Journal articles: 'Chromosomes, Artificial, Bacterial'

1

Sambrook, Joseph, and David W. Russell. "Working with Bacterial Artificial Chromosomes." Cold Spring Harbor Protocols 2006, no. 1 (2006): pdb.prot4010. http://dx.doi.org/10.1101/pdb.prot4010.

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Lai, Cary, Tobias Fischer, and Elizabeth Munroe. "Homologous Recombination Using Bacterial Artificial Chromosomes." Cold Spring Harbor Protocols 2015, no. 2 (2015): pdb.prot072397. http://dx.doi.org/10.1101/pdb.prot072397.

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Song, Junqi, Fenggao Dong, and Jiming Jiang. "Construction of a bacterial artificial chromosome (BAC) library for potato molecular cytogenetics research." Genome 43, no. 1 (2000): 199–204. http://dx.doi.org/10.1139/g99-099.

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Lack of reliable techniques for chromosome identification is the major obstacle for cytogenetics research in plant species with large numbers of small chromosomes. To promote molecular cytogenetics research of potato (Solanum tuberosum, 2n = 4x = 48) we developed a bacterial artificial chromosome (BAC) library of a diploid potato species S. bulbocastanum. The library consists of 23 808 clones with an average insert size of 155 kb, and represents approximately 3.7 equivalents to the potato genome. The majority of the clones in the BAC library generated distinct signals on specific potato chromosomes using fluorescence in situ hybridization (FISH). The hybridization signals provide excellent cytological markers to tag individual potato chromosomes. We also demonstrated that the BAC clones can be mapped to specific positions on meiotic pachytene chromosomes. The excellent resolution of pachytene FISH can be used to construct a physical map of potato by mapping molecular marker-targeted BAC clones on pachytene chromosomes. Key words: potato, BAC library, chromosome identification, physical mapping, molecular cytogenetics.

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4

Hanson, Robert E., Michael S. Zwick, Sangdun Choi, et al. "Fluorescent in situ hybridization of a bacterial artificial chromosome." Genome 38, no. 4 (1995): 646–51. http://dx.doi.org/10.1139/g95-082.

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Fluorescent in situ hybridization (FISH) of a 130 kilobase cotton (Gossypium hirsutum L.) bacterial artificial chromosome (BAC) clone containing a high proportion of single-copy DNA produced a large pair of FISH signals on the distal end of the long arm of a pair of chromosomes of the D-genome species G. raimondii Ulbr. and produced a fainter pair of signals on a small submetacentric pair of chromosomes of the A-genome species G. herbaceum L. The signals were syntenic with a nucleolar organizer region in G. raimondii and G. herbaceum. Signal pairs were easily recognized in interphase and metaphase cells either with or without suppression of repetitive sequences with unlabeled G. hirsutum C0t-1 DNA. High quality FISH results were consistently obtained and image analysis was not required for viewing or photography. Results indicate that FISH of BAC clones is an excellent tool for the establishment of new molecular cytogenetic markers in plants and will likely prove instrumental in the development of useful physical maps for many economically important crop species.Key words: bacterial artificial chromosome, BAC, Gossypium, in situ hybridization, physical mapping.

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Yang, Zhongan, Hong Jiang, Thawinee Chachainasakul, et al. "Modified bacterial artificial chromosomes for zebrafish transgenesis." Methods 39, no. 3 (2006): 183–88. http://dx.doi.org/10.1016/j.ymeth.2006.04.011.

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6

Adler, Heiko, Martin Messerle, and Ulrich H. Koszinowski. "Cloning of herpesviral genomes as bacterial artificial chromosomes." Reviews in Medical Virology 13, no. 2 (2003): 111–21. http://dx.doi.org/10.1002/rmv.380.

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Swaminathan, Srividya, Hilary M. Ellis, Laura S. Waters, et al. "Rapid engineering of bacterial artificial chromosomes using oligonucleotides." genesis 29, no. 1 (2000): 14–21. http://dx.doi.org/10.1002/1526-968x(200101)29:1<14::aid-gene1001>3.0.co;2-x.

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Juhas, Mario, and James W. Ajioka. "Integrative bacterial artificial chromosomes for DNA integration into the Bacillus subtilis chromosome." Journal of Microbiological Methods 125 (June 2016): 1–7. http://dx.doi.org/10.1016/j.mimet.2016.03.017.

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Cao, Yihua, Shuiichi Kimura, Takayuki Itoi, Kohsuke Honda, Takeshi Omasa, and Hisao Ohtake. "Physical mapping of Chinese hamster ovary chromosomes using bacterial artificial chromosome library." Journal of Bioscience and Bioengineering 108 (November 2009): S8. http://dx.doi.org/10.1016/j.jbiosc.2009.08.032.

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10

Ball, Kristen D., and J. T. Trevors. "Bacterial genomics: the use of DNA microarrays and bacterial artificial chromosomes." Journal of Microbiological Methods 49, no. 3 (2002): 275–84. http://dx.doi.org/10.1016/s0167-7012(01)00375-x.

