Since the first reports of the complete nucleotide sequences of the tobacco  and liverwort  chloroplast (cp) genomes, a number of other land plant cp genomic sequences have been determined. These complete cp genomic sequences have enabled various comparative analyses, including phylogenetic studies, that are based on these data [3–7]. In contrast, however, the complete cp genome nucleotide sequences of only three gymnosperm species, Cycas taitungensis , Pinus thunbergii , and Pinus koraiensis  have been determined.
The cp genomes of gymnosperms, especially in coniferous species, have distinctive features compared with those of angiosperms, including paternal inheritance [11–17], relatively high levels of intra-specific variation [18–21], and a different pattern of RNA editing . Generally, the cp genomes of angiosperms range in size from 130 to 160 kb, and contain two identical inverted repeats (IRs) that divide the genomes into large (LSC) and small single copy (SSC) regions. The relative sizes of these LSC, SSC and IRs remain constant, with both gene content and gene order being highly conserved [23, 24]. On the other hand, the relative sizes of the gymnosperm IRs vary significantly among taxa [25–27]; for example, the IRs of Ginkgo biloba are 17 kbp , those of Cycas taitungensis are 23 kbp , whereas those of Pinus thunbergii are very short, at just 495 bp [9, 29]. It has been suggested that, like P. thunbergii, some coniferous species also lack the large IRs that exist in other gymnosperms [25, 26, 30, 31]. This lack of IRs is considered to have preceded the extensive genomic rearrangements of the conifer cp genome . Steane  compared the complete cp genome of Eucalyptus globulus with that of other angiosperm taxa and P. thunbergii, and found that the cp genome of P. thunbergii was arranged very differently to that of angiosperms. However, there is only limited information available about the cp genomic sequences of coniferous species, with the complete cp genome nucleotide sequences of only two species of pine, Pinus thunbergii  and Pinus koraiensis  in the family Pinaceae, having been determined. The cp genomes of these two pine species were very similar in terms of both gene content and gene order and so provided little information about the complexity of the conifer cp genome.
In previous phylogenetic studies, of the four extant gymnosperm groups (Cycads, Conifers, Ginkgoales, and Gnetales), the conifers were considered to be divisible into two distinct groups; a Pinaceae group and a group consisting of five other families (Cupressaceae sensu lato, Taxaceae, Podocarpaceae, Araucariaceae, and Sciadopityaceae) [33, 34]. The cp nucleotide sequences from this five member group, excluding the Pinaceae group, can provide interesting information about the conifer cp genome, not only in terms of genome structure but also concerning their evolutionary history. Despite the lack of complete cp genome sequences from any family member of the Cupressaceae sensu lato, Tsumura et al.  suggested, on the basis of physical maps and Southern hybridization analyses, that the cp genome of Cryptomeria japonica differs from that of other land plants, including pine species, in terms of genome size and gene order as well as in the absence of the large IRs. Thus, the complete cp genome sequence of C. japonica would drastically increase our understanding of the divergence of coniferous cp genome structures and gene content, and additionally clearly identify the differences with the Pinaceae group.
There are two particular questions that need to be addressed using the complete cp genome sequence of C. japonica: (1) how different is the C. japonica cp genome from those of other plants, including gymnosperms, and (2) is the loss of the large IRs involved with the instability and diversification of the cp genome, especially between coniferous groups? To respond to these questions, we present in this paper the complete nucleotide sequence of the cp genome of C. japonica [DDBJ: AP009377], and compare its overall gene content and genomic structure with those of two other angiosperms (Eucalyptus globulus and Oryza sativa), a liverwort (Marchantia polymorpha), a fern (Adiantum capillus), and two gymnosperms (Cycas taitungensis and Pinus thunbergii).