Brückner et al., Fig. 1b 1 2 3 4 5 7 8 9 10 11 12 Brückner et al., Fig. 1B a c b 6 Fig. 1. Circular representation of Streptococcus pneumoniae genome comparisons.

Slides:



Advertisements
Similar presentations
1 3. genome analysis. 2 The first DNA-based genome to be sequenced in its entirety was that of bacteriophage Φ-X174; (5,368 bp), sequenced by Frederick.
Advertisements

MGH-PGA Genomic Analysis of Stress and Inflammation: Sequence Analysis of Pseudomonas aeruginosa Strain PA14 Nicole T. Liberati, Dan G. Lee, Jacinto M.
Figure 1: (A) A microarray may contain thousands of ‘spots’. Each spot contains many copies of the same DNA sequence that uniquely represents a gene from.
What is comparative genomics? Analyzing & comparing genetic material from different species to study evolution, gene function, and inherited disease Understand.
Genome annotation and search for homologs. Genome of the week Discuss the diversity and features of selected microbial genomes. Link to the paper describing.
What do we already know ? The rice disease resistance gene Pi-ta Genetically mapped to chromosome 12 Rybka et al. (1997). It has also been sequenced Bryan.
From: Duggan et.al. Nature Genetics 21:10-14, 1999 Microarray-Based Assays (The Basics) Each feature or “spot” represents a specific expressed gene (mRNA).
Visualizing Biosciences Genomics & Proteomics. “Scientists Complete Rough Draft of Human Genome” - New York Times, June 26, 2000 The problem: –3 billion.
The first report of detecting the blaSIM-2 gene and determining the complete sequence of the SIM-encoding plasmid  F. Sun, D. Zhou, Q. Wang, J. Feng,
3. genome analysis.
Bacterial genomics: The controlled chaos of shifty pathogens
Reciprocal Crossovers and a Positional Preference for Strand Exchange in Recombination Events Resulting in Deletion or Duplication of Chromosome 17p11.2 
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters by Pascal Preker, Jesper Nielsen, Susanne Kammler, Søren Lykke-Andersen,
Genomic Insights into the Immune System of the Sea Urchin
Recombination between Palindromes P5 and P1 on the Human Y Chromosome Causes Massive Deletions and Spermatogenic Failure  Sjoerd Repping, Helen Skaletsky,
OTX2 is associated with higher levels of activity when paired with NEUROD1 and arranged in clusters. OTX2 is associated with higher levels of activity.
Genomic rearrangements of E
The first report of detecting the blaSIM-2 gene and determining the complete sequence of the SIM-encoding plasmid  F. Sun, D. Zhou, Q. Wang, J. Feng,
Exon Circularization Requires Canonical Splice Signals
The ETS-CRE array identifies genomic sequences specifically cobound by CREB1 and GABPα. The ETS-CRE array identifies genomic sequences specifically cobound.
Schematic representation of the lbk gene, positions of gRNAs, and knock-in cassette. Schematic representation of the lbk gene, positions of gRNAs, and.
A Map for Horizontal Disparity in Monkey V2
Volume 18, Issue 5, Pages (November 2015)
Supplemental Figure 3 A B C T-DNA 1 2 RGLG1 2329bp 3 T-DNA 1 2 RGLG2
Molecular cloning of pms916 salt hypersensitive T-DNA mutant.
Genomic context, sequence identity, and structural homology modeling of the aadA31 gene detected in P. multocida PM13 and H. somni HS31. Genomic context,
Recurrent 10q22-q23 Deletions: A Genomic Disorder on 10q Associated with Cognitive and Behavioral Abnormalities  Jorune Balciuniene, Ningping Feng, Kelly.
Volume 11, Issue 5, Pages (May 2015)
Map of the pSSE ATCC plasmid.
Volume 126, Issue 6, Pages (September 2006)
The Complete Genome Sequence of Escherichia coli K-12
Phylogenetic tree of perA A2-domain DNA sequence.
Comparison of the variable regions of (A) pHNZY32, pHNZY118, and pHNAH24; (B) pHNMCC14; (C) pHNFKU92; (D) pE80; (E) pECB11; (F) p42-2; and (G) pSLK172-2.
Volume 17, Issue 6, Pages (November 2016)
Copy-Number Variations Measured by Single-Nucleotide–Polymorphism Oligonucleotide Arrays in Patients with Mental Retardation  Janine Wagenstaller, Stephanie.
Matthew W Jones-Rhoades, David P Bartel  Molecular Cell 
The mosaic genome structure and phylogeny of Shiga toxin-producing Escherichia coli O104:H4 is driven by short-term adaptation  K. Zhou, M. Ferdous, R.F.
Comparative analysis of Aeromonas sp.
A DNA Replication Mechanism for Generating Nonrecurrent Rearrangements Associated with Genomic Disorders  Jennifer A. Lee, Claudia M.B. Carvalho, James.
A Physical Map, Including a BAC/PAC Clone Contig, of the Williams-Beuren Syndrome– Deletion Region at 7q11.23  Risa Peoples, Yvonne Franke, Yu-Ker Wang,
Recursive construction and error correction of a simple combinatorial library. Recursive construction and error correction of a simple combinatorial library.
Michael A. Rogers, Hermelita Winter, Christian Wolf, Jürgen Schweizer 
Volume 23, Issue 10, Pages (June 2018)
Reciprocal Crossovers and a Positional Preference for Strand Exchange in Recombination Events Resulting in Deletion or Duplication of Chromosome 17p11.2 
E.J. Hollox, J.A.L. Armour, J.C.K. Barber 
Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number.
A Novel Family of Mammalian Taste Receptors
Mutagenesis through Cas9/sgRNA-induced HDR
An AT-Rich Sequence in Human Common Fragile Site FRA16D Causes Fork Stalling and Chromosome Breakage in S. cerevisiae  Haihua Zhang, Catherine H. Freudenreich 
Whole-genome comparison of E
iraL shares sequence identity with iraM from E
Tagging of the endogenous Py03652 gene with the gfp gene in Plasmodium yoelii. Tagging of the endogenous Py03652 gene with the gfp gene in Plasmodium yoelii.
Multidrug resistance-encoding plasmid from Aeromonas sp. strain P2GI
Zvi Tamari, Naama Barkai  Cell Reports 
Genomewide profiling of chromatin accessibility in prostate cancer specimens Genomewide profiling of chromatin accessibility in prostate cancer specimens.
Brandon Ho, Anastasia Baryshnikova, Grant W. Brown  Cell Systems 
Kinetics of clone appearance, size, persistence, and lineage content.
Fig. 2. Validating the efficiency of smc3 MOs
Comparative genomic expressive hybridisation detection and quantification. Comparative genomic expressive hybridisation detection and quantification. (A)
Figure 1. An outline of the novel ∼3
Relationship between blood cell and plasma miRNA expression among published circulating cancer biomarkers. Relationship between blood cell and plasma miRNA.
Alignment of Wt1 genomic regions reveals a highly conserved element upstream of zebrafish wt1a. Alignment of Wt1 genomic regions reveals a highly conserved.
Manfred Schmid, Agnieszka Tudek, Torben Heick Jensen  Cell Reports 
Flow field adjacent to an eel (body length L=0
Volume 21, Issue 23, Pages (December 2011)
Phylogenetic trees of S. oralis and S. mitis strains.
Chromosomal maps of three M
Long noncoding RNAs are distributed throughout the genome and are characteristically distinct from annotated mRNAs. Long noncoding RNAs are distributed.
Driver pathways and key genes in OSCC
Most virus-related pyrosequencing reads found in raw sewage represent previously unknown viruses. Most virus-related pyrosequencing reads found in raw.
Presentation transcript:

