Open Access

Complete nucleotide sequence of the Cryptomeria japonicaD. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species

  • Tomonori Hirao1, 2,
  • Atsushi Watanabe2,
  • Manabu Kurita2,
  • Teiji Kondo2 and
  • Katsuhiko Takata1Email author
BMC Plant Biology20088:70

DOI: 10.1186/1471-2229-8-70

Received: 23 January 2008

Accepted: 23 June 2008

Published: 23 June 2008



The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms.


The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements.


The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.


Since the first reports of the complete nucleotide sequences of the tobacco [1] and liverwort [2] 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 [37]. In contrast, however, the complete cp genome nucleotide sequences of only three gymnosperm species, Cycas taitungensis [8], Pinus thunbergii [9], and Pinus koraiensis [10] have been determined.

The cp genomes of gymnosperms, especially in coniferous species, have distinctive features compared with those of angiosperms, including paternal inheritance [1117], relatively high levels of intra-specific variation [1821], and a different pattern of RNA editing [22]. 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 [2527]; for example, the IRs of Ginkgo biloba are 17 kbp [28], those of Cycas taitungensis are 23 kbp [8], 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 [26]. Steane [32] 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 [9] and Pinus koraiensis [10] 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. [27] 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).

Results and Discussion

General characteristics of the C. japonicacp genome

The total size of the C. japonica cp genome was determined to be 131,810 bp, which is larger than the cp genomes of both P. thunbergii (119,707 bp) and M. polymorpha (121,024 bp), but smaller than those of A. capillus (150,568 bp), E. globulus (160,286 bp), and C. taitungensis (163,403 bp), and approximately the same size as that of O. sativa (134,558 bp). This size is only slightly smaller than that previously estimated by RFLP southern hybridization analysis [27]. The large IR region, which is found in other land plants except Pinus, could also not be observed in the C. japonica cp genome, and so we were unable to define the large (LSC) and small (SSC) single copy regions in this genome. A total of 116 genes were identified in the C. japonica cp genome, of which 112 genes were single copy and two genes, trnI-CAU and trnQ-UUG, were duplicated and occurred as inverted repeat sequences. There were four ribosomal RNA genes (3.5%), 30 individual transfer RNA genes (25.9%), 21 genes encoding large and small ribosomal subunits (18.1%), four genes encoding DNA-dependent RNA polymerases (3.5%), 48 genes encoding photosynthesis-related proteins (41.4%), and 9 genes encoding other proteins, including those with unknown functions (7.8%). Among the 112 single copy genes, 17 genes contained introns, and three genes, clpP, trnT-GGU, and ycf68, were identified as pseudogenes. The locations of the genes and pseudogenes are shown in Figure 1 (gene map) and Table 1 (gene content). The C. japonica cp genome has an AT content of 64.6%, which is higher than those of A. capillus (58.0%), C. taitungensis (60.5%), O. sativa (61.0%), and P. thunbergii (61.2%), similar to that of E. globulus (63.4%), but lower than that of M. polymorpha (71.2%).
Table 1

List of genes found in C. japonica chloroplast genome (see Figure 1)