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11

Gómez, Martha I., M. Nurul Islam-Faridi, Sung-Sick Woo, et al. "FISH of a maize sh2-selected sorghum BAC to chromosomes of Sorghum bicolor." Genome 40, no. 4 (1997): 475–78. http://dx.doi.org/10.1139/g97-063.

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Fluorescence in situ hybridization (FISH) of a 205 kb Sorghum bicolor bacterial artificial chromosome (BAC) containing a sequence complementary to maize sh2 cDNA produced a large pair of FISH signals at one end of a midsize metacentric chromosome of S. bicolor. Three pairs of signals were observed in metaphase spreads of chromosomes of a sorghum plant containing an extra copy of one arm of the sorghum chromosome arbitrarily designated with the letter D. Therefore, the sequence cloned in this BAC must reside in the arm of chromosome D represented by this monotelosome. This demonstrates a novel procedure for physically mapping cloned genes or other single-copy sequences by FISH, sh2 in this case, by using BACs containing their complementary sequences. The results reported herein suggest homology, at least in part, between one arm of chromosome D in sorghum and the long arm of chromosome 3 in maize.Key words: sorghum, maize, shrunken locus, physical mapping, fluorescence in situ hybridization, bacterial artificial chromosomes.

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Zhang, Peng, Wanlong Li, Bernd Friebe, and Bikram S. Gill. "Simultaneous painting of three genomes in hexaploid wheat by BAC-FISH." Genome 47, no. 5 (2004): 979–87. http://dx.doi.org/10.1139/g04-042.

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Fluorescence in situ hybridization (FISH) is widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts, making them amenable for FISH mapping. In our BAC-FISH experiments, we selected 56 restriction fragment length polymorphism (RFLP)-locus-specific BAC clones from the libraries of Triticum monococcum and Aegilops tauschii, which are the A- and D-genome donors of wheat (Triticum aestivum, 2n = 6x = 42), respectively. The BAC clone 676D4 from the T. monococcum library contains a dispersed repeat that preferentially hybridizes to A-genome chromosomes, and two BAC clones, 9I10 and 9M13, from the Ae. tauschii library contain a dispersed repeat that preferentially hybridizes to the D-genome chromosomes. These repeats are useful in simultaneously discriminating the three different genomes in hexaploid wheat, and in identifying intergenomic translocations in wheat or between wheat and alien chromosomes. Sequencing results show that both of these repeats are transposable elements, indicating the importance of transposable elements, especially retrotransposons, in the genome evolution of wheat.Key words: bacterial artificial chromosome (BAC), fluorescence in situ hybridization (FISH), transposable elements (TEs), wheat, Triticum aestivum.

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13

Islam-Faridi, M. N., K. L. Childs, P. E. Klein, et al. "A Molecular Cytogenetic Map of Sorghum Chromosome1: Fluorescencein SituHybridization Analysis With Mapped Bacterial Artificial Chromosomes." Genetics 161, no. 1 (2002): 345–53. http://dx.doi.org/10.1093/genetics/161.1.345.

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AbstractWe used structural genomic resources for Sorghum bicolor (L.) Moench to target and develop multiple molecular cytogenetic probes that would provide extensive coverage for a specific chromosome of sorghum. Bacterial artificial chromosome (BAC) clones containing molecular markers mapped across sorghum linkage group A were labeled as probes for fluorescence in situ hybridization (FISH). Signals from single-, dual-, and multiprobe BAC-FISH to spreads of mitotic chromosomes and pachytene bivalents were associated with the largest sorghum chromosome, which bears the nucleolus organizing region (NOR). The order of individual BAC-FISH loci along the chromosome was fully concordant to that of marker loci along the linkage map. In addition, the order of several tightly linked molecular markers was clarified by FISH analysis. The FISH results indicate that markers from the linkage map positions 0.0-81.8 cM reside in the short arm of chromosome 1 whereas markers from 81.8-242.9 cM are located in the long arm of chromosome 1. The centromere and NOR were located in a large heterochromatic region that spans ∼60% of chromosome 1. In contrast, this region represents only 0.7% of the total genetic map distance of this chromosome. Variation in recombination frequency among euchromatic chromosomal regions also was apparent. The integrated data underscore the value of cytological data, because minor errors and uncertainties in linkage maps can involve huge physical regions. The successful development of multiprobe FISH cocktails suggests that it is feasible to develop chromosome-specific “paints” from genomic resources rather than flow sorting or microdissection and that when applied to pachytene chromatin, such cocktails provide an especially powerful framework for mapping. Such a molecular cytogenetic infrastructure would be inherently cross-linked with other genomic tools and thereby establish a cytogenomics system with extensive utility in development and application of genomic resources, cloning, transgene localization, development of plant “chromonomics,” germplasm introgression, and marker-assisted breeding. In combination with previously reported work, the results indicate that a sorghum cytogenomics system would be partially applicable to other gramineous genera.

