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• Wisniewski-Dyé, F
• Lozano, L
• Acosta-Cruz, E
• Borland, S
• Drogue, B
• Prigent-Combaret, C
• Rouy, Z
• Barbe, V
• Herrera, A
• González, V
• Mavingui, P
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• Wisniewski-Dyé, F
• Lozano, L
• Acosta-Cruz, E
• Borland, S
• Drogue, B
• Prigent-Combaret, C
• Rouy, Z
• Barbe, V
• Herrera, A
• González, V
• Mavingui, P
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• Wisniewski-Dyé, F
• Lozano, L
• Acosta-Cruz, E
• Borland, S
• Drogue, B
• Prigent-Combaret, C
• Rouy, Z
• Barbe, V
• Herrera, A
• González, V
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Genes 2012, 3(4), 576-602; doi:10.3390/genes3040576

Article

Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation

Florence Wisniewski-Dyé ^1,* , Luis Lozano ² , Erika Acosta-Cruz ¹ , Stéphanie Borland ¹ , Benoît Drogue ¹ , Claire Prigent-Combaret ¹ , Zoé Rouy ^3,4 , Valérie Barbe ⁴ , Alberto Mendoza Herrera ⁵ , Victor González ²  and Patrick Mavingui ¹

¹ Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France ² Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México ³ Laboratoire d’Analyse Bioinformatique en Génomique et Métabolisme CNRS UMR8030, France ⁴ Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France ⁵ Centro de Biotecnología Genómica, Instituto politécnico Nacional, 88710 Reynosa, Tamaulipas, México

* Author to whom correspondence should be addressed.

Received: 14 May 2012; in revised form: 24 August 2012 / Accepted: 13 September 2012 / Published: 28 September 2012

(This article belongs to the Special Issue Bacterial Genomes and Their Evolution)

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Abstract: Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.

Keywords: Azospirillum; core genome; chromid; horizontal gene transfer; orthologous groups; rhizosphere

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