Category for genes

Group of gene

Name of gene

Self replication

Ribosomal RNA genes

rrn 16

rrn 23

rrn 5

rrn 4.5


Transfer RNA genes

trn A-UGC *

trn C-GCA

trn D-GUC

trn E-UUC

trn F-GAA

trnf M-CAU


trn G-GCC

trn G-UCC *

trn H-GUG

trn I-CAU × 2

trn I-GAU *

trn K-UUU *


trn L-CAA

trn L-UAA *

trn L-UAG

trn M-CAU

trn N-GUU

trn P-GGG


trn P-UGG

trn Q-UUG × 2

trn R-ACG

trn R-UCU

trn S-GCU

trn S-UGA


trn S-GGA

trn T-UGU

trn V-GAC

trn V-UAC *

trn W-CCA

trn Y-GUA


Small subunit of ribosome

rps 2

rps 3

rps 4

rps 7

rps 8

rps 11


rps 12*

rps 14

rps 15

rps 16 *

rps 18

rps 19


Large subunit of ribosome

rpl 2 *

rpl 14

rpl 16 *

rpl 20

rpl 22

rpl 23


rpl 32

rpl 33

rpl 36


DNA dependent RNA polymerase

rpo A

rpo B

rpo C1 *

rpo C2


Translational initiation factor

inf A


Genes for photosynthesis

Subunits of photosystem I

psa A

psa B

psa C

psa I

psa J

psa M


Subunits of photosystem II

psb A

psb B

psb C

psb D

psb E

psb F


psb H

psb I

psb J

psb K

psb L

psb M


psb N

psb T



Subunits of Cytochrome

pet A

pet B *

pet D *

pet G

pet L



Subunits of ATP synthase

atp A

atp B

atp E

atp F *

atp H

atp I


Large subunit of Rubisco

rbc L


Chlorophyll biosynthesis

chl B

chl N

chl L


Subunits of NADH dehydrogenase

ndh A*

ndh B *

ndh C

ndh D

ndh E

ndh F


ndh G

ndh H

ndh I

ndh J

ndh K


Other genes


mat K


Envelop membrane protein



Subunit of Acetyl-CoA-carboxylase



c-type cytochrome synthesis gene



Genes of Unknown function

Conserved Open Reading Frames

ycf 1

ycf 2

ycf 3 *

ycf 4





Pseudo-trn T-GGU


Pseudo-ycf 68


* Genes containing introns.
Figure 1

Gene organization of the C. japonica chloroplast genome (see Table 1). Genes shown outside the circle are transcribed clockwise, while those located inside are transcribed counter-clockwise. Intron-containing genes are indicated by asterisks. Red boxes, ribosomal RNA genes; black boxes, transfer RNA genes; light orange boxes, large subunit of ribosomal protein genes; dark orange boxes, small subunit of ribosomal protein genes; dark purple boxes, DNA dependent RNA polymerase genes; dark green boxes, rbcL gene; yellowish-green boxes, subunits of photosystem I genes; green boxes, subunits of photosystem II genes; light blue boxes, subunits of cytochrome genes; dark blue boxes, subunits of ATP synthase genes; light yellow boxes, ORF genes; dark yellow boxes, subunits of NADH dehydrogenase genes; light purple boxes, chlorophyll biosynthesis genes. The pseudogene is indicated by ψ (pseudo-).

A marked difference in gene content between gymnosperms including C. japonica

There are marked differences in several genes between gymnosperms, even though the C. japonica cp genome shares several common features with other plants, and some of these are described below. For example, there is considerable difference in gene content between C. japonica and P. thunbergii; the 11 intact ndh (NADH dehydrogenase) genes found in C. japonica, as well as in five other plants, are absent from P. thunbergii [9]. The loss of these ndh genes is thought to be due to specific mutations in the Pinus cp genome.

Another functional gene, rps16, which encodes a small ribosomal subunit, is found in the angiosperms, E. globulus and O. sativa, in the fern, A. capillus, and in gymnosperms, C. taitungensis and C. japonica (Figure 2). However, the location of rps16 is halfway between the trnK-UUU and chlB genes in the cp genome of gymnosperms, and halfway between matK and chlB, and between the trnK-UUU and trnQ-UUG genes in fern and angiosperms, respectively. In contrast, rps16 is completely absent from the M. polymorpha and P. thunbergii [29, 35] cp genomes, in addition to a large number of unrelated taxa of land plants, including Connarus, Epifagus, Eucommia, Fugus, Krameria, Linum, Malpighia, Passiflora, Securidaca, Turnera, Viola, Adonis, Medicago, Selaginella [3641]. Doyle et al. [38] postulated the functional transfer of rps16 from the chloroplast to the nucleus in order to explain the absence of this gene in such a large number of unrelated taxa of land plants. Similarly, the loss of rps16 and its functional transfer to the nucleus might have occurred independently in gymnosperms, especially in coniferous species.
Figure 2

Amino acid sequences of the rps 16 genes from five plant cp genomes, including C. japonica. The histogram below the sequences represents the degree of similarity. Peaks indicate positions of high similarity, and valleys positions of low similarity. Numbers at the C-terminal ends indicate the length of the amino acid sequences in each species.

