2366–2378 Nucleic Acids Research, 2008, Vol. 36, No. 7 doi:10.1093/nar/gkn081 Published online 24 February 2008 The complete nucleotide sequences of the five genetically distinct plastid genomes of Oenothera, subsection Oenothera: I. Sequence evaluation and plastome evolutiony Stephan Greiner1, Xi Wang1,2, Uwe Rauwolf1, Martina V. Silber1, Klaus Mayer2, J o¨rg Meurer1, Georg Haberer2 and Reinhold G. Herrmann1,* 1Department Biologie I, Bereich Botanik, Ludwig-Maximilians-Universita¨ t, Menzinger Strasse 67, 80 638 Munich and 2MIPS/IBI Institute for Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health GmbH, Ingolsta¨ dter Landstrasse 1, 85 764 Neuherberg, Germany Received November 30, 2007; Revised February 1, 2008; Accepted February 8, 2008 ABSTRACT The flowering plant genus Oenothera is uniquely suited for studying molecular mechanisms of speci- ation. It assembles an intriguing combination of genetic features, including permanent translocation heterozygosity, biparental transmission of plastids, and a general interfertility of well-defined species. This allows an exchange of plastids and nuclei between species often resulting in plastome– genome incompatibility. For evaluation of its molec- ular determinants we present the complete nucleotide sequences of the five basic, genetically distinguishable plastid chromosomes of subsection Oenothera (=Euoenothera) of the genus, which are associated in distinct combinations with six basic genomes. Sizes of the chromosomes range from 163 365 bp (plastome IV) to 165 728 bp (plastome I), display between 96.3% and 98.6% sequence simi- larity and encode a total of 113 unique genes. Plastome diversification is caused by an abundance of nucleotide substitutions, small insertions, dele- tions and repetitions. The five plastomes deviate from the general ancestral design of plastid chromosomes of vascular plants by a subsection- specific 56 kb inversion within the large single-copy segment. This inversion disrupted operon struc- tures and predates the divergence of the subsection presumably 1 My ago. Phylogenetic relationships suggest plastomes I–III in one clade, while plastome IV appears to be closest to the common ancestor. INTRODUCTION Plastid chromosomes have received considerable attention to examine phylogenetic relationships among plants as well as to probe into eukaryotic genome evolution. Their endosymbiotic ancestry, limited coding potential, rela- tively conserved organization and well-deﬁned structure provide a unique source of information to address a wide range of fundamental questions. At present, sequences of entire plastid chromosomes are available from more than 100, generally distantly related taxa including protist, thallophytic, bryophytic and vascular plants (www.ncbi.nlm.nih.gov). This information has clariﬁed overall evolutionary relationships for most groups of photoautotrophs as well as the outlines of the evolution of the eukaryotic cell with its compartmental- ized genome. It emerged that three basic processes shaped that evolution: (i) the restructuring of the genetic potentials of the symbiotic partners (1); this conversion occurred predominantly at the unicellular level (2); (ii) the generation of novel gene sets and genetic programs with the advent of multicellular organisms and (iii) a co- evolution of the cellular genetic compartments that together constitute an integrated genetic system (3,4). The impact of this latter process that operates in relatively short evolutionary time scales becomes apparent after interspeciﬁc organelle exchanges, which even between related species can frequently cause serious disturbances *To whom correspondence should be addressed. Tel: + 49 8917861271; Fax: +49 89171683; Email: r.herrmann@lrz.uni-muenchen.de yDedicated to the senior Oenothera geneticist Prof. Wilfried Stubbe. The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors 2008 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.