The evolutionary fate of the chloroplast and nuclear rps16 genes as revealed through the sequencing and comparative analyses of four novel legume chloroplast genomes from Lupinus.
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins. To study the evolutionary fate of the rps16 gene, we explored all available plant chloroplast, mitochondrial and nuclear genomes. Whereas no plant mitochondrial genomes carry an rps16 gene, many plants still have a functional nuclear and chloroplast rps16 gene. Ka/Ks ratios revealed that both chloroplast and nuclear rps16 copies were under purifying selection. However, due to the dual targeting of the nuclear rps16 gene product and the absence of a mitochondrial copy, the chloroplast gene may be lost. We also performed comparative analyses of lupine plastomes (SNPs, indels and repeat elements), identified the most variable regions and examined their phylogenetic utility. The markers identified here will help to reveal the evolutionary history of lupines, Genistoids and closely related clades.
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
J
J
Keller
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.|IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France.
M
M
Rousseau-Gueutin
CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, F-34398 Montpellier, France.
G E
GE
Martin
IGEPP, INRA, Agrocampus Ouest, Université de Rennes 1, BP35327, 35653 Le Rheu Cedex, France.
J
J
Morice
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
J
J
Boutte
Laboratoire d'Ecologie Alpine, CNRS - Université de Grenoble 1 - Université de Savoie, 38041 Grenoble, France.
E
E
Coissac
Département des Sciences Biologiques, Faculté des Sciences de la Nature et de la Vie, Université Abderrahmane Mira, 06000 Bejaia, Algeria.
M
M
Ourari
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
M
M
Aïnouche
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
A
A
Salmon
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
F
F
Cabello-Hurtado
UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), Université de Rennes 1, 35042 Rennes, France.
A
A
Aïnouche
D002467:Cell Nucleus / Q000235:genetics; D018744:DNA, Plant; D019143:Evolution, Molecular; D017343:Genes, Plant; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D054643:INDEL Mutation; D031297:Lupinus / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA
D018744:DNA, Plant
Lupinus; chloroplast genomes; functional gene relocation; phylogeny; repeated sequences