scholarly journals Combined Genetic and Physical Map of the Complex Genome of Agrobacterium tumefaciens

1999 ◽  
Vol 181 (17) ◽  
pp. 5160-5166 ◽  
Author(s):  
Brad W. Goodner ◽  
Brian P. Markelz ◽  
M. Casey Flanagan ◽  
Chris B. Crowell ◽  
Jodi L. Racette ◽  
...  
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Physical Mapping ◽  
Physical Map ◽  
Genomic Structure ◽  
Genetic Maps ◽  
Mapping Data ◽  
Circular Chromosome ◽  
Linear Chromosome ◽  
Single Chromosome ◽  
Complex Genome

ABSTRACT A combined genetic and physical map of the Agrobacterium tumefaciens A348 (derivative of C58) genome was constructed to address the discrepancy between initial single-chromosome genetic maps and more recent physical mapping data supporting the presence of two nonhomologous chromosomes. The combined map confirms the two-chromosome genomic structure and the correspondence of the initial genetic maps to the circular chromosome. The linear chromosome is almost devoid of auxotrophic markers, which probably explains why it was missed by genetic mapping studies.

scholarly journals Draft Genome Sequence of Agrobacterium tumefaciens Strain 1D1526

2019 ◽  
Vol 8 (45) ◽  
Author(s):  
Naxin Huo ◽  
Yong Gu ◽  
Kent F. McCue ◽  
Diaa Alabed ◽  
James G. Thomson
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Circular Chromosome ◽  
Linear Chromosome ◽  
Content Type

This work reports the draft genome sequence of Agrobacterium tumefaciens strain 1D1526. The assembled genome is composed of a 2,881,823-bp circular chromosome, a 2,235,711-bp linear chromosome, and a 44,582-bp unassembled contig.

scholarly journals Replicon-Specific Regulation of Small Heat Shock Genes in Agrobacterium tumefaciens

2004 ◽  
Vol 186 (20) ◽  
pp. 6824-6829 ◽  
Author(s):  
Sylvia Balsiger ◽  
Curdin Ragaz ◽  
Christian Baron ◽  
Franz Narberhaus
Keyword(s):  
Agrobacterium Tumefaciens ◽  
Heat Shock ◽  
Elevated Temperatures ◽  
Heat Shock Gene ◽  
Circular Chromosome ◽  
Linear Chromosome ◽  
Shsp Gene ◽  
Shine Dalgarno Sequence ◽  
Specific Regulation ◽  
Shock Proteins

ABSTRACT Four genes coding for small heat shock proteins (sHsps) were identified in the genome sequence of Agrobacterium tumefaciens, one on the circular chromosome (hspC), one on the linear chromosome (hspL), and two on the pAT plasmid (hspAT1 and hspAT2). Induction of sHsps at elevated temperatures was revealed by immunoblot analyses. Primer extension experiments and translational lacZ fusions demonstrated that expression of the pAT-derived genes and hspL is controlled by temperature in a regulon-specific manner. While the sHsp gene on the linear chromosome turned out to be regulated by RpoH (σ32), both copies on pAT were under the control of highly conserved ROSE (named for repression of heat shock gene expression) sequences in their 5′ untranslated region. Secondary structure predictions of the corresponding mRNA strongly suggest that it represses translation at low temperatures by masking the Shine-Dalgarno sequence. The hspC gene was barely expressed (if at all) and not temperature responsive.

scholarly journals Mapping of Escherichia coli chromosomal Tn5 and F insertions by pulsed field gel electrophoresis.

Genetics ◽  
1988 ◽  
Vol 119 (2) ◽  
pp. 227-236
Author(s):  
C L Smith ◽  
R D Kolodner
Keyword(s):  
Escherichia Coli ◽  
Physical Mapping ◽  
Gel Electrophoresis ◽  
Physical Map ◽  
Pulsed Field Gel Electrophoresis ◽  
Genetic Maps ◽  
Low Resolution ◽  
Transposon Tn5 ◽  
Pulsed Field ◽  
E Coli

Abstract A low resolution Not I physical map of Escherichia coli was recently constructed. In this report we demonstrated that this map can be used to map Tn5 and F insertions physically. The transposon, Tn5, contains Not I recognition sequences in its IS50 sequences. F plasmid contains an unmapped Not I site. Hence, the location of Tn5 and F in the chromosome can be mapped by identifying the location of the introduced Not I sites using pulsed field gel electrophoresis. The physical mapping of genetically mapped Tn5 insertions confirm the previously constructed Not I map and helps align the E. coli physical and genetic maps. The use of Tn5 can assist the construction of both physical and genetic maps for microorganisms lacking such maps. Variations on this approach will facilitate physical mapping with a wide variety of organisms, enzymes, and genetic elements.

scholarly journals Segregation of fourAgrobacterium tumefaciensreplicons during polar growth: PopZ and PodJ control segregation of essential replicons

