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

Martin Guillaume, Rousseau-Gueutin Mathieu, Cordonnier Solenn, Lima Oscar, Michon-Coudouel Sophie, Naquin Delphine, de Carvalho Julie Ferreira, Ainouche Malika Lily, Salmon Armel, Ainouche Abdelkader. 2014. 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. Annals of Botany, 113 (7) : 1197-1210.

https://doi.org/10.1093/aob/mcu050

Article de revue ; Article de revue à facteur d'impact

Prévisualisation

Version Online first - Anglais
Utilisation soumise à autorisation de l'auteur ou du Cirad.
Lupinus luteus chloroplast_2014.pdf
Télécharger (758kB) | Prévisualisation

Prévisualisation

Version publiée - Anglais
Utilisation soumise à autorisation de l'auteur ou du Cirad.
580078.pdf
Télécharger (723kB) | Prévisualisation

Quartile : Q1, Sujet : PLANT SCIENCES

Résumé : 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 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. Key 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.

Mots-clés Agrovoc : Lupinus luteus, Fabaceae, génome, transfert de gène, chloroplaste, séquence nucléotidique, acide aminé, phylogénie

Mots-clés géographiques Agrovoc : Algérie

Mots-clés libres : 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