The trnP-GGG and trnR-CCG genes are considered to be pseudogenes, possibly relics of plastid genome evolution in gymnosperms and moss [22, 42, 43]. The trnP-GGG gene is found in C. japonica, as well as in the two gymnosperms, P. thunbergii and C. taitungensis, in the liverwort, M. polymorpha, and in the fern, A. capillus, but not in angiosperm cp genomes. The gene is also found in Gnetum and Ginkgo of gymnosperms [8], suggesting that this is a relic gene in a large number of gymnosperms. In contrast, the trnR-CCG gene, which is found in P. thunbergii, C. taitungensis, M. polymorpha, and A. capillus, is absent from the C. japonica and angiosperm cp genomes, suggesting that trnR-CCG is not conserved in all gymnosperm cp genomes and might have been completely lost in taxa, such as Cupressaceae sensu lato, that have relatively recently diverged during the long evolutionary history of plants.

The tRNA gene, trnT-GGU, in the C. japonica cp genome contains only 43 bp of its 3' end and was therefore too short to form its complete secondary structure (Figure 3). Furthermore, this trnT-GGU gene occurs as a single copy gene in the cp genomes of A. capillus, M. polymorpha, E. globulus, and O. sativa, is present as two copies in P. thunbergii, but is completely missing from the C. taitungensis cp genome. In Pelagonium, the loss of trnT-GGU from its cp genome has been considered to be associated with genomic rearrangements [44]. Although this relationship is considered further below, the duplication or incomplete lost of tRNA genes in P. thunbergii and C. japonica is also thought to be associated with genome rearrangements. However, the question remains as to why the trnT-GGU of C. taitungensis is completely lost despite the fact that no genomic rearrangements were found in comparison with standard cp genomes, such as of E. globulus.
Figure 3

Nucleotide sequences of the trn T-GGU genes of six land plant cp genomes, including C. japonica. The trnT-GGU gene is missing from the C. taitungensis genome and is too short to form a secondary structure in C. japonica. The bold characters show the anti-codon GGU. The position of the trnT-GGU gene in each cp genome is shown above each sequence. The secondary structure of the trnT-GGU gene is described at the top.

Diversification of genes in the C. japonicacp genome

The accD gene, which encodes acetyl-CoA-carboxylase (ACCase), is found in the cp genomes of all seven plants analyzed in this study, however, their reading frame lengths vary considerably. The reading frame length of the C. japonica cp genome is 700 codons, which is larger than that of A. capillus (309 codons), M. polymorpha (316 codons), P. thunbergii (321 codons), and C. taitungensis (359 codons) (Figure 4). The alignments do not include those of the angiosperms, E. globulus (490 codons), and O. sativa (106 codons), because of the complicated nature of the alignments. In monocot angiosperms, the accD reading frame length is reduced from 106 codons in O. sativa to zero in Z. mays, and this reduction is considered to be the cause of accD loss in monocot species [45]. In contrast to this reduction, the accD reading frame in coniferous species, especially in Cupressaceae sensu lato including C. japonica, may have diversified in an increasing direction.
Figure 4

Alignment of amino acid sequences of the acc D gene in five land plant cp genomes. The histogram indicates the degree of similarity (see Figure 2). The number on the right indicates the length of the accD reading frame in each cp genome. The amino acid length of the accD gene product in C. japonica is approximately twice that of the other five plant cp genomes.

The clpP gene, which encodes a proteolytic subunit of the ATP-dependent Clp protease, is found intact in the cp genomes of the six land plants, C. taitungeinsis, E. globulus, A. capillus, and M. polymorpha, with three exons and two introns, and in the P. thunbergii and O. sativa cp genomes with no introns [22]. However, in the C. japonica cp genome, only the second exon of the gene remains and so it occurs as a pseudogene. Furthermore, the clpP gene is co-transcribed with the 5'-end of the rps12 gene and the rpl20 gene (M. polymorpha; [46], P. contorta; [47], O. sativa; [48]), so that the clpP to rpl20 gene order is extremely conserved in the cp genomes of all the land plants of this study. However, the clpP gene in the C. japonica cp genome is found halfway between the psbJ and accD genes, and is clearly not co-transcribed with the rps12-5'end and rpl20 genes (Figure 5). As the loss of function of the clpP gene in the Adonis annua cp genome is thought to be due to genome rearrangements (inverted mutations) [39], it is possible that genome rearrangements are also the reason why clpP is a non-functional pseudogene in the C. japonica cp genome, as discussed further below.
Figure 5