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Gschwend, Andrea R., Qingyi Yu, Paul Moore, et al. "Construction of Papaya Male and Female BAC Libraries and Application in Physical Mapping of the Sex Chromosomes." Journal of Biomedicine and Biotechnology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/929472.

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Papaya is a major fruit crop in the tropics and has recently evolved sex chromosomes. Towards sequencing the papaya sex chromosomes, two bacterial artificial chromosome (BAC) libraries were constructed from papaya male and female genomic DNA. The female BAC library was constructed using restriction enzymeBstY I and consists of 36,864 clones with an average insert size of 104 kb, providing 10.3x genome equivalents. The male BAC library was constructed using restriction enzymeEcoR I and consists of 55,296 clones with an average insert size of 101 kb, providing 15.0x genome equivalents. The male BAC library was used in constructing the physical map of the male-specific region of the male Y chromosome (MSY) and in filling gaps and extending the physical map of the hermaphrodite-specific region of the Yhchromosome (HSY) and the X chromosome physical map. The female BAC library was used to extend the X physical map gap. The MSY, HSY, and X physical maps offer a unique opportunity to study chromosomal rearrangements, Y chromosome degeneration, and dosage compensation of the papaya nascent sex chromosomes.

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15

Cowell, J. K., Y. D. Wang, K. Head, J. Conroy, D. McQuaid, and N. J. Nowak. "Identification and characterisation of constitutional chromosome abnormalities using arrays of bacterial artificial chromosomes." British Journal of Cancer 90, no. 4 (2004): 860–65. http://dx.doi.org/10.1038/sj.bjc.6601588.

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16

McGregor, Alistair, and Mark R. Schleiss. "Recent Advances in Herpesvirus Genetics Using Bacterial Artificial Chromosomes." Molecular Genetics and Metabolism 72, no. 1 (2001): 8–14. http://dx.doi.org/10.1006/mgme.2000.3123.

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17

Muyrers, Joep P. P., Youming Zhang, Vladimir Benes, Giuseppe Testa, Wilhelm Ansorge, and A. Francis Stewart. "Point mutation of bacterial artificial chromosomes by ET recombination." EMBO reports 1, no. 3 (2000): 239–43. http://dx.doi.org/10.1093/embo-reports/kvd049.

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18

Muyrers, J. "Rapid modification of bacterial artificial chromosomes by ET- recombination." Nucleic Acids Research 27, no. 6 (1999): 1555–57. http://dx.doi.org/10.1093/nar/27.6.1555.

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19

Kus, Arita, Joanna Szymanowska-Pułka, Jolanta Kwasniewska, and Robert Hasterok. "Detecting Brachypodium distachyon Chromosomes Bd4 and Bd5 in MH- and X-Ray-Induced Micronuclei Using mcFISH." International Journal of Molecular Sciences 20, no. 11 (2019): 2848. http://dx.doi.org/10.3390/ijms20112848.

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Micronuclei are biomarkers of genotoxic effects and chromosomal instability. They are formed when chromosome fragments or whole chromosomes fail to disjoin into daughter nuclei. We present qualitative and quantitative analyses of the involvement of specific chromosome regions of chromosomes Bd4 and Bd5 in the formation of micronuclei of Brachypodium distachyon root tip cells following maleic hydrazide (MH) treatment and X-radiation. This is visualised by cytomolecular approaches using bacterial artificial chromosome (BAC)-based multicolour fluorescence in situ hybridisation (mcFISH) in combination with 5S and 25S rDNA probes. The results showed that the long arm of submetacentric chromosome Bd4 forms micronuclei at twice the frequency of its short arm, suggesting that the former is more prone to double-strand breaks (DSBs). In contrast, no difference was observed in the frequency of micronuclei derived from the long and short arms of submetacentric chromosome Bd5. Interestingly, the proximal region of the short arm of Bd5 is more prone to DSBs than its distal part. This demonstrates that 5S rDNA and 35S rDNA loci are not “hot spots” for DNA breaks after the application of these mutagens.

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20

Blaas, Leander, Monica Musteanu, Robert Eferl, Anton Bauer, and Emilio Casanova. "Bacterial artificial chromosomes improve recombinant protein production in mammalian cells." BMC Biotechnology 9, no. 1 (2009): 3. http://dx.doi.org/10.1186/1472-6750-9-3.

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21

Asami, Junko, Yukiko U. Inoue, Youhei W. Terakawa, Saki F. Egusa, and Takayoshi Inoue. "Bacterial artificial chromosomes as analytical basis for gene transcriptional machineries." Transgenic Research 20, no. 4 (2010): 913–24. http://dx.doi.org/10.1007/s11248-010-9469-3.

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22

Bird, Alexander W., and Anthony A. Hyman. "Building a spindle of the correct length in human cells requires the interaction between TPX2 and Aurora A." Journal of Cell Biology 182, no. 2 (2008): 289–300. http://dx.doi.org/10.1083/jcb.200802005.

