Optical mapping as a routine tool for bacterial genome sequence finishing

Latreille, Phil; Norton, Stacie; Goldman, Barry S.; Henkhaus, John; Miller, Nancy; Barbazuk, Brad; Bode, Helge B.; Darby, Creg; Du, Zijin; Forst, Steve; Gaudriault, Sophie; Goodner, Brad; Goodrich-Blair, Heidi; Slater, Steven

doi:10.1186/1471-2164-8-321

Cited by 96 publications

(99 citation statements)

References 28 publications

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“…Thus, optical mapping was used to obtain a de novo BamHI restriction map with no requirement for previous sequence information (60). The in silico restriction maps of scaffolds were aligned to this structural map to reveal the correct alignment and orientation of all the contigs as shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificit

et al. 2011

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Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campestris pv. vesicatoria 85-10, with a completely different host range. We also compared X. axonopodis pv. citrumelo to the genome of citrus canker pathogen X. axonopodis pv. citri 306. Comparative genomic analysis showed differences in several gene clusters, like those for type III effectors, the type IV secretion system, lipopolysaccharide synthesis, and others. In addition to pthA, effectors such as xopE3, xopAI, and hrpW were absent from X. axonopodis pv. citrumelo while present in X. axonopodis pv. citri. These effectors might be responsible for survival and the low virulence of this pathogen on citrus compared to that of X. axonopodis pv. citri. We also identified unique effectors in X. axonopodis pv. citrumelo that may be related to the different host range as compared to that of X. axonopodis pv. citri. X. axonopodis pv. citrumelo also lacks various genes, such as syrE1, syrE2, and RTX toxin family genes, which were present in X. axonopodis pv. citri. These may be associated with the distinct virulences of X. axonopodis pv. citrumelo and X. axonopodis pv. citri. Comparison of the complete genome sequence of X. axonopodis pv. citrumelo to those of X. axonopodis pv. citri and X. campestris pv. vesicatoria provides valuable insights into the mechanism of bacterial virulence and host specificity.Xanthomonas is an important genus of plant pathogenic bacteria (87). These Gram-negative rod-shaped pathogens belong to the class Gammaproteobacteria and can infect over 350 species of plants (12). Among the diseases on citrus, citrus bacterial canker (CBC) and citrus bacterial spot (CBS) are caused by distinct pathovars of Xanthomonas species. Citrus canker is caused by several pathogenic variants of X. axonopodis pv. citri (synonyms Xanthomonas citri, Xanthomonas campestris pv. citri, or Xanthomonas citri subsp. citri) (90, 109), whereas CBS is caused by X. axonopodis pv. citrumelo. X. axonopodis pv. citri strain 306 with a suspected origin in southeastern Asia causes Asiatic type A canker and is the most widespread and virulent form of CBC. It produces hyperplasic and hypertrophic (corky) lesions surrounded by oily or watersoaked margins and a yellow halo on leaves, stems, and fruits.In 1984, a disease similar to citrus canker was discovered in citrus nurseries in central Florida, leading to the destruction of millions of seedlings (98). This new form of citrus canker was described as the "E-strain" group, also known as nursery strain canker. Leaf spots of this strain are irregular to round, 3 to 5 mm in diameter, flat, water so...

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Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificit

et al. 2011

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“…paratuberculosis strain K-10, including identification of two new genes. In fact, it has been shown that Whole Genome Mapping could be routinely used as an aid to bacterial genome sequence assembly (11) and closure of sequence gaps (31). Using comparative whole-genome mapping, we (24) have also shown the presence of a large genetic inversion event in a methicillin-resistant S. aureus (MRSA).…”

Section: Discussionmentioning

confidence: 99%

Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality

et al. 2012

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cDespite being a clonal pathogen, Staphylococcus aureus continues to acquire virulence and antibiotic-resistant genes located on mobile genetic elements such as genomic islands, prophages, pathogenicity islands, and the staphylococcal chromosomal cassette mec (SCCmec) by horizontal gene transfer from other staphylococci. The potential virulence of a S. aureus strain is often determined by comparing its pulsed-field gel electrophoresis (PFGE) or multilocus sequence typing profiles to that of known epidemic or virulent clones and by PCR of the toxin genes. Whole-genome mapping (formerly optical mapping), which is a highresolution ordered restriction mapping of a bacterial genome, is a relatively new genomic tool that allows comparative analysis across entire bacterial genomes to identify regions of genomic similarities and dissimilarities, including small and large insertions and deletions. We explored whether whole-genome maps (WGMs) of methicillin-resistant S. aureus (MRSA) could be used to predict the presence of methicillin resistance, SCCmec type, and Panton-Valentine leukocidin (PVL)-producing genes on an S. aureus genome. We determined the WGMs of 47 diverse clinical isolates of S. aureus, including well-characterized reference MRSA strains, and annotated the signature restriction pattern in SCCmec types, arginine catabolic mobile element (ACME), and PVL-carrying prophage, PhiSa2 or PhiSa2-like regions on the genome. WGMs of these isolates accurately characterized them as MRSA or methicillin-sensitive S. aureus based on the presence or absence of the SCCmec motif, ACME and the unique signature pattern for the prophage insertion that harbored the PVL genes. Susceptibility to methicillin resistance and the presence of mecA, SCCmec types, and PVL genes were confirmed by PCR. A WGM clustering approach was further able to discriminate isolates within the same PFGE clonal group. These results showed that WGMs could be used not only to genotype S. aureus but also to identify genetic motifs in MRSA that may predict virulence.

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“…The xpt genes are homologues of the Photorhabdus tc, while the xaxAB were discovered in Xenorhabdus as an apoptotic toxin, which Photorhabdus ortholog is phlA (Vigneux, 2007). The future publication of the X. nematophilus genome sequence will enable genome-wide comparisons of the two related genera (Latreille et al, 2007). Such analysis will shed light on the similarities and differences between these two parallel entomopathogenic lifestyles.…”

Section: Xenorhabdus and Photorhabdusmentioning

confidence: 99%

The Diversity of Insect-bacteria Interactions and its Applications for Disease Control

Sánchez-Contreras

Vlisidou

2008

Biotechnology and Genetic Engineering Reviews

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Prokaryotic microorganisms are widespread in all environments on Earth, establishing diverse interactions with many eukaryotic taxa, including insects. These associations may be symbiotic, pathogenic and vectoring. Independently of the type of interaction, each association starts with the adhesion of the microorganism to the host, entry and "invasion" of the host, then progresses to establishment and dissemination within the host, by avoiding host immune responses, and concludes with transmission back to the environment or to a new host. Advances in genomics and genetics have allowed the dissection of these processes and provided important information on the elements driving the shaping of the members of each association. Furthermore, many mechanisms involved in the establishment of the associations have been scrutinised, along with the development of new methods for the management of insect populations.

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Optical mapping as a routine tool for bacterial genome sequence finishing

Cited by 96 publications

References 28 publications

Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificit

Comparative Genomic Analysis of Xanthomonas axonopodis pv. citrumelo F1, Which Causes Citrus Bacterial Spot Disease, and Related Strains Provides Insights into Virulence and Host Specificit

Comparative Whole-Genome Mapping To Determine Staphylococcus aureus Genome Size, Virulence Motifs, and Clonality

The Diversity of Insect-bacteria Interactions and its Applications for Disease Control

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