Percentage identity plots and gene order surrounding the clp P gene. Gene identities between C. japonica and C. taitungensis (A), and between C. taitungensis and six other plants including C. japonica (B-G) are shown by MultiPipMaker. The directions of arrows indicate the transcribed sense/antisense strands. The colored boxes show the group of genes and the relevant coding region of each gene. Mutual comparisons of the clpP gene between C. japonica and C. taitungensis (A, B), show the first and third exon are completely absence in the C. japonica cp genome. For the gene order surrounding the clpP gene, the clpP to rpl20 gene order is extremely conserved to be co-transcribed in the cp genomes of all the land plants of this study (see Figure 7 for the detailed gene order). On the other hand, the clpP gene in the C. japonica cp genome is found halfway between the psbJ and accD gene, and is clearly not co-transcribed with the rps12 and rpl20 genes.

Although four major ycf genes have been partially characterized in the cp genomes of other land plants, their precise functions remain unclear to date. Four ycf genes, ycf1, ycf2, ycf3, and ycf4, were also identified in the C. japonica cp genome. The highly conserved ycf3 and ycf4 are believed to be involved in the formation of photosystem I in Chlamydomonas reinhardtii [49]. The deduced amino acid sequences of the ycf3 and ycf4 products show 81–96% and 71–76% sequence identity, respectively, with their homologues in other land plants. In contrast, ycf1 and ycf2 show considerable divergence relative to other land plants, with their deduced proteins having only 24–54% (partially 54% identity with that of P. thunbergii) and 25–37% sequence identity, respectively, with their homologues in other land plants. The two divergent ycf1 and ycf2 genes are thought to be involved in cellular metabolism or to play a structural role in plastids [50]. Both the maize and rice cp genomes lack these two reading frames [45, 51], and the results from the present comparative analysis show that there are no regions homologous to ycf1 and ycf2 in C. japonica. Furthermore, although the ycf68 gene of C. japonica shows 63% identity to that of P. thunbergii, the C. japonica ycf68 may not encode a protein. The ycf68 sequence, which occurs in the trnI-GAU intron, could represent a functional protein encoding gene in rice, corn, and Pinus, although alignments of the ycf68 region in 14 angiosperms revealed that, in the majority of cases, it contained numerous frameshifts and stop codons [52]. Similarly, we found numerous frameshifts and stop codons in the ycf68 region, although the C. japonica and C. taitungensis ycf68 regions have a comparatively high level of homology with that of P. thunbergii (Figure 6).
Figure 6

Alignment of the ycf 68 regions of seven land plant cp genomes. Sequences of the ycf68 region of P. thunbergii and O. sativa were obtained from databases of each complete cp genome sequence, and relevant regions of the other plants were obtained by alignment with that of P. thunbergii or O. sativa. Codons highlighted in red represent stop codons.

Loss of large IR region within coniferous cp genomes

Figure 7 details the gene order and locations of the LSC, SSC, and IRs of the cp genomes of the seven land plants, E. globulus (A), O. sativa (B), A. capillus (C), M. polymorpha (D), C. taitungensis (E), P. thunbergii (F), and C. japonica (G). The C. japonica and P. thunbergii cp genomes have lost one of the large inverted repeats (IRs) that are found in the cp genomes of other plants. When compared to the C. taitungensis cp genome (Figure 7E), which has a large IR region, the corresponding IR of the C. japonica cp genome was divided into two segments, and the relevant SSC region was divided into three segments (Figure 7G). Similarly, in the P. thunbergii cp genome, the relevant IR region was divided into three segments (Figure 7F). Although the IR of P. thunbergii, which is 495-bp in length, contains a duplicated trnI-CAU gene and a partial psbA gene (red boxes in Figure 7F), presumably due to incomplete loss of the large IR [29], the IRs of Pinus cp genomes are thought to be structurally different from those of other plants, being composed of two or more genes including the trnI-CAU gene. There are two pairs of short inverted repeats in the C. japonica cp genome, consisting of 284-bp and 114-bp inverted repeats containing duplicated trnQ-UUG (white arrows in Figure 7G) and trnI-CAU (black arrows in Figure 7G) genes, respectively. Based on the defined IRs of the Pinus cp genome, the residual IR of C. japonica may be the 114-bp inverted repeat containing the duplicated trnI-CAU gene. However, it is structurally different from the IRs of other plants that contain several duplicated genes in their cp genomes.
Figure 7

