Annals of Botany 113: 1197–1210, 2014 doi:10.1093/aob/mcu050, available online at www.aob.oxfordjournals.org The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family Guillaume E. Martin1,†‡, Mathieu Rousseau-Gueutin1,†, Solenn Cordonnier1, Oscar Lima1, Sophie Michon-Coudouel2, Delphine Naquin1,§, Julie Ferreira de Carvalho1, Malika Aı¨nouche1, Armel Salmon1 and Abdelkader Aı¨nouche1,* 1UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l’Univers de Rennes), Universite´ de Rennes 1/Universite´ Europe´enne de Bretagne, 35 042 Rennes, France and 2Plate-forme Ge´nomique Environnementale et Fonctionnelle, OSUR-CNRS, Universite´ de Rennes 1, 35042 Rennes, France †These two authors contributed equally to this work Downloaded from ‡Present address: CIRAD (Centre de coope´ration Internationale en Recherche Agronomique pour le De´veloppement), UMR AGAP, F-34398 Montpellier, France §Present address: Plate-forme IMAGIF, FRC3115 CNRS, 91198 Gif sur Yvette Cedex, France * For correspondence. E-mail
[email protected] Received: 10 December 2013 Returned for revision: 3 February 2014 Accepted: 26 February 2014 Published electronically: 25 April 2014 http://aob.oxfordjournals.org/ † Background and Aims To date chloroplast genomes are available only for members of the non-protein amino acid- accumulating clade (NPAAA) Papilionoid lineages in the legume family (i.e. Millettioids, Robinoids and the ‘inverted repeat-lacking clade’, IRLC). It is thus very important to sequence plastomes from other lineages in order to better understand the unusual evolution observed in this model flowering plant family. To this end, the plas- tome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group.