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Announcement
29 August 2013

Draft Genome Sequence of the Xanthomonas cassavae Type Strain CFBP 4642

ABSTRACT

We report the draft genome sequence of the Xanthomonas cassavae type strain CFBP 4642, the causal agent of bacterial necrosis on cassava plants. These data will allow the comparison of this nonvascular pathogen with the vascular pathogen Xanthomonas axonopodis pv. manihotis, both infecting the same host, which will facilitate the development of diagnostic tools.

GENOME ANNOUNCEMENT

Cassava (Manihot esculenta Crantz) is the third most important source of calories in the tropics, after rice and maize, and millions of people in Africa, Asia, and Latin America depend on cassava. South America, probably the Amazon region, is considered the center of origin for the cassava species. It was only in the 16th century that Portuguese navigators introduced cassava to the west coast of Africa, from where it later disseminated to East Africa. Most of the spread within the African continent, however, took place only during the 20th century due to colonial powers encouraging its cultivation (1). Nowadays, cassava is grown in all Sub-Saharan countries, and Africa produces more cassava than the rest of the world combined (1). Cassava plants are frugal with respect to environmental conditions (drought, poor soil) and hold great promise as a future staple crop in Africa, since this species might not only tolerate but even profit from climate change (2).
Cassava plants can suffer from two bacterial diseases, bacterial blight and bacterial necrosis, caused by two species of Xanthomonas. The causal agent of bacterial blight, X. axonopodis pv. manihotis, is a vascular pathogen which has been well studied over the last years (3). Recently, draft genome sequences of 65 strains have been elucidated (4). Much less is known about the nonvascular pathogen X. cassavae, which causes bacterial necrosis in Africa (5). The comparison of a vascular and a nonvascular pathogen, both infecting cassava, might give important clues about determinants of tissue specificity during colonization of the host plant. This prompted us to sequence the X. cassavae type strain CFBP 4642 (NCPPB 101, ICMP 204, LMG 673), which was isolated in Malawi in 1951.
Type strain CFBP 4642 was sequenced using the Illumina Hi-Seq2000 platform (GATC Biotech, Germany). The shotgun sequencing yielded 95,437,238 read pairs (64,851,255 100-bp paired-end reads with an insert size of 250 bp and 30,585,983 50-bp mate-pair reads with an insert size of 3 kb). A combination of Velvet (6), SOAPdenovo, and SOAPGapCloser (7) yielded 83 contigs larger than 500 bp (N50, 158,383 bp) with the largest contig of 425 kb for a total assembly size of 5,263,056 bp.
Multilocus sequence analysis of four housekeeping genes described earlier for xanthomonads (8) revealed that the four internal fragments are 99.94% identical (3,371/3,373) to those of the X. cassavae type strain ICMP 204 at PAMDB (9). The genome encodes a canonical type III protein secretion system (10) and several type III effectors, such as transcriptional activator-like (TAL) effectors (5). Interestingly, a CRISPR/cas defense system is present, which might be exploited to develop a powerful tool for Pan-African epidemiological surveillance (11).

Nucleotide sequence accession number.

This whole-genome shotgun project has been deposited in GenBank under the accession no. ATMC00000000.

ACKNOWLEDGMENTS

This work was supported by grant ANR-2010-GENM-013 from the French Agence Nationale de la Recherche.
Strain CFBP 4642 is available at the CIRM-CFBP, French Collection for Plant-associated Bacteria, http://www.angers-nantes.inra.fr/cfbp.

REFERENCES

1.
Hillocks RJ. 2002. Cassava in Africa, p 41–54. In Hillocks RJ, Thresh JM, and Bellotti AC (ed), Cassava: biology, production and utilization. CAB International, Wallingford, Oxfordshire, United Kingdom.
2.
Jarvis A, Ramirez-Villegas J, Herrera Campo BV, and Navarro-Racines C. 2012. Is cassava the answer to African climate change adaptation? Trop. Plants Biol. 5:9–29.
3.
López CE and Bernal AJ. 2012. Cassava bacterial blight: using genomics for the elucidation and management of an old problem. Trop. Plants Biol. 5:117–126.
4.
Bart R, Cohn M, Kassen A, McCallum EJ, Shybut M, Petriello A, Krasileva K, Dahlbeck D, Medina C, Alicai T, Kumar L, Moreira LM, Rodrigues Neto J, Verdier V, Santana MA, Kositcharoenkul N, Vanderschuren H, Gruissem W, Bernal A, and Staskawicz BJ. 2012. High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. Proc. Natl. Acad. Sci. U. S. A. 109:E1972–E1979.
5.
Verdier V, Boher B, Maraite H, and Geiger JP. 1994. Pathological and molecular characterization of Xanthomonas campestris strains causing diseases of cassava (Manihot esculenta). Appl. Environ. Microbiol. 60:4478–4486.
6.
Zerbino DR and Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829.
7.
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.
8.
Young JM, Park DC, Shearman HM, and Fargier E. 2008. A multilocus sequence analysis of the genus Xanthomonas. Syst. Appl. Microbiol. 31:366–377.
9.
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.
10.
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.
11.
Horvath P and Barrangou R. 2010. CRISPR/Cas, the immune system of bacteria and archaea. Science 327:167–170.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 1Number 429 August 2013
eLocator: 10.1128/genomea.00679-13

History

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

Contributors

Authors

Stéphanie Bolot
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, LIPM, UMR 2594, Castanet-Tolosan, France
Alejandra Munoz Bodnar
UMR 186 IRD-Cirad-Université Montpellier 2 Résistance des Plantes aux Bioaggresseurs, Montpellier, France
Sébastien Cunnac
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), UMR 441, Castanet-Tolosan, France
CNRS, LIPM, UMR 2594, Castanet-Tolosan, France
Matthieu Arlat
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, LIPM, UMR 2594, Castanet-Tolosan, France
Université de Toulouse, Université Paul Sabatier, Toulouse, France
Marie-Agnès Jacques
INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L'UNAM, Angers, France
Lionel Gagnevin
UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), CIRAD, Saint-Pierre, La Réunion, France
Perrine Portier
INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L'UNAM, Angers, France
INRA, CIRM-CFBP Collection Française de Bactéries associées aux Plantes, Angers, France
Marion Fischer-Le Saux
INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France
Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, PRES L'UNAM, Angers, France
INRA, CIRM-CFBP Collection Française de Bactéries associées aux Plantes, Angers, France
Sébastien Carrere
INRA, Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, LIPM, UMR 2594, Castanet-Tolosan, 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].
S.B. and A.M.B. contributed equally to this study.

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