Gene order and cp genomic architecture of the seven land plant species, including C. japonica. Each colored gene segment shows the same gene order region among the seven land plants cp genomes. Gray, blue and orange boxes for each gene order show the relevant regions of LSC (Large Single Copy), SSC (Small Single Copy) and IR (Inverted Repeat) regions in the E. globulus (A), O. sativa (B), A. capillus (C), M. polymorpha (D), and C. taitungensis (E) cp genomes, respectively. In the P. thunbergii (F) and C. japonica (G) cp genomes, gray, blue and orange boxes show the relevant regions of the SSC and IR regions of the C. taitungensis cp genome. Red boxes in the P. thunbergii cp genome show the defined IR in the P. thunbergii cp genome. In the C. japonica cp genome, the black and white arrows show duplicated genes; trnI-CAU (black arrows), trnQ-UUG (white arrows).

Structural differences between cp genomes of C. japonicaand other land plants

In addition to the loss of the large IR, genome rearrangements appear to have played an important role in the evolution of the coniferous cp genome. Harr-plot analyses also indicate that the cp genome of C. japonica has lost its large IR and that its structure differs significantly from that of the cp genomes of the other six plants in terms of gene order. We estimated the minimum rearrangements via inversions in pairwise comparisons of cp genomes in order to determine the structural differences between cp genomes (Table 2), even though inversions may not be the only mutational events causing gene order changes in the cp genome. A minimum of five inversions would be required to transform the gene structure of the gymnosperm C. taitungensis cp genome into that of the angiosperm E. globulus cp genome (Table 2, additional file 1A). In contrast, many genome rearrangements have occurred in the cp genomes of coniferous species within gymnosperms; we found that deletion of the large IR and a minimum of 12 inversions would be required to transform the gene structure of the C. taitungensis cp genome into that of C. japonica (Table 2, Figure 8A), and that deletion of the large IR and a minimum of seven inversions would be required to transform the gene structure of the C. taitungensis cp genome into that of P. thunbergii (Table 2, additional file 1B). Furthermore, it is interesting to note that 15 inversions would be required to transform the gene structure of C. japonica into that of P. thunbergii (Table 2, Figure 8B).
Table 2

Minimum rearrangements via inversions in pairwise comparisons of seven chloroplast genomes

comparison species

large inversion*

one gene inversion**

loss of a large IR

total inversion

C. japonica vs P. thunbergii





C. japonica vs C. taitungensis





C. japonica vs A. capillus





C. japonica vs M. polymorpha





C. japonica vs E. globulus





C. japonica vs O. sativa





P. thunbergii vs C. taitungensis





P. thunbergii vs A. capillus





P. thunbergii vs M. polymorpha





P. thunbergii vs E. globulus





P. thunbergii vs O. sativa





C. taitungensis vs A. capillus





C. taitungensis vs M. polymorpha





C. taitungensis vs E. globulus





C. taitungensis vs O. sativa





A. capillus vs M. polymorpha





A. capillus vs E. globulus





A. capillus vs O. sativa





M. polymorpha vs E. globulus





M. polymorpha vs O. sativa





E. globulus vs O. sativa





* large inversions indicate an inversion event of the segment composed of two or more genes.

** one gene inversion indicates the inversion event of one gene.
Figure 8

Harr plot analyses comparing the cp genome of C. japonica with those of C. taitungensis and P. thunbergii. Each dotplot shows the positions where 45 out of 50 nucleotides match in the two sequences. The plot analysis was carried out using Pipmaker software. Sequences along the Y-axis are set from the top to the bottom, and along the X-axis are from left to right. Relative lengths of sequences are shown to the side and below the boxes. The colored gene segments along the X- and Y-axes correspond with common gene units of the seven cp genomes (shown in Figure 7). At the expected endpoint of inversion or translocation mutation, the gene name is attached based on the X-axis (C. japonica cp genome). The pseudogene is indicated by ψ (pseudo-). The representative inversion and translocation are represented by gene segment I (the trnT-UGU to trnQ-UUG of C. japonica cp genome) and gene segment II (thr trnV-GAC to pseudo-clpP of C. japonica cp genome). The detailed comparisons of the gene segment I and II are shown in the following Figure 9 and Figure 10.

The large IR is thought to stabilize the cp genome against major structural rearrangements [5355]. Among angiosperm species, structural changes in the cp genome have occurred within tribes of the legume family (Fabaceae), which have also lost their IR, and so it appears that most genomes that have lost their IRs have undergone more rearrangements than those that have not [53, 56]. With respect to other conifers, it has been shown that Douglas fir (Pseudotsuga menziesii) and radiata pine (Pinus radiata) lack the large IR, and that both of these conifer genomes have undergone a greater number of rearrangements relative to ferns, angiosperms, and even Ginkgo, a gymnosperm [26]. The differences in genome structure between C. japonica and other land plants, including pines, strongly confirms that the presence of large IRs plays a role in the structural stability of the cp genome.

Tsumura et al. [27] suggested that the cp genome structure of C. japonica differs significantly from that of pine species, implying that independent changes have occurred and that no simple evolutionary path can be determined. In fact, phylogenetic studies have revealed the significant divergence of Coniferales [33, 34], with a phylogenetic tree using the rbcL gene in one of these studies indicating that C. japonica (Cupressaceae sensu lato) and pine species (Pinaceae) are not very closely related and are in fact located in different clade (additional file 2 in this study). In a study of 18 Campanulaceae species, Cosner et al. [57] suggested that data regarding cp genome rearrangements were useful for inferring phylogenetic relationships, and actually found that the results of analysis using gene order closely paralleled the results of phylogenetic analysis using Internal Transcribed Spacer (ITS) and rbcL sequence data. Hence, data on rearrangements in the conifer cp genome might reflect phylogenetic relationships and serve as a new evolutionary-related parameter. Furthermore, insights obtained from these studies will provide a clearer detail of the process of cp genome evolution. However, in order to better understand the complex changes in the cp genome structure that have occurred during the long process of evolution, data on the cp genomes of other coniferous taxa, such as Taxaceae, Sciadopityaceae, Podocarpaceae, and Araucariaceae will be required.

The vestiges of genome rearrangement within the C. japonicacp genome

Dispersed repetitive sequences with duplicated tRNA genes have been reported in the cp genomes of other Pinus species [58, 59], and are associated with numerous DNA rearrangements, including the loss of IRs [59]. In addition, intact tRNA genes and dispersed repeats that are segments of tRNA sequences have a relationship with the inversion endpoints [23, 6062], although not all inversion borders are near tRNA genes [61]. In this study, the gene order between psbA or matK and trnS-GCU in the cp genome of six other plants examined was highly conserved, whereas that of the C. japonica cp genome differed significantly from these six plants (Figure 9). Assuming a C. taitungensis-like ancestral cp genome, we postulate an inversion event, which occurred at the segment from trnQ-UUG to trnT-UGU, to explain the cause of the duplicated trnQ-UUG gene (gene segment I in Figure 8A, and Figure 9).
Figure 9

Expected inversion event in the C. japonica cp genome. The expected inversion corresponds with the gene segment I in Figure 8. Genes are represented by boxes extending above or below the base-line depending on the direction of transcription. The colored boxes indicate the same gene units among the seven cp genomes, including C. japonica. The tRNA anti-codon is abbreviated in the six plant cp genomes excluding C. japonica. The character highlighted in red represents the duplicated trnQ-UUG in the C. japonica cp genome. The pseudogene is indicated by ψ (pseudo-).

Within the large inversion from trnT-UGU to trnQ-UUG, we found another vestige of the genome rearrangement. As mentioned above, the incomplete loss of trnT-GGU (halfway between trnE-UUC and psbD in the C. japonica cp genome, Figure 9) from the C. japonica cp genome may have been the result of genome rearrangement. In grasses, such as O. sativa, it has been suggested that rearrangements in the region surrounding trnT-GGU were derived from two independent inversions [49, 61, 62]. In the A. capillus cp genome, the segment from trnT-GGU to trnG-GCC is inverted when compared to that of E. globulus. In the P. thunbergii cp genome, a translocation and inversion event occurred at the segment from trnT-GGU to the pseudogene ndhC (as indicated within gene segment I in additional file 1B). It is worth noting that trnT-GGU is located at the borders of the sites of the genome rearrangements. Although the rearrangement associated with trnT-GGU was not found in the C. japonica cp genome when compared to that of E. globulus, the incomplete loss of trnT-GGU in the C. japonica cp genome suggests the possibility of a re-inversion event.