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To assemble mitotic spindles, cells nucleate microtubules from a variety of sources including chromosomes and centrosomes. We know little about how the regulation of microtubule nucleation contributes to spindle bipolarity and spindle size. The Aurora A kinase activator TPX2 is required for microtubule nucleation from chromosomes as well as for spindle bipolarity. We use bacterial artificial chromosome–based recombineering to introduce point mutants that block the interaction between TPX2 and Aurora A into human cells. TPX2 mutants have very short spindles but, surprisingly, are still bipolar and segregate chromosomes. Examination of microtubule nucleation during spindle assembly shows that microtubules fail to nucleate from chromosomes. Thus, chromosome nucleation is not essential for bipolarity during human cell mitosis when centrosomes are present. Rather, chromosome nucleation is involved in spindle pole separation and setting spindle length. A second Aurora A–independent function of TPX2 is required to bipolarize spindles.

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23

Silva, Silvokleio da Costa, Sandra Mendes, Thallitha Régis, Orlando Sampaio Passos, Walter dos Santos Soares Filho, and Andrea Pedrosa-Harand. "Cytogenetic Map of Pummelo and Chromosome Evolution of True Citrus Species and the Hybrid Sweet Orange." Journal of Agricultural Science 11, no. 14 (2019): 148. http://dx.doi.org/10.5539/jas.v11n14p148.

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Pummelo (Citrus maxima) is considered as one of the true citrus species. Together with mandarin (C. reticulata), it gave rise to the hybrid sweet orange (C. sinensis) and other important citrus crops. Although these species have 2n = 18, each has a unique heterochromatin distribution. The aims of this study were to identify chromosome homoeologies between pummelo and other true citrus species, to investigate the karyotypic changes involved in the chromosomal evolution between true citrus and to shed light into the origin of sweet orange hybrid karyotype. Mitotic metaphase chromosomes of pummelo and sweet orange were double stained with the fluorochromes CMA/DAPI (Chromomycin A3/4&rsquo;-6-diamidino-2-phenylindole), and identified by FISH (Fluorescence in Situ Hybridization) with chromosome-specific BAC (Bacterial Artificial Chromosome) markers. The results were compared to previously established cytogenetic maps of mandarin, C. medica and Poncirus trifoliata. Only chromosomes 1, 4 and 8 were maintained unaltered among species, with chromosomes 2 and 3 being among the least conserved in heterochromatin distribution. BACs were conserved in position among homoeologs and the markers mapped to chromosomes 2 and 3 indicated that sweet orange karyotype largely conserved one chromosome from pummelo and one from mandarin. Despite conserved synteny, expansion and contraction of heterochromatic blocks accounted for the differences between karyotypes, even between the hybrid sweet orange and pummelo.

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Dong, Fenggao, J. Mitchell McGrath, John P. Helgeson, and Jiming Jiang. "The genetic identity of alien chromosomes in potato breeding lines revealed by sequential GISH and FISH analyses using chromosome-specific cytogenetic DNA markers." Genome 44, no. 4 (2001): 729–34. http://dx.doi.org/10.1139/g01-043.

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Genomic in situ hybridization (GISH) is one of the most popular and effective techniques for detecting alien chromatin introgressed into breeding lines; however, GISH analysis alone does not reveal the genetic identity of the alien chromosomes. We previously isolated a set of bacterial artificial chromosomes (BACs) specific to each of the 12 potato chromosomes. These BAC clones can be used as chromosome-specific cytogenetic DNA markers (CSCDMs) for potato chromosome identification. Here we demonstrate that GISH and fluorescence in situ hybridization (FISH), using CSCDMs, can be performed sequentially on the same chromosome preparations. Somatic metaphase chromosomes prepared using an enzymatic digestion and "flame-drying" procedure allows repeated probing up to five times without significant damage to chromosome morphology. The sequential GISH and FISH analyses reveal the genomic origin and genetic identity of the alien chromosomes in a single experiment and also determine whether an alien chromosome has been added to the genetic background of potato or is substituting for a homoeologous potato chromosome. The sequential GISH and FISH procedures should be widely applicable for germplasm characterization, especially in plant species with small-sized chromosomes.Key words: FISH, GISH, chromosome indentification, molecular cytogenetics, potato.

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Fujii, Tsuguru, Seigo Kuwazaki, Kimiko Yamamoto, et al. "Identification and molecular characterization of a sex chromosome rearrangement causing a soft and pliable (spli) larval body phenotype in the silkworm, Bombyx mori." Genome 53, no. 1 (2010): 45–54. http://dx.doi.org/10.1139/g09-083.