2020 ◽  
Vol 117 (42) ◽  
pp. 26366-26373
Author(s):  
J. S. Robalino-Espinosa ◽  
J. R. Zupan ◽  
A. Chavez-Arroyo ◽  
P. Zambryski
Keyword(s):  
Cell Cycle ◽  
Agrobacterium Tumefaciens ◽  
Single Cell ◽  
Essential Role ◽  
Polar Growth ◽  
Cell Compartment ◽  
Circular Chromosome ◽  
Linear Chromosome ◽  
Growth Pole ◽  
Cell Compartments

Agrobacterium tumefaciensC58 contains four replicons, circular chromosome (CC), linear chromosome (LC), cryptic plasmid (pAt), and tumor-inducing plasmid (pTi), and grows by polar growth from a single growth pole (GP), while the old cell compartment and its old pole (OP) do not elongate. We monitored the replication and segregation of these four genetic elements during polar growth. The three largest replicons (CC, LC, pAt) reside in the OP compartment prior to replication; post replication one copy migrates to the GP prior to division. CC resides at a fixed location at the OP and replicates first. LC does not stay fixed at the OP once the cell cycle begins and replicates from varied locations 20 min later than CC. pAt localizes similarly to LC prior to replication, but replicates before the LC and after the CC. pTi does not have a fixed location, and post replication it segregates randomly throughout old and new cell compartments, while undergoing one to three rounds of replication during a single cell cycle. Segregation of the CC and LC is dependent on the GP and OP identity factors PopZ and PodJ, respectively. Without PopZ, replicated CC and LC do not efficiently partition, resulting in sibling cells without CC or LC. Without PodJ, the CC and LC exhibit abnormal localization to the GP at the beginning of the cell cycle and replicate from this position. These data reveal PodJ plays an essential role in CC and LC tethering to the OP during early stages of polar growth.

scholarly journals Advances in BAC-Based Physical Mapping and Map Integration Strategies in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Ruvini Ariyadasa ◽  
Nils Stein
Keyword(s):  
High Throughput ◽  
Physical Mapping ◽  
Physical Map ◽  
Genetic Maps ◽  
Gold Standard Reference ◽  
Reference Quality ◽  
Sequencing Strategy ◽  
Map Integration ◽  
Integration Strategies ◽  
Next Generation Sequencing Ngs

In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1299-1313
Author(s):  
Zheng Xu ◽  
Britton Lance ◽  
Claudia Vargas ◽  
Budak Arpinar ◽  
Suchendra Bhandarkar ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Dna Sequences ◽  
Pneumocystis Carinii ◽  
Single Copy ◽  
Fungal Genome ◽  
Mapping Data ◽  
Genome Database ◽  
Rdna Genes ◽  
Genome Map ◽  
Mapping By Sequencing

Abstract A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock Ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

Physical mapping of 38 highly informative genetic markers to 10 intervals of chromosome 11q: integration of the physical and genetic maps

1994 ◽  
Vol 58 (2) ◽  
pp. 81-85 ◽  
Author(s):  
D. HUNT ◽  
V. VAN HEYNINGEN ◽  
C. JONES ◽  
C. McCONVILLE ◽  
F. J. BENHAM
Keyword(s):  
Genetic Markers ◽  
Physical Mapping ◽  
Genetic Maps

Construction of a genomic map ofMoraxella (Branhamella) catarrhalisATCC 25238 and physical mapping of virulence-associated genes

1999 ◽  
Vol 45 (4) ◽  
pp. 299-303 ◽  
Author(s):  
K T Nguyen ◽  
E J Hansen ◽  
M A Farinha
Keyword(s):  
Gel Electrophoresis ◽  
Moraxella Catarrhalis ◽  
Southern Hybridization ◽  
Physical Map ◽  
Outer Membrane Proteins ◽  
Restriction Enzymes ◽  
Pulsed Field Gel Electrophoresis ◽  
Respiratory Pathogens ◽  
Circular Chromosome ◽  
Pulsed Field

A physical genome map of the Moraxella catarrhalis type strain (ATCC 25238) has been constructed using pulsed field gel electrophoresis. Macrorestriction analyses of the genome of M. catarrhalis were performed by digestion with the restriction enzymes SmaI, NotI, and RsrII, which cleave the single circular chromosome into 9, 10, and 6 fragments, respectively. The chromosomal fragments generated by pulsed field gel electrophoresis were converted to a linkage map utilizing a combination of partial digestions, and cross-hybridizations. Moraxella catarrhalis, like a number of other respiratory pathogens, has a relatively small genome estimated at 1750 kilobase pairs or about 40% of the size of the Escherichia coli genome. The locations of the four ribosomal RNA operons (rrnLS) were determined by Southern hybridization and by digestion with I-CeuI endonuclease. A number of genes involved in virulence have been placed onto the physical map by Southern hybridization including those encoding the predominant outer-membrane proteins and the chromosomal gene encoding beta-lactamase.Key words: Moraxella catarrhalis, physical map, genome analysis, pulsed-field gel electrophoresis, virulence.

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