title: Plastome organization and evolution of chloroplast genes in Cardamine species adapted to contrasting habitats.
abstract: BACKGROUND
  Plastid genomes, also known as plastomes, are shaped by the selective forces acting on the fundamental cellular functions they code for and thus they are expected to preserve signatures of the adaptive path undertaken by different plant species during evolution. To identify molecular signatures of positive selection associated to adaptation to contrasting ecological niches, we sequenced with Solexa technology the plastomes of two congeneric Brassicaceae species with different habitat preference, Cardamine resedifolia and Cardamine impatiens.
  
  
  RESULTS
  Following in-depth characterization of plastome organization, repeat patterns and gene space, the comparison of the newly sequenced plastomes between each other and with 15 fully sequenced Brassicaceae plastomes publically available in GenBank uncovered dynamic variation of the IR boundaries in the Cardamine lineage. We further detected signatures of positive selection in ten of the 75 protein-coding genes of the examined plastomes, identifying a range of chloroplast functions putatively involved in adaptive processes within the family. For instance, the three residues found to be under positive selection in RUBISCO could possibly be involved in the modulation of RUBISCO aggregation/activation and enzymatic specificty in Brassicaceae. In addition, our results points to differential evolutionary rates in Cardamine plastomes.
  
  
  CONCLUSIONS
  Overall our results support the existence of wider signatures of positive selection in the plastome of C. resedifolia, possibly as a consequence of adaptation to high altitude environments. We further provide a first characterization of the selective patterns shaping the Brassicaceae plastomes, which could help elucidate the driving forces underlying adaptation and evolution in this important plant family.
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. shilang.hu@fmach.it.
authors.forename: Shiliang
authors.initials: S
authors.lastname: Hu
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. gaurav.sablok@fmach.it.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Sablok
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. bo.wang@fmach.it.
authors.forename: Bo
authors.initials: B
authors.lastname: Wang
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. qudong@gmail.com.|College of Horticulture, Northwest Agricultural and Forest University, 712100, Yangling, Shaanxi, PR China. qudong@gmail.com.
authors.forename: Dong
authors.initials: D
authors.lastname: Qu
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. enrico.barbaro@fmach.it.
authors.forename: Enrico
authors.initials: E
authors.lastname: Barbaro
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. roberto.viola@fmach.it.
authors.forename: Roberto
authors.initials: R
authors.lastname: Viola
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. mingai.li@fmach.it.
authors.forename: Mingai
authors.initials: M
authors.lastname: Li
authors.affiliation: Ecogenomics Laboratory, Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 S, Michele all'Adige (TN), Italy. claudio.varotto@fmach.it.
authors.forename: Claudio
authors.initials: C
authors.lastname: Varotto
mesh_terms: D000220:Adaptation, Biological; D031217:Cardamine / Q000145:classification / Q000166:cytology / Q000235:genetics / Q000502:physiology*; D002736:Chloroplasts / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D054628:Genome, Chloroplast; D008969:Molecular Sequence Data; D010802:Phylogeny; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity