Lotus japonicus with a 6-to 7-fold genome coverage. We used vector PCLD04541, which allows direct plant transformation by BACs. The average insert size is 94 kb. Clones were stable in Escherichia coli and Agrobacterium tumefaciens.

Construction and characterization of a bacterial artificial chromosome (BAC) library of hexaploid wheat (Triticum aestivum L.) and validation of genome coverage using locus-specific primers

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 870-878 ◽  
Author(s):  
Sasanda D Nilmalgoda ◽  
Sylvie Cloutier ◽  
Andrzej Z Walichnowski
Keyword(s):  
Triticum Aestivum ◽  
Hexaploid Wheat ◽  
Bac Library ◽  
Triticum Aestivum L ◽  
Resistance Locus ◽  
Insert Size ◽  
Specific Primers ◽  
Hindiii Site ◽  
Genome Coverage ◽  
Hmw Glutenin

A BAC library of hexaploid wheat was constructed using the spring wheat cultivar Triticum aestivum L. 'Glenlea'. Fresh shoot tissue from 7- to 10-day-old seedlings was used to obtain HMW DNA. The library was constructed using the HindIII site of pIndigoBAC-5 and the BamHI site of pIndigoBAC-5 and pECBAC1. A total of 12 ligations were used to construct the entire library, which contains over 650 000 clones. Ninety-six percent of the clones had inserts. The insert size ranged from 5 to 189 kb with an average of 79 kb. The entire library was gridded onto 24 high-density filters using a 5 × 5 array. A subset of these membranes was hybridized with two intergenic chloroplast probes and the percentage of clones containing chloroplast DNA (cpDNA) was calculated to be 2.2%. The genome coverage was estimated to be 3.1 × haploid genome equivalents, giving a 95.3% probability of identifying a clone corresponding to any wheat DNA sequence. BAC pools were constructed and screened using markers targeting the Glu-B1 locus (1BL), the hardness loci (5AS, 5BS, 5DS), the leaf rust resistance locus Lr1 (5DL), and the major fusarium head blight QTL locus located on 3BS. These markers were either locus-specific amplicons or microsatellites. A total of 49 BAC clones were identified for 14 markers giving an average of 3.5 clones/marker, thereby corroborating the estimated 3.1× genome coverage. An example using the gene encoding the HMW glutenin Bx7 is illustrated.Key words: BAC library, BAC pools, hexaploid wheat, locus-specific primers, HMW glutenin.

scholarly journals Distribution of Genes and Repetitive Elements in theDiabrotica virgifera virgiferaGenome Estimated Using BAC Sequencing

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Brad S. Coates ◽  
Analiza P. Alves ◽  
Haichuan Wang ◽  
Kimberly K. O. Walden ◽  
B. Wade French ◽  
...  
Keyword(s):  
Bac Library ◽  
Diabrotica Virgifera Virgifera ◽  
Diabrotica Virgifera ◽  
Genome Coverage ◽  
Haplotype Variation ◽  
Endogenous Genes ◽  
Evolution Of Resistance ◽  
Haploid Genome Size ◽  
Corn Plants ◽  
Paired End Sequencing

Feeding damage caused by the western corn rootworm,Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with104±34.5 kb inserts was created, which has an~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that theD. virgifera virgiferagenome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding.

Characterization and applications of an expanded canine BAC library with fourfold genome coverage

2004 ◽  
Vol 121 (5) ◽  
pp. 345-349 ◽  
Author(s):  
C. Schelling ◽  
A. Billault ◽  
B. Colomb ◽  
B. Pineroli ◽  
K. Guziewicz ◽  
...  
Keyword(s):  
Bac Library ◽  
Genome Coverage

scholarly journals Construction of a Llama Bacterial Artificial Chromosome Library with Approximately 9-Fold Genome Equivalent Coverage

