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.
OBJECTIVE
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 plastome of a lupine species, Lupinus luteus, was sequenced to represent the Genistoid lineage, a noteworthy but poorly studied legume group.


METHODS
The plastome of L. luteus was reconstructed using Roche-454 and Illumina next-generation sequencing. Its structure, repetitive sequences, gene content and sequence divergence were compared with those of other Fabaceae plastomes. PCR screening and sequencing were performed in other allied legumes in order to determine the origin of a large inversion identified in L. luteus.


RESULTS
The first sequenced Genistoid plastome (L. luteus: 155 894 bp) resulted in the discovery of a 36-kb inversion, embedded within the already known 50-kb inversion in the large single-copy (LSC) region of the Papilionoideae. This inversion occurs at the base or soon after the Genistoid emergence, and most probably resulted from a flip-flop recombination between identical 29-bp inverted repeats within two trnS genes. Comparative analyses of the chloroplast gene content of L. luteus vs. Fabaceae and extra-Fabales plastomes revealed the loss of the plastid rpl22 gene, and its functional relocation to the nucleus was verified using lupine transcriptomic data. An investigation into the evolutionary rate of coding and non-coding sequences among legume plastomes resulted in the identification of remarkably variable regions.


CONCLUSIONS
This study resulted in the discovery of a novel, major 36-kb inversion, specific to the Genistoids. Chloroplast mutational hotspots were also identified, which contain novel and potentially informative regions for molecular evolutionary studies at various taxonomic levels in the legumes. Taken together, the results provide new insights into the evolutionary landscape of the legume plastome.
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Guillaume E
GE
Martin
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Mathieu
M
Rousseau-Gueutin
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Solenn
S
Cordonnier
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Oscar
O
Lima
Plate-forme Génomique Environnementale et Fonctionnelle, OSUR-CNRS, Université de Rennes 1, 35042 Rennes, France.
Sophie
S
Michon-Coudouel
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Delphine
D
Naquin
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Julie Ferreira
JF
de Carvalho
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Malika
M
Aïnouche
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France.
Armel
A
Salmon
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1/Université Européenne de Bretagne, 35 042 Rennes, France kader.ainouche@univ-rennes1.fr.
Abdelkader
A
Aïnouche
D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D031297:Lupinus / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
36-kb inversion; European yellow lupine; Fabaceae phylogeny; Genistoid clade; Lupinus luteus; Papilionoidae; chloroplast genome evolution; flip–flop recombination; functional gene transfer; inverted repeats; legume; lineage-specific marker; plastome hotspots; repeated plastid sequences; sequence divergence; structural plastid rearrangement