Comparative genomics of aeschynomene symbionts: insights into the ecological lifestyle of nod-independent photosynthetic bradyrhizobia.
Tropical aquatic species of the legume genus Aeschynomene are stem- and root-nodulated by bradyrhizobia strains that exhibit atypical features such as photosynthetic capacities or the use of a nod gene-dependent (ND) or a nod gene-independent (NI) pathway to enter into symbiosis with legumes. In this study we used a comparative genomics approach on nine Aeschynomene symbionts representative of their phylogenetic diversity. We produced draft genomes of bradyrhizobial strains representing different phenotypes: five NI photosynthetic strains (STM3809, ORS375, STM3847, STM4509 and STM4523) in addition to the previously sequenced ORS278 and BTAi1 genomes, one photosynthetic strain ORS285 hosting both ND and NI symbiotic systems, and one NI non-photosynthetic strain (STM3843). Comparative genomics allowed us to infer the core, pan and dispensable genomes of Aeschynomene bradyrhizobia, and to detect specific genes and their location in Genomic Islands (GI). Specific gene sets linked to photosynthetic and NI/ND abilities were identified, and are currently being studied in functional analyses.
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. dmornico@genoscope.cns.fr.
Damien
D
Mornico
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. lucie.miche@univ-provence.fr.
Lucie
L
Miché
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. gilles.bena@ird.fr.
Gilles
G
Béna
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. nico.nouwen@ird.fr.
Nico
N
Nouwen
Laboratoire de Bioénergétique Cellulaire, CEA Cadarache, DSV, IBEB, 13108 Saint Paul-lez-Durance, France. andre.vermeglio@cea.fr.
André
A
Verméglio
LABGeM, CEA-Genoscope & CNRS-UMR8030, 91057 Evry, France. vallenet@genoscope.cns.fr.
David
D
Vallenet
LABGeM, CEA-Genoscope & CNRS-UMR8030, 91057 Evry, France. asmith@genoscope.cns.fr.
Alexander A T
AA
Smith
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. eric.giraud@ird.fr.
Eric
E
Giraud
LABGeM, CEA-Genoscope & CNRS-UMR8030, 91057 Evry, France. cmedigue@genoscope.cns.fr.
Claudine
C
Médigue
IRD-LSTM, UMR113, Campus de Baillarguet, 34398 Montpellier cedex 5, France. lionel.moulin@ird.fr.
Lionel
L
Moulin