Nucleic Acids Research, 2008, Vol. 36, No. 7 2371 Figure 3. Overall distribution of sequence divergence and repeat content in the Oenothera plastid chromosomes. Percentage repeat content and divergence on the y-axis were calculated using sliding sequence intervals of 1 kb with a step size of 10 bp along a multiple chromosome alignment. Whole chromosome alignments have been deduced from concatenated multiple alignments of intergenic regions and genes (see ‘Materials and Methods’ section). Repetitive regions frequently overlap with areas of high divergence. Indels occur less often in genes and are present in only relatively few polypeptide genes, notably in accD, clpP, ndhD, ndhF, rps18, rpl22, ycf1 and ycf2. These changes in coding potential will be discussed separately (see later and Supplementary Figures 1–4 and Supplementary Tables 4 and 5). Overall distribution and types of repeats are highly similar between all ﬁve plastomes. On average 61 tandem repeats from 55 in plastome IV up to 70 in plastome I were detected, with a mean copy number of 4.5 copies per tandem and an average size of 41 bp per copy. The largest tandem repeat regions which span more than 1 kb and consist of variants of the AAG/TTC trinucleotide sequence are found in all plastomes at the two ycf2 genes in the IR. Expanded tandem repeats are also frequent and overlapping in accD and ycf1 contributing to the substantial sequence divergence of these genes. Rpl32, ndhF and the tandemly repeated trnfMCAUI and trnfMCAUII are associated with small identical tandem repeats in all ﬁve plastomes. More interesting are tandem repeats within coding regions, which are speciﬁc for particular plastomes, generally of moderate size and low copy number. Such repeats that change coding potential are found in clpP, ndhF and rps18 (Supplementary Figures 2 and 3). The plastome-speciﬁc repeat diﬀerences associated with ccsA, rpl22, rpl32, rps19 and trnSGCU are located outside the respective coding sequences. On average approximately 70 palindromic repeats with a maximal gap size of 3 kb or less were detected within the ﬁve plastome sequences. Palindrome sizes, however, are smaller and far less variable than tandem sizes, ranging from 32 bp (detection limit given by the threshold applied) up to 56 bp. They were detected in accD, ccsA, matK, ndhD, ndhF, ndhJ, petD, psaA, psaB, psbH, rpl32, rpoA, rpoB, rps18, ycf1, ycf2 and ycf4, but no notable changes in coding sequences are caused by palindrome repeats among the plastome types. Exceptions are the highly polymorphic genes accD and ycf2 as well as ndhD in which a palindromic repeat associated with a polyA-stretch shows a frame changing insertion of a single nucleotide (Supplementary Figure 2). Presence and absence of repetitive elements and divergent regions correlate well, but repeat content and high divergence are not strongly linked (Figure 3). The large inversion Except for the 56 kb inversion mentioned earlier, no other inversion has been detected in the ﬁve plastome sequences. The junctions of the inversion in the intergenic regions between trnQUUG/accD and rps16/rbcL are highly diver- gent and contain palindromes as well as tandem repeats (Figure 3). Overall the trnQUUG/accD spacer contains more tandem repeats (ﬁve to eight, depending on the plastome) than the rps16/rbcL spacer, with a maximum of