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We carried out genetic and cytogenetic analyses of X-ray-induced deleterious Z chromosomes that result in a soft and pliable (spli) phenotype in the silkworm, Bombyx mori . In a B. mori strain with a spli phenotype, we found the Z chromosome broken between the sch (1–21.5) and od (1–49.6) loci. We also found a chromosomal fragment bearing a fifth-chromosome locus for egg and eye pigmentation fused to a Z chromosome fragment. By means of fluorescence in situ hybridization using bacterial artificial chromosome clones as probes, we confirmed that the fused chromosome is composed of a fragment of chromosome 5 and a fragment of the Z chromosome. Moreover, a predicted gene, GA002017, the Bombyx ortholog of the Drosophila gene acj6 (Bmacj6), was completely deleted by the Z chromosome breakage event. The relationship between Bmacj6 and the spli phenotype is discussed.

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Wolny, Elzbieta, Wojciech Fidyk, and Robert Hasterok. "Karyotyping of Brachypodium pinnatum (2n = 18) chromosomes using cross-species BAC–FISH." Genome 56, no. 4 (2013): 239–43. http://dx.doi.org/10.1139/gen-2013-0012.

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Identification of individual chromosomes in a complement is usually a difficult task in the case of most plant species, especially for those with small, numerous, and morphologically uniform chromosomes. In this paper, we demonstrate that the landmarks produced by cross-species fluorescence in situ hybridisation (FISH) of Brachypodium distachyon derived bacterial artificial chromosome (BAC) clones can be used for discrimination of Brachypodium pinnatum (2n = 18) chromosomes. Selected sets of clones were hybridised in several sequential experiments performed on exactly the same chromosome spreads, using reprobing of cytological preparations. Analysis of the morphometric features of B. pinnatum chromosomes was performed to establish their total length, the position of centromeres, and the position of BAC-based landmarks in relation to the centromere, thereby enabling their effective karyotyping, which is a prerequisite for more complex study of the grass genome structure and evolution at the cytomolecular level.

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Meksem, Khalid, Jeffry Shultz, Faiza Tebbji, et al. "A bacterial artificial chromosome based physical map of the Ustilago maydis genome." Genome 48, no. 2 (2005): 207–16. http://dx.doi.org/10.1139/g04-099.

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Ustilago maydis, a basidiomycete, is a model organism among phytopathogenic fungi. A physical map of U. maydis strain 521 was developed from bacterial artificial chromosome (BAC) clones. BAC fingerprints used polyacrylamide gel electrophoresis to separate restriction fragments. Fragments were labeled at the HindIII site and codigested with HaeIII to reduce fragments to 50–750 bp. Contiguous overlapping sets of clones (contigs) were assembled at nine stringencies (from P ≤ 1 x 10–6 to 1 x 10–24). Each assembly nucleated contigs with different percentages of bands overlapping between clones (from 20% to 97%). The number of clones per contig decreased linearly from 41 to 12 from P ≤ 1 x 10–7 to 1 x 10–12. The number of separate contigs increased from 56 to 150 over the same range. A hybridization-based physical map of the same BAC clones was compared with the fingerprint contigs built at P ≤ 1 × 10–7. The two methods provided consistent physical maps that were largely validated by genome sequence. The combined hybridization and fingerprint physical map provided a minimum tile path composed of 258 BAC clones (18–20 Mbp) distributed among 28 merged contigs. The genome of U. maydis was estimated to be 20.5 Mbp by pulsed-field gel electrophoresis and 24 Mbp by BAC fingerprints. There were 23 separate chromosomes inferred by both pulsed-field gel electrophoresis and fingerprint contigs. Only 11 of the tile path BAC clones contained recognizable centromere, telomere, and subtelomere repeats (high-copy DNA), suggesting that repeats caused some false merges. There were 247 tile path BAC clones that encompassed about 17.5 Mbp of low-copy DNA sequence. BAC clones are available for repeat and unique gene cluster analysis including tDNA-mediated transformation. Program FingerPrint Contigs maps aligned with each chromosome can be viewed at http://www.siu.edu/~meksem/ustilago_maydis/.Key words: Ustilago maydis, physical map, bacterial artificial chromosomes, whole-genome sequencing.

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28

Boysen, Cecilie, Melvin I. Simon, and Leroy Hood. "Fluorescence-Based Sequencing Directly from Bacterial and P1-Derived Artificial Chromosomes." BioTechniques 23, no. 6 (1997): 978–82. http://dx.doi.org/10.2144/97236bm01.

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29

Beier, Sebastian, Axel Himmelbach, Thomas Schmutzer, et al. "Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes." Plant Biotechnology Journal 14, no. 7 (2016): 1511–22. http://dx.doi.org/10.1111/pbi.12511.

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30

Heintz, Nathaniel, and Shiaoching Gong. "Working with Bacterial Artificial Chromosomes (BACs) and Other High-Capacity Vectors." Cold Spring Harbor Protocols 2020, no. 10 (2020): pdb.top097998. http://dx.doi.org/10.1101/pdb.top097998.