Furthermore, the gene order between the clpP and trnV-UAC genes is extremely conserved among the six other land plants studied, whereas that of the C. japonica cp genome is significantly different (Figure 10). Within the trnN-GUU to chlL gene segment of the C. japonica cp genome, we identified three inverted repeats and one direct repeat which were 50 bp or longer and showed a sequence identity of at least 90%, together with a duplicated partial trnL-CAA gene (repetitive sequences of I-IV in Figure 10 and additional file 3). We infer that these repetitive sequences are associated with the inversion and translocation events, because the repetitive sequences were not observed in the other six plant cp genomes and they coincided with rearrangement endpoints that were significantly different from the six other plant cp genomes. However, it is difficult to unequivocally establish the process of genome rearrangement in the C. japonica cp genome based solely on the positional information of these repetitive sequences. In particular, we cannot infer why several repetitive sequences are concentrated within the region between trnL-CAA and ycf1 (repetitive sequences of I-III in Figure 10 and additional file 3).
Figure 10

Expected inversion or translocation endpoints and dispersed repetitive sequences of the C. japonica cp genome. The expected inversion corresponds with gene segment II in Figure 8. Genes are represented by boxes extending above or below the base-line depending on the direction of transcription. The colored boxes indicate the same gene units among the seven cp genomes including C. japonica. The number above the gene segments of the C. japonica cp genome correspond with positions of each repetitive sequence, and the character (similarity, length, repeat type, location, and sequence) of each repetitive sequence is shown in additional file 3. The trnL-CAA gene sequence of the C. japonica cp genome is shown with its secondary structure. The trnL-CAA with ψ (pseudo-) is incomplete in length to form its secondary structure.

We described above the relationship between the clpP pseudogene, within the trnN-GUU gene to chlL gene segment, and genome rearrangements. In the Adonis annua cp genome [37], the functions of the clpP gene are thought to have been lost as a result of genome rearrangement (inversion event). In the petA to clpP region of the C. japonica cp genome, assuming a C. taitungensis-like ancestral cp genome, we can construct a genome rearrangement model in which a minimum of three inversions would be required to transform the gene order of the C. taitungensis cp genome into that of C. japonica (Figure 11). The clpP pseudogene in the C. japonica cp genome was apparently caused by such genome rearrangements, and the repetitive sequences halfway between psbJ and clpP, and between ccsA and petA in the C. japonica cp genome should therefore be vestiges of the genome rearrangements.
Figure 11

A three-step model for genome rearrangement with the clp P pseudogene in C. japonica cp genome. (A) the hypothesized ancestral cp genome of C. japonica; (B), (C) the hypothesized genome rearrangement; (D) the present form of C. japonica. The number (IV) in the figure indicate the formed repetitive sequence (see Figure 10 and additional file 3), and its transition position during genome rearrangement.


This study has revealed that the coniferous species, C. japonica, has a distinct cp genome compared to previously reported land plant cp genomes. In terms of gene content, several genes in the C. japonica cp genome differ significantly, having either been lost or diverged, from those of other land plants, while the gene order and genome structure also differ significantly. The deleted large IRs and the numerous genome rearrangements that have occurred in the C. japonica cp genome have provided new insights into the evolutionary lineage of conifers. However, as the complete cp genome nucleotide sequences of only three conifer species that belong to two distinct genera have been determined, our present results will certainly advance our understanding of the complex evolutionary history of the coniferous cp genome.


Isolation of chloroplast DNA

Open-pollinated C. japonica seeds were collected from several clones, and were germinated and grown for 1 month in a greenhouse. C. japonica chloroplasts were isolated from the needle tissues of these seedlings using the sucrose density gradient method [63]. The chloroplast pellet was resuspended in 250 ml of Kool's buffer A (50 mM Tris-HCl, pH 8.0, 0.35 M sucrose, 7 mM EDTA, 5 mM 2-mercaptoethanol) containing 0.1% bovine serum albumin, and the suspension was filtered through layers of cheesecloth and Miracloth (Calbiochem; without squeezing). The filtrate was centrifuged, and the resulting green pellet was resuspended in 2.5 ml of Kool's buffer A. This second suspension was then loaded onto a stepwise 20–45–55% sucrose gradient in 50 mM Tris-HCl, pH 8.0, 0.3 M sorbitol, 7 mM EDTA, and centrifuged for 30 min. The green band at the 20–45% sucrose interphase was collected, diluted 1:3 with Kool's buffer B (50 mM Tris-HCl, pH 8.0, 20 mM EDTA), centrifuged for 10 min, and the chloroplast pellet then resuspended in Kool's buffer B. The chloroplasts were lysed by adding SDS to a final concentration of 3%. A 1/20th volume of 10 mg/ml pronase E was added to the solution, and the mixture incubated overnight at 37°C. DNA was extracted twice from the lysate with phenol and once with phenol/chloroform/isoamyl alcohol (25:24:1), and the DNA was precipitated with 0.1 volumes of 3 M sodium acetate and 2.5 volumes of ethanol. The precipitate was washed twice with 70% ethanol and dissolved in water. The extracted DNAs were further purified using the DNeasy Plant Mini Kit (QIAGEN) and treated with ATP-dependent DNase (TOYOBO) to remove linear double- or single-stranded DNA.

