Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

Salzberg, Steven L.; Sommer, Daniel; Schatz, Michael C.; Phillippy, Adam M.; Rabinowicz, Pablo D.; Tsuge, Seiji; Furutani, Ayako; Ochiai, Hirokazu; Delcher, Arthur L.; Kelley, David R.; Puiu, Daniela; Radune, Diana; Shumway, Martin; Trapnell, Cole; Gudlur, Aparna; Jha, Gopaljee; Pandey, Alok; Patil, Prabhu B.; Ishihara, Hisashi; Meyer, Damien; Szurek, Boris; Koebnik, Ralf; Ryan, Robert P.; Hirata, Haruyuki; Tsuyumu, Shinji; Lee, Sang Won; Seo, Young-Su; Sriariyanum, Malinee; Ronald, Pamela C.; Sonti, Ramesh V.; Sluys, Marie‐Anne Van; Leach, Jan E.; White, Frank F.; Bogdanove, Adam J.

doi:10.1186/1471-2164-9-534

Cited by 118 publications

(129 citation statements)

References 2 publications

(1 reference statement)

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“…For example, one study looking at the acquisition of antibiotic-resistance integrons by susceptible strains in the gut In recent years, it has become clear that IS elements play an important role in pathogen evolution through genome rearrangements and in genome reduction. Salzberg et al 63 reported that a strain of the rice pathogen Xanthomonas oryzae pv. oryzae has an unusually long tandem duplication (each region is 212,087 bp long) with an IS element in between the two regions and two IS elements each flanking the other end of the two regions.…”

Section: Comparative Genomics Of Strains Of S Equi and S Zooepidemicusmentioning

confidence: 99%

The influence of the accessory genome on bacterial pathogen evolution

Jackson

Vinatzer

Arnold

et al. 2011

Mobile Genetic Elements

111

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Section: Comparative Genomics Of Strains Of S Equi and S Zooepidemicusmentioning

confidence: 99%

The influence of the accessory genome on bacterial pathogen evolution

Jackson

Vinatzer

Arnold

et al. 2011

Mobile Genetic Elements

111

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“…The BLS and PXO datasets were derived from X. oryzae strains BLS256 and PXO99A previously assembled using Sanger reads (47,48) and reassembled using Pacific Biosciences P6-C4 reads in Booher et al (11). The BLS dataset contains 89,634 reads (≈234× coverage), and the PXO dataset contains 55,808 reads (≈141× coverage).…”

Section: Resultsmentioning

confidence: 99%

Assembly of long error-prone reads using de Bruijn graphs

Lin

Yuan

Kolmogorov

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

257

208

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The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical paradigm for assembling long error-prone reads. We show how to generalize de Bruijn graphs for assembling long error-prone reads and describe the ABruijn assembler, which combines the de Bruijn graph and the OLC approaches and results in accurate genome reconstructions.de Bruijn graph | genome assembly | single-molecule sequencing T he key challenge to the success of single-molecule sequencing (SMS) technologies lies in the development of algorithms for assembling genomes from long but inaccurate reads. The pioneer in long reads technologies, Pacific Biosciences, now produces accurate assemblies from long error-prone reads (1, 2). Goodwin et al. (3) and Loman et al. (4) demonstrated that high-quality assemblies can be obtained from even less-accurate Oxford Nanopore reads. Advances in assembly of long errorprone reads recently resulted in the accurate reconstructions of various genomes (5-10). However, as illustrated in Booher et al. (11), the problem of assembling long error-prone reads is far from being resolved even in the case of relatively small bacterial genomes.Previous studies of SMS assemblies were based on the overlaplayout-consensus (OLC) approach (12) or a similar string graph approach (13), which require an all-against-all comparison of reads (14) and remain computationally challenging (see refs. 15-17 for a discussion of the pros and cons of this approach). Moreover, there is an assumption that the de Bruijn graph approach, which has dominated genome assembly for the last decade, is inapplicable to long reads. This is a misunderstanding, because the de Bruijn graph approach, as well as its variation called the A-Bruijn graph approach, was developed to assemble rather long Sanger reads (18). There is also a misunderstanding that the de Bruijn graph approach can only assemble highly accurate reads and fails when assembling long error-prone reads. Although this is true for the original de Bruijn graph approach to assembly (15-17), the A-Bruijn graph approach was originally designed to assemble inaccurate reads as long as any similarities between reads can be reliably identified. Moreover, A-Bruijn graphs have proven to be useful even for assembling mass spectra, which represent highly inaccurate fingerprints of amino acid sequences of peptides (19,20). However, although A-Bruijn graphs have proven to be useful in assembling Sanger reads and mass spectra, the question of how to apply A-Bruijn graphs for assembling long error-prone reads remains open.de Bruijn graphs are a key algorithmic technique in genome assembly (15,(21)(22)(23)(24). In addition, de Bruijn graphs have been used for sequencing by hybridization (...

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“…The genomic sequences are available for three strains of Xoo and one strain of Xoc (Lee et al, 2005;Ochiai et al, 2005;Lu et al, 2008;Salzberg et al, 2008). The full complement of TAL T3 effectors are now known for two strains of Xoo and one strain of Xoc, and both pathogens are unusual due to the high number of TAL effector genes within their individual genomes.…”

Section: Implication Of Interaction Between T3 Effectors and The Corrmentioning

confidence: 99%

“…A and MAFF311018 (also named T7174) have 19 and 17 genes, respectively, organized in nine and eight regions of their respective genomes (Ochiai et al, 2005;Salzberg et al, 2008;Fig. 5).…”

Section: Implication Of Interaction Between T3 Effectors and The Corrmentioning

confidence: 99%