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Announcement
29 August 2013

High-Quality Draft Genome Sequences of Two Xanthomonas citri pv. malvacearum Strains

ABSTRACT

We report high-quality draft genome sequences of two strains (race 18 and 20) of Xanthomonas citri pv. malvacearum, the causal agent of bacterial blight of cotton. Comparative genomics will help to decipher mechanisms provoking disease and triggering defense responses and to develop new molecular tools for epidemiological surveillance.

GENOME ANNOUNCEMENT

Xanthomonas citri pv. malvacearum is the causal agent of bacterial blight (BB), one of the most devastating diseases of cotton (Gossypium spp.). BB of cotton was first reported in the United States by Atkinson, who described several symptoms, such as angular leaf spots, water-soaked lesions, stem black arm, boll rot, and plantlet burning (1). In the second half of the 20th century, BB became a limiting factor of fiber production in all major cotton-producing regions of Africa, Asia, Australia, and North America (2). The use of resistant cultivars is usually the most efficient way to manage disease. However, resistance was repeatedly overcome by the appearance of new races. More than 20 races have been described, including highly virulent strains that were isolated in Central Africa in the 1980s (2). To better understand the molecular basis of provoking disease and of triggering defense responses and to develop new molecular markers for epidemiological surveillance, we sequenced the genomes of two strains originating from Burkina Faso and belonging to the highly virulent race 20 and the less virulent race 18 (3).
Both strains were sequenced using the Illumina Hi-Seq2000 platform (GATC Biotech, Germany). The shotgun sequencing yielded 40,654,599 read pairs (29,066,551 100-bp paired-end reads with an insert size of 250 bp and 11,588,048 50-bp mate-pair reads with an insert size of 3 kb) and 43,359,649 read pairs (19,340,592 100-bp paired-end reads and 24,019,057 50-bp mate-pair reads) for strains X18 and X20, respectively. A combination of Velvet (4), SOAPdenovo, and SOAPGapCloser (5) yielded 22 contigs larger than 500 bp (N50, 705,301 bp), with the largest contig of 2,062 kb, for a total assembly size of 4,989,917 bp for strain X18 and 17 contigs larger than 500 bp (N50, 1,006,603 bp), with the largest scaffold of 1,770 kb, for a total assembly size of 5,216,199 bp for strain X20.
Multilocus sequence analyses of six housekeeping genes described earlier for xanthomonads confirmed that strains X18 and X20 belong to X. citri pv. malvacearum (2,745 bp with 100% identity) (6), corresponding to DNA-DNA homology group 9.5, which also includes X. citri pv. citri (2,730 identical residues) and X. citri pv. glycines (2,729 identical residues) (7). The genome encodes a canonical type III protein secretion system (8) and several type III effectors, including transcriptional activator-like (TAL) effectors, which are responsible for symptom formation and avirulence reactions on cotton (9). The availability of two genome sequences of X. citri pv. malvacearum will critically aid in developing new molecular typing tools for epidemiological surveillance and guiding breeding programs based on rapid and accurate identification of predominant lineages.

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited in GenBank under the accession numbers ATMA00000000 for strain X18 and ATMB00000000 for strain X20.

ACKNOWLEDGMENT

This work was supported by grant ANR-2010-GENM-013 from the French Agence Nationale de la Recherche.

REFERENCES

1.
Atkinson GF. 1891. The black rust of cotton. Ala. Agric. Exp. Stn. Bull. 27:1–16.
2.
Delannoy E, Lyon BR, Marmey P, Jalloul A, Daniel JF, Montillet JL, Essenberg M, and Nicole M. 2005. Resistance of cotton towards Xanthomonas campestris pv. malvacearum. Annu. Rev. Phytopathol. 43:63–82.
3.
Martinez C, Baccou JC, Bresson E, Baissac Y, Daniel JF, Jalloul A, Montillet JL, Geiger JP, Assigbetsé K, and Nicole M. 2000. Salicylic acid mediated by the oxidative burst is a key molecule in local and systemic responses of cotton challenged by an avirulent race of Xanthomonas campestris pv. malvacearum. Plant Physiol. 122:757–766.
4.
Zerbino DR and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829.
5.
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu SM, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam TW, and Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18.
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Almeida NF, Yan S, Cai R, Clarke CR, Morris CE, Schaad NW, Schuenzel EL, Lacy GH, Sun X, Jones JB, Castillo JA, Bull CT, Leman S, Guttman DS, Setubal JC, and Vinatzer BA. 2010. PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100:208–215.
7.
Rademaker JL, Louws FJ, Schultz MH, Rossbach U, Vauterin L, Swings J, and de Bruijn FJ. 2005. A comprehensive species to strain taxonomic framework for Xanthomonas. Phytopathology 95:1098–1111.
8.
Büttner D. 2012. Protein export according to schedule: architecture, assembly, and regulation of type III secretion systems from plant- and animal-pathogenic bacteria. Microbiol. Mol. Biol. Rev. 76:262–310.
9.
Yang Y, De Feyter R, and Gabriel DW. 1994. Host-specific symptoms and increased release of Xanthomonas citri and X. campestris pv. malvacearum from leaves are determined by the 102-bp tandem repeats of pthA and avrb6, respectively. Mol. Plant Microbe Interact. 7:345–355.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 1Number 429 August 2013
eLocator: 10.1128/genomea.00674-13

History

Received: 30 July 2013
Accepted: 31 July 2013
Published online: 29 August 2013

Contributors

Authors

Sébastien Cunnac
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
Stéphanie Bolot
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
Natalia Forero Serna
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
Erika Ortiz
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
Boris Szurek
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
Laurent D. Noël
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
Matthieu Arlat
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
Université de Toulouse, Université Paul Sabatier, Toulouse, France
Marie-Agnès Jacques
INRA, Institut de Recherche en Horticulture et Semences (IRHS), Beaucouzé, France
Lionel Gagnevin
UMR “Peuplements Végétaux et Bioagresseurs en Milieu Tropical” (PVBMT), La Réunion, France
Sébastien Carrere
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-organismes (LIPM), Castanet-Tolosan, France
Michel Nicole
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
Ralf Koebnik
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France

Notes

Address correspondence to Ralf Koebnik, [email protected].
Sébastien Cunnac and Stéphanie Bolot contributed equally to this study.

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