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Petherbridge, Lawrence, Andrew C. Brown, Susan J. Baigent, et al. "Oncogenicity of Virulent Marek's Disease Virus Cloned as Bacterial Artificial Chromosomes." Journal of Virology 78, no. 23 (2004): 13376–80. http://dx.doi.org/10.1128/jvi.78.23.13376-13380.2004.

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ABSTRACT Marek's disease virus (MDV) is an oncogenic alphaherpesvirus that induces T-cell lymphomas in poultry. We report the construction of bacterial artificial chromosome (BAC) clones of the highly oncogenic RB-1B strain by inserting mini-F vector sequences into the US2 locus. MDV reconstituted from two BAC clones induced rapid-onset lymphomas similar to those induced by the wild-type virus. Virus reconstituted from another BAC clone that showed a 7.7-kbp deletion in the internal and terminal unique long repeat regions was nononcogenic, suggesting that the deleted region may be associated with oncogenicity. The generation of the oncogenic BAC clones of MDV is a significant step in unraveling the oncogenic determinants of this virus.

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32

Jackson, Scott A., Fenggao Dong, and Jiming Jiang. "Digital mapping of bacterial artificial chromosomes by fluorescence in situ hybridization." Plant Journal 17, no. 5 (1999): 581–87. http://dx.doi.org/10.1046/j.1365-313x.1999.00398.x.

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33

Dubcovsky, Jorge, Wusirika Ramakrishna, Phillip J. SanMiguel, et al. "Comparative Sequence Analysis of Colinear Barley and Rice Bacterial Artificial Chromosomes." Plant Physiology 125, no. 3 (2001): 1342–53. http://dx.doi.org/10.1104/pp.125.3.1342.

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34

Zhou, Fuchun, and Shou-Jiang Gao. "Recent advances in cloning herpesviral genomes as infectious bacterial artificial chromosomes." Cell Cycle 10, no. 3 (2011): 434–40. http://dx.doi.org/10.4161/cc.10.3.14708.

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35

Qian, Yaping, Li Jin, and Bing Su. "Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)." Genome 47, no. 2 (2004): 239–45. http://dx.doi.org/10.1139/g03-122.

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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.

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Pagel, Janice, Jason G. Walling, Nevin D. Young, Randy C. Shoemaker, and Scott A. Jackson. "Segmental duplications within the Glycine max genome revealed by fluorescence in situ hybridization of bacterial artificial chromosomes." Genome 47, no. 4 (2004): 764–68. http://dx.doi.org/10.1139/g04-025.

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Soybean (Glycine max L. Merr.) is presumed to be an ancient polyploid based on chromosome number and multiple RFLP fragments in genetic mapping. Direct cytogenetic observation of duplicated regions within the soybean genome has not heretofore been reported. Employing flourescence in situ hybridization (FISH) of genetically anchored bacterial artificial chromosomes (BACs) in soybean, we were able to observe that the distal ends of molecular linkage group E had duplicated regions on linkage groups A2 and B2. Further, using fiber-FISH, it was possible to measure the molecular size and organization of one of the duplicated regions. As FISH did not require repetitive DNA for blocking fluorescence signals, we assume that the 200-kb genome region is relatively low in repetitive sequences. This observation, along with the observation that the BACs are located in distal euchromatin regions, has implications for genome structure/evolution and the approach used to sequence the soybean genome.Key words: soybean, genome evolution, FISH, chromosomes, physical mapping.

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Alam, Shayer Mahmood Ibney, Marie Altmanová, Tulyawat Prasongmaneerut, et al. "Cross-Species BAC Mapping Highlights Conservation of Chromosome Synteny across Dragon Lizards (Squamata: Agamidae)." Genes 11, no. 6 (2020): 698. http://dx.doi.org/10.3390/genes11060698.

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Dragon lizards (Squamata: Agamidae) comprise about 520 species in six subfamilies distributed across Asia, Australasia and Africa. Only five species are known to have sex chromosomes. All of them possess ZZ/ZW sex chromosomes, which are microchromosomes in four species from the subfamily Amphibolurinae, but much larger in Phrynocephalus vlangalii from the subfamily Agaminae. In most previous studies of these sex chromosomes, the focus has been on Australian species from the subfamily Amphibolurinae, but only the sex chromosomes of the Australian central bearded dragon (Pogona vitticeps) are well-characterized cytogenetically. To determine the level of synteny of the sex chromosomes of P. vitticeps across agamid subfamilies, we performed cross-species two-colour FISH using two bacterial artificial chromosome (BAC) clones from the pseudo-autosomal regions of P. vitticeps. We mapped these two BACs across representative species from all six subfamilies as well as two species of chameleons, the sister group to agamids. We found that one of these BAC sequences is conserved in macrochromosomes and the other in microchromosomes across the agamid lineages. However, within the Amphibolurinae, there is evidence of multiple chromosomal rearrangements with one of the BACs mapping to the second-largest chromosome pair and to the microchromosomes in multiple species including the sex chromosomes of P. vitticeps. Intriguingly, no hybridization signal was observed in chameleons for either of these BACs, suggesting a likely agamid origin of these sequences. Our study shows lineage-specific evolution of sequences/syntenic blocks and successive rearrangements and reveals a complex history of sequences leading to their association with important biological processes such as the evolution of sex chromosomes and sex determination.

