A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes

Clémence Chaintreuil (1) , Ronan Rivallan (2) , David Bertioli , Christophe C. Klopp (3) , Jerome Gouzy (4) , Brigitte Courtois (2) , Philippe Leleux (5) , Jean-Francois Rami (2) , Djamel Gully (1) , Hugues Parrinello (6, 7) , Dany Severac (7) , Delphine Patrel (1) , Joël Fardoux (1) , William Ribière , Marc Boursot , Fabienne Cartieaux (1) , Pierre Czernic (1) , Pascal Ratet (8) , Pierre Mournet (9) , Eric Giraud (10) , Jean-François Arrighi (1) , Guillaume Martin

1 UMR LSTM - Laboratoire des symbioses tropicales et méditerranéennes
2 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
3 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)
4 LIPM - Laboratoire des interactions plantes micro-organismes
5 IBC - Institut de Biologie Computationnelle
6 BCM - BioCampus
7 IGF MGX - Institut de Génomique Fonctionnelle - Montpellier GenomiX
8 ISV - Institut des sciences du végétal
9 UMR DAP - Développement et amélioration des plantes
10 CRRM - Centre de recherche rétrospective de Marseille

Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far fo-cused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F 2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n ¼ 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a Downloaded from https://academic.oup.com/dnaresearch/article-abstract/23/4/365/2469965 by BIU Montpellier user on 12 March 2020 basis for a genome sequencing project and pave the way for forward genetic analysis of symbio-sis in A. evenia.

Keywords: symbiosis; Aeschynomene evenia; legume; comparative genomics; genetic map

Domains: Life Sciences [q-bio]; Life Sciences [q-bio]; Vegetal Biology

Clémence Chaintreuil, Ronan Rivallan, David Bertioli, Christophe C. Klopp, Jerome Gouzy, et al.. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes. DNA Research, 2016, 23 (4), pp.365-376. ⟨10.1093/dnares/dsw020⟩. ⟨hal-02410329⟩