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

Keller J., Rousseau-Gueutin Mathieu, Martin Guillaume, Morice Jérôme, Boutte Julien, Coissac E., Ourari M., Ainouche Malika Lily, Salmon Armel, Cabello-Hurtado F., Ainouche Abdelkader. 2017. 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. DNA Research, 24 (4) : 343-358.

Quartile : Q1, Sujet : GENETICS & HEREDITY

Résumé : 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.

Mots-clés Agrovoc : phylogénie, chloroplaste, génome, séquence nucléotidique, évolution, Fabaceae, Oryza sativa, Musa paradisiaca

Classification Agris : F30 - Génétique et amélioration des plantes
F70 - Taxonomie végétale et phytogéographie

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

• Keller J., CNRS (FRA)
• Rousseau-Gueutin Mathieu, Université de Rennes I (FRA)
• Martin Guillaume, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-1801-7500
• Morice Jérôme, Université de Rennes I (FRA)
• Boutte Julien, Université de Rennes I (FRA)
• Coissac E., CNRS (FRA)
• Ourari M., Université Abderrahmane Mira (DZA)
• Ainouche Malika Lily, Université de Rennes I (FRA)
• Salmon Armel, Université de Rennes I (FRA)
• Cabello-Hurtado F., CNRS (FRA)
• Ainouche Abdelkader, Université de Rennes I (FRA)

Source : Cirad-Agritrop (https://agritrop.cirad.fr/583759/)

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