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Bierle, Craig J., Kaitlyn M. Anderholm, Jian Ben Wang, Michael A. McVoy, and Mark R. Schleiss. "Targeted Mutagenesis of Guinea Pig Cytomegalovirus Using CRISPR/Cas9-Mediated Gene Editing." Journal of Virology 90, no. 15 (2016): 6989–98. http://dx.doi.org/10.1128/jvi.00139-16.

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ABSTRACTThe cytomegaloviruses (CMVs) are among the most genetically complex mammalian viruses, with viral genomes that often exceed 230 kbp. Manipulation of cytomegalovirus genomes is largely performed using infectious bacterial artificial chromosomes (BACs), which necessitates the maintenance of the viral genome inEscherichia coliand successful reconstitution of virus from permissive cells after transfection of the BAC. Here we describe an alternative strategy for the mutagenesis of guinea pig cytomegalovirus that utilizes clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing to introduce targeted mutations to the viral genome. Transient transfection and drug selection were used to restrict lytic replication of guinea pig cytomegalovirus to cells that express Cas9 and virus-specific guide RNA. The result was highly efficient editing of the viral genome that introduced targeted insertion or deletion mutations to nonessential viral genes. Cotransfection of multiple virus-specific guide RNAs or a homology repair template was used for targeted, markerless deletions of viral sequence or to introduce exogenous sequence by homology-driven repair. As CRISPR/Cas9 mutagenesis occurs directly in infected cells, this methodology avoids selective pressures that may occur during propagation of the viral genome in bacteria and may facilitate genetic manipulation of low-passage or clinical CMV isolates.IMPORTANCEThe cytomegalovirus genome is complex, and viral adaptations to cell culture have complicated the study of infectionin vivo. Recombineering of viral bacterial artificial chromosomes enabled the study of recombinant cytomegaloviruses. Here we report the development of an alternative approach using CRISPR/Cas9-based mutagenesis in guinea pig cytomegalovirus, a small-animal model of congenital cytomegalovirus disease. CRISPR/Cas9 mutagenesis can introduce the same types of mutations to the viral genome as bacterial artificial chromosome recombineering but does so directly in virus-infected cells. CRISPR/Cas9 mutagenesis is not dependent on a bacterial intermediate, and defined viral mutants can be recovered after a limited number of viral genome replications, minimizing the risk of spontaneous mutation.

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Ziolkowski, Piotr A., and Jan Sadowski. "FISH-mapping of rDNAs and Arabidopsis BACs on pachytene complements of selected Brassicas." Genome 45, no. 1 (2002): 189–97. http://dx.doi.org/10.1139/g01-101.

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To improve resolution of physical mapping on Brassica chromosomes, we have chosen the pachytene stage of meiosis where incompletely condensed bivalents are much longer than their counterparts at mitotic metaphase. Mapping with 5S and 45S rDNA sequences demonstrated the advantage of pachytene chromosomes in efficient physical mapping and confirmed the presence of a novel 5S rDNA locus in Brassica oleracea, initially identified by genetic mapping using restriction fragment length polymorphism (RFLP). Fluorescence in situ hybridization (FISH) analysis visualized the presence of the third 5S rDNA locus on the long arm of chromosome C2 and confirmed the earlier reports of two 45S rDNA loci in the B. oleracea genome. FISH mapping of low-copy sequences from the Arabidopsis thaliana bacterial artificial chromosome (BAC) clones on the B. oleracea chromosomes confirmed the expectation of efficient and precise physical mapping of meiotic bivalents based on data available from A. thaliana and indicated conserved organization of these two BAC sequences on two B. oleracea chromosomes. Based on the heterologous in situ hybridization with BACs and their mapping applied to long pachytene bivalents, a new approach in comparative analysis of Brassica and A. thaliana genomes is discussed.Key words: Brassicaceae, pachytene chromosomes, FISH, rDNA, BACs.

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Mendes, Sandra, Thallita Régis, Javier Terol, Walter dos Santos Soares Filho, Manuel Talon, and Andrea Pedrosa-Harand. "Integration of mandarin (Citrus reticulata) cytogenetic map with its genome sequence." Genome 63, no. 9 (2020): 437–44. http://dx.doi.org/10.1139/gen-2020-0046.

