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.
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.
Authors: Alan M Magee; Sue Aspinall; Danny W Rice; Brian P Cusack; Marie Sémon; Antoinette S Perry; Sasa Stefanović; Dan Milbourne; Susanne Barth; Jeffrey D Palmer; John C Gray; Tony A Kavanagh; Kenneth H Wolfe Journal: Genome Res Date: 2010-10-26 Impact factor: 9.043
Authors: Stephen H Kazakoff; Michael Imelfort; David Edwards; Jasper Koehorst; Bandana Biswas; Jacqueline Batley; Paul T Scott; Peter M Gresshoff Journal: PLoS One Date: 2012-12-14 Impact factor: 3.240
Authors: Linda A Raubeson; Rhiannon Peery; Timothy W Chumley; Chris Dziubek; H Matthew Fourcade; Jeffrey L Boore; Robert K Jansen Journal: BMC Genomics Date: 2007-06-15 Impact factor: 3.969
Authors: Sue Sherman-Broyles; Aureliano Bombarely; Jane Grimwood; Jeremy Schmutz; Jeff Doyle Journal: G3 (Bethesda) Date: 2014-08-25 Impact factor: 3.154
Authors: Pasquale L Curci; Domenico De Paola; Donatella Danzi; Giovanni G Vendramin; Gabriella Sonnante Journal: PLoS One Date: 2015-03-16 Impact factor: 3.240
Authors: Diana V Dugas; David Hernandez; Erik J M Koenen; Erika Schwarz; Shannon Straub; Colin E Hughes; Robert K Jansen; Madhugiri Nageswara-Rao; Martijn Staats; Joshua T Trujillo; Nahid H Hajrah; Njud S Alharbi; Abdulrahman L Al-Malki; Jamal S M Sabir; C Donovan Bailey Journal: Sci Rep Date: 2015-11-23 Impact factor: 4.379