Brückner et al., Fig. 1b Brückner et al., Fig. 1B a c b 6 Fig. 1. Circular representation of Streptococcus pneumoniae genome comparisons. A. S. pneumoniae R6 versus TIGR. B. S. pneumoniae TIGR versus R6. The outer two circles show the predicted coding regions according to the NCBI accession number NC_ (R6) and NC_ (TIGR). The third circle in red shows the result of blast hits with a minimum length of 1000 bp; white areas represent genomic regions present in one strain only (closed circles). The forth circle indicates the GC content, and innermost circle represents the GC skew. The dots mark regions of high diversity between the two strains; the numbers refer to the clusters outlined in tables 1 and 3. The arrows marked a, b and c indicate regions of unusual GC content and GC skew. Diagrams were created with the programme ARTEMIS. Standard parameters were used (window size: 1000 bp, window step: 100 bp).

Brückner et al., Fig. 1a Brückner et al., Fig. 1A a c 6

Brückner et al., Fig , , , ,279 spr pspA spr argG SP pspA 126, , , , , , , , , , ,000 Fig. 2. The R6 cluster 1 region. The numbers refer to the borders of sequence divergence between S. pneumoniae TIGR and R6 strains. The arrows depict the orientation of the genes as annotated. Regions with >98% sequence identities are connected by lines. The regions of homology are indicated by different shades of gray.

Brückner et al., Fig. 4 4 R6/D39 ATCC D219 F1 2303R Hu-11/15/ S /2349/456/ * 2* 3* 4* 5* 6* 7* 8* 9* 10* 11* 12* 13* Fig. 4. Gene clusters of S. pneumoniae TIGR detectable on oligonucleotide microarrays in hybridization with genomic DNA of genetically distinct S. pneumoniae strains. The genes are arranged according to the annotated genome with the replication start on top. Low hybridization signals are indicated by black lines, and only those genes that differ by an intensity ratio smaller than –4 in at least one of the strains shown are marked by black lines. Clusters that are not contained in the R6 strain are marked by arrows on the left side (1-12); other clusters noticeable in other strains are marked on the right (1* - 13*). The strains used for hybridization are described in detail in (Hakenbeck et al. 2001): strain 4 (serotype 4 from Papua), the pair R6/D39, serotype 22 ATCC 49619, serotype 23F D219 from Germany; serotype 23F F1 (France); three representatives of the Hungarian seroytpe 19A multiresistant clone (Hu-11, Hu-15, Hu-9); the two serotype 3 strains 1711 (Switzerland) and 4241 (France); serotype 23F from Finland; four representatives of the multiresistant Spanish 23F clone 17 (South Africa), 2349, 456 and the 19F capsular variant 496 from Spain; and the multiresistant serotype 6B from Spain.