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Announcement
12 December 2013

High-Quality Draft Genome Sequences of Xanthomonas axonopodis pv. glycines Strains CFBP 2526 and CFBP 7119

ABSTRACT

We report here the high-quality draft genome sequences of two strains of Xanthomonas axonopodis pv. glycines, the causal agent of bacterial pustule on soybeans. Comparison of these genomes with those of phylogenetically closely related pathovars of Xanthomonas spp. will help to understand the mechanisms involved in host specificity and adaptation to host plants.

GENOME ANNOUNCEMENT

The soybean (Glycine max) is an economically important crop legume for seed proteins and oil content (1), particularly in America and Asia (2). Xanthomonas axonopodis pv. glycines causes the bacterial pustule on soybeans. Typical symptoms are pale green spots with elevated pustules due to the hypertrophy of parenchyma cells (3). Expanding lesions become necrotic and cause premature defoliation. Symptoms may develop on pods, and the pathogen is transmitted via the seeds. The disease reduces yield and crop quality and occurs during warm and wet weather (4).
A single recessive locus, rxp, which carries resistance to bacterial pustules, has been identified (5) and is present in the resistant cultivar Williams 82, whose genome is sequenced (6). Several studies on the diversity of Xanthomonas axonopodis pv. glycines described at least 3 races (7, 8) according to the distribution of transcription activator-like (TAL) type III effectors, which are major pathogenicity factors of Xanthomonas axonopodis pv. glycines on soybeans (911). Several genes involved in various infection processes are controlled by two major regulators (12, 13). The genome of Xanthomonas axonopodis pv. glycines strain 12-2, isolated in Thailand, was recently published (12). We present the genomes of two Xanthomonas axonopodis pv. glycines strains, CFBP 2526 and CFBP 7119, isolated in Sudan and Brazil, respectively. These strains were included in several phylogenetic studies (1417). The strain CFBP 2526 is the pathotype strain of Xanthomonas axonopodis pv. glycines (18).
Both strains were sequenced using the Illumina HiSeq 2000 platform (GATC Biotech, Germany). Shotgun sequencing yielded 77,326,552 read pairs (75,568,393 100-bp paired-end reads with an insert size of 250 bp and 1,758,159 50-bp mate-pair reads with an insert size of 3 kb) and 59,188,498 read pairs (47,138,978 100-bp paired-end reads and 12,049,520 50-bp mate-pair reads) for strains CFBP 2526 and CFBP 7119, respectively. A combination of Velvet (19), SOAPdenovo, and SOAP Gapcloser (20) yielded 25 contigs >500 bp (N50, 423,865 bp), with the largest contig being 1,231,354 bp, for a total assembly size of 5,250,836 bp for strain CFBP 2526, and 16 contigs >500 bp (N50, 1,218,836 bp), with the largest contig being 2,302,514 bp, for a total assembly size of 5,518,822 bp for strain CFBP 7119.
Both strains are fully equipped to sense and move in their environment, to protect themselves, and to acquire nutrients. The main secretion systems described in Gram-negative bacteria were present, including the type III secretion system, a major pathogenicity determinant that delivers effectors (T3Es) directly into the plant cell. At least 20 T3E genes were present in each genome. Partial tal sequences, which were not assembled due to their highly conserved and repeated structures, were also found. Further studies will confirm if these tal sequences correspond to functional genes. Most of the observed differences between the genomes correspond to plasmid sequences and to several clusters mainly featuring phage-related genes.

Nucleotide sequence accession numbers.

These whole-genome shotgun projects have been deposited in GenBank under accession no. AUWO00000000 for strain CFBP 2526 and AUWM00000000 for strain CFBP 7119. The versions described in this paper are the first versions, AUWO01000000 and AUWM01000000, for CFBP 2526 and CFBP 7119, respectively.

ACKNOWLEDGMENTS

This work was supported by the French Agence Nationale de la Recherche (no. ANR-2010-GENM-013) and the LABEX TULIP (no. ANR-10-LABX-41).

REFERENCES

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Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 1Number 626 December 2013
eLocator: 10.1128/genomea.01036-13

History

Received: 2 November 2013
Accepted: 11 November 2013
Published online: 12 December 2013

Contributors

Authors

A. Darrasse
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
S. Bolot
INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, France
L. Serres-Giardi
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
E. Charbit
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
T. Boureau
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
M. Fisher-Le Saux
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
M. Briand
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
M. Arlat
INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, France
Université de Toulouse, Université Paul Sabatier, Toulouse, France
L. Gagnevin
UMR “Peuplements Végétaux et Bioagresseurs en Milieu Tropical” (PVBMT), CIRAD, Saint-Pierre, La Réunion, France
R. Koebnik
UMR 186 IRD-Cirad-Université Montpellier 2 “Résistance des Plantes aux Bioaggresseurs,” Montpellier, France
L. D. Noël
INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, France
S. Carrère
INRA, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 441, Castanet-Tolosan, France
CNRS, Laboratoire des Interactions Plantes Micro-Organismes (LIPM), UMR 2594, Castanet-Tolosan, France
M. A. Jacques
INRA, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Université d'Angers, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France
Agrocampus Ouest, Institut de Recherche en Horticulture et Semences (IRHS), UMR 1345 SFR 4207 QUASAV, Beaucouzé, France

Notes

Address correspondence to M. A. Jacques, [email protected].
A.D. and S.B. contributed equally to this study.

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