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Citrus is an extremely important genus in terms of world fruit production. Despite its economic importance and the small genome sizes of its species (2n = 18, 1C = 430 ± 68 Mbp), entire genomic assemblies have only recently become available for some of its representatives. Together with the previous CMA/DAPI banding and fluorescence in situ hybridization (FISH) in the group, these data are important for understanding the complex relationships between its species and for assisting breeding programs. To anchor genomic data with the cytogenetic map of mandarin (Citrus reticulata), the parental species of several economically important hybrids such as sweet orange and clementine, 18 BAC (bacterial artificial chromosome) clones were used. Eleven clementine BACs were positioned by BAC-FISH, doubling the number of chromosome markers so far available for BAC-FISH in citrus. Additionally, six previously mapped BACs were end-sequenced, allowing, together with one BAC previously sequenced, their assignment to scaffolds and the subsequent integration of chromosomes and the genome assembly. This study therefore established correlations between mandarin scaffolds and chromosomes, allowing further structural genomic and comparative study with the sweet orange genome, as well as insights into the chromosomal evolution of the group.

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41

Sima, Jiao, Daniel A. Bartlett, Molly R. Gordon, and David M. Gilbert. "Bacterial artificial chromosomes establish replication timing and sub-nuclear compartment de novo as extra-chromosomal vectors." Nucleic Acids Research 46, no. 4 (2017): 1810–20. http://dx.doi.org/10.1093/nar/gkx1265.

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42

Miller, Joseph T., Fenggao Dong, Scott A. Jackson, Junqi Song, and Jiming Jiang. "Retrotransposon-Related DNA Sequences in the Centromeres of Grass Chromosomes." Genetics 150, no. 4 (1998): 1615–23. http://dx.doi.org/10.1093/genetics/150.4.1615.

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Abstract Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.

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Yang, Zhong-Nan, and T. Erik Mirkov. "Isolation of large terminal sequences of BAC inserts based on double-restriction-enzyme digestion followed by anchored PCR." Genome 43, no. 2 (2000): 412–15. http://dx.doi.org/10.1139/g99-120.

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Isolation of the terminal portions of genomic DNA cloned in bacterial artificial chromosomes (BACs) is an important step in map-based cloning, and several methods have been developed. Here, we present a new method based on double-restriction-enzyme digestion followed by anchored PCR. BAC DNA was digested with two enzymes: NotI and one of four enzymes (EcoRV, HpaI, StuI, or XmnI) that produce blunt termini. After dephosphorylation, these digestions were ligated to NotI- and EcoRV-digested pMSK, a new cloning vector developed in this work that is derived from pBluescript SK(+). PCR products representing the left- and right-terminal sequences of BAC inserts were obtained using a primer complementary to pMSK and a primer complementary to sequences in either the left arm or the right arm of the BAC vector pBeloBAC11. We have tested this method with 15 different BAC clones, and PCR products representing both the left- and right-terminal sequences have been obtained from all 15 BAC clones. This method is simple, fast, reproducible, and uses the same set of primers for any restriction enzyme used. With some modifications, it can also be used for isolating the terminal portions of genomic DNA cloned in yeast artificial chromosomes and P1-derived artificial chromosomes. Key words: BAC, anchored PCR, terminal sequence isolation, chromosome walk.

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Bautista, R., D. P. Villalobos, S. Díaz-Moreno, F. R. Cantón, F. M. Cánovas, and M. Gonzalo Claro. "New strategy for Pinus pinaster genomic library construction in bacterial artificial chromosomes." Investigación Agraria: Sistemas y Recursos Forestales 17, no. 3 (2008): 238. http://dx.doi.org/10.5424/srf/2008173-01038.

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Bird, Alexander W., Axel Erler, Jun Fu, et al. "High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes." Nature Methods 9, no. 1 (2011): 103–9. http://dx.doi.org/10.1038/nmeth.1803.

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Testa, Giuseppe, Youming Zhang, Kristina Vintersten, et al. "Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles." Nature Biotechnology 21, no. 4 (2003): 443–47. http://dx.doi.org/10.1038/nbt804.

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Cai, W., J. Jing, B. Irvin, et al. "High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping." Proceedings of the National Academy of Sciences 95, no. 7 (1998): 3390–95. http://dx.doi.org/10.1073/pnas.95.7.3390.

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Tischer, B. Karsten, and Benedikt B. Kaufer. "Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences." Journal of Biomedicine and Biotechnology 2012 (2012): 1–14. http://dx.doi.org/10.1155/2012/472537.

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Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques inEscherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members ofCoronaviridaeandFlaviviridaecould be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

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DiLeone, R. J., G. A. Marcus, M. D. Johnson, and D. M. Kingsley. "Efficient studies of long-distance Bmp5 gene regulation using bacterial artificial chromosomes." Proceedings of the National Academy of Sciences 97, no. 4 (2000): 1612–17. http://dx.doi.org/10.1073/pnas.97.4.1612.

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Qi, X., S. Lindup, T. S. Pittaway, S. Allouis, M. D. Gale, and K. M. Devos. "Development of Simple Sequence Repeat Markers from Bacterial Artificial Chromosomes without Subcloning." BioTechniques 31, no. 2 (2001): 355–62. http://dx.doi.org/10.2144/01312st08.

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Journal articles on the topic 'Chromosomes, Artificial, Bacterial'

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