2012 ◽  
Vol 2012 ◽  
pp. 1-4 ◽  
Author(s):  
K. W. Airmet ◽  
J. D. Hinckley ◽  
L. T. Tree ◽  
M. Moss ◽  
S. Blumell ◽  
...  
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Bac Library ◽  
Artificial Chromosome ◽  
The United States ◽  
Modern Technology ◽  
Average Insert Size ◽  
Genome Equivalent ◽  
Insert Size ◽  
Genome Coverage ◽  
Genomic Studies

The Ilama is an important agricultural livestock in much of South America. The llama is increasing in popularity in the United States as a companion animal. Little work has been done to improve llama production using modern technology. A paucity of information is available regarding the llama genome. We report the construction of a llama bacterial artificial chromosome (BAC) library of about 196,224 clones in the vector pECBAC1. Using flow cytometry and bovine, human, mouse, and chicken as controls, we determined the llama genome size to be2.4×109 bp. The average insert size of the library is 137.8 kb corresponding to approximately 9-fold genome coverage. Further studies are needed to further characterize the library and llama genome. We anticipate that this new library will help facilitate future genomic studies in the llama.

Identification of the kinanthraquinone biosynthetic gene cluster by expression of an atypical response regulator

2021 ◽  
Vol 85 (3) ◽  
pp. 714-721
Author(s):  
Risa Takao ◽  
Katsuyuki Sakai ◽  
Hiroyuki Koshino ◽  
Hiroyuki Osada ◽  
Shunji Takahashi
Keyword(s):  
Heterologous Expression ◽  
Gene Cluster ◽  
Secondary Metabolite ◽  
Response Regulator ◽  
Bac Library ◽  
Gene Clusters ◽  
Biosynthetic Gene Cluster ◽  
Gene Organization ◽  
Biosynthetic Gene ◽  
Streptomyces Sp

ABSTRACT Recent advances in genome sequencing have revealed a variety of secondary metabolite biosynthetic gene clusters in actinomycetes. Understanding the biosynthetic mechanism controlling secondary metabolite production is important for utilizing these gene clusters. In this study, we focused on the kinanthraquinone biosynthetic gene cluster, which has not been identified yet in Streptomyces sp. SN-593. Based on chemical structure, 5 type II polyketide synthase gene clusters were listed from the genome sequence of Streptomyces sp. SN-593. Among them, a candidate gene cluster was selected by comparing the gene organization with grincamycin, which is synthesized through an intermediate similar to kinanthraquinone. We initially utilized a BAC library for subcloning the kiq gene cluster, performed heterologous expression in Streptomyces lividans TK23, and identified the production of kinanthraquinone and kinanthraquinone B. We also found that heterologous expression of kiqA, which belongs to the DNA-binding response regulator OmpR family, dramatically enhanced the production of kinanthraquinones.

A Graph-Theoretic Approach to Comparing and Integrating Genetic, Physical and Sequence-Based Maps

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2235-2247
Author(s):  
Immanuel V Yap ◽  
David Schneider ◽  
Jon Kleinberg ◽  
David Matthews ◽  
Samuel Cartinhour ◽  
...  
Keyword(s):  
Directed Graph ◽  
Source Material ◽  
Complete Picture ◽  
Theoretic Approach ◽  
Research Groups ◽  
Genome Coverage ◽  
Graph Theoretic ◽  
Novel Approach ◽  
Graph Theoretic Approach ◽  
Locus Order

AbstractFor many species, multiple maps are available, often constructed independently by different research groups using different sets of markers and different source material. Integration of these maps provides a higher density of markers and greater genome coverage than is possible using a single study. In this article, we describe a novel approach to comparing and integrating maps by using abstract graphs. A map is modeled as a directed graph in which nodes represent mapped markers and edges define the order of adjacent markers. Independently constructed graphs representing corresponding maps from different studies are merged on the basis of their common loci. Absence of a path between two nodes indicates that their order is undetermined. A cycle indicates inconsistency among the mapping studies with regard to the order of the loci involved. The integrated graph thus produced represents a complete picture of all of the mapping studies that comprise it, including all of the ambiguities and inconsistencies among them. The objective of this representation is to guide additional research aimed at interpreting these ambiguities and inconsistencies in locus order rather than presenting a “consensus order” that ignores these problems.

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

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