Chloroplast DNA sequencing and genome assembly

The cp DNA isolated was sheared by ultrasonication, and the sheared fragments then blunted and cloned into pBluescript II vector. The cp DNA fragments were shotgun sequenced using the BigDye Terminator Cycle Sequencing v3.1™ Kit with an ABI 3100 Genetic Analyzer (both PE Applied Biosystems). Sequencher 3.1 (Gene Codes Corporation) software was used for sequence analysis and assembly. The sonication-derived cloned fragments were found to cover 80% of the whole genome after contig assembly. Any remaining sequence gaps were amplified by PCR and sequenced directly from the amplification products.

Gene annotation

The cp genome of C. Japonica was annotated using DOGMA [Dual Organellar GenoMe Annotator, 64] after a FASTA-formatted file of the complete cp genome was uploaded to the program's server. Gene annotation and comparative genome analyses (BLASTN, BLASTX) were performed against a custom database of 11 previously published cp genomes using default parameters of 60% for protein coding genes and 85% for tRNAs and rRNAs. For genes with low amino acid sequence identity, manual annotation was performed using a percentage identity threshold of 25–50%. The fully annotated cp genome of Cryptomeria japonica was submitted to DDBJ GenBank with the following accession number [DDBJ: AP009377].

Exploration of the differences in gene contents and diversified genes

Exploration of the differences in gene contents and diversified genes between the C. japonica cp genome and the six previously published cp genomes was performed using PipMaker [65]. The six cp genomes compared are as follows: the dicot angiosperm, E. globulus (Myrtaceae, 160,286 bp, AY780259); the monocot angiosperm, O. sativa (Poaceae, 134,525 bp, X15901); the liverwort, M. polymorpha (Marchantiaceae, 121,024 bp, NC001319); the fern, A. capillus (Pteridaceae, 150,568 bp, AY178864); and the two gymnosperms, C. taitungensis (Cycadaceae, 163,403 bp, AP009339) and P. thunbergii (Pinaceae, 119,707 bp, D17510). The variable genes identified within the C. japonica cp genome by gene annotations were aligned with the corresponding coding genes of the six land plant cp genomes using ClustalX [66] followed by screening for nucleotide and amino acid sequence differences.

Comparative analysis of genome structure

Comparative analysis of the genome structure of the seven cp genomes, including that of the C. japonica cp genome, was performed using the Harr-plot analysis of PipMaker [65]. For estimates of genome rearrangement, the GRIMM web server [67] was used to identify the minimum number of rearrangements by inversion in pairwise comparisons of the cp genome. GRIMM cannot deal with duplicated genes and requires that the genomes that are compared have the same gene content, so that one of the two IR copies and their genes were arbitrarily excluded.

Examination of dispersed repeat sequences

FASTPCR software [68] was used to locate and count the direct (forward) and inverted (palindromic) repeats within the C. japonica cp genome. The identification of repeat sequences was assessed with the following parameters: options at a minimum length of 50 bp and 90% or greater sequence identity.

Phylogenetic analysis using the rbcL gene of chloroplast genome

Based on the rbcL gene sequence of the C. japonica cp genome, the rbcL gene nucleotide sequences of 132 gymnosperm species and eight out-group species were obtained by a FASTA search of GenBank. The DNA sequences were aligned using ClustalX [66], with excluded gap regions. Phylogenetic analysis using the neighbor-joining (NJ) method was performed using ClustalW from the DDBJ web server [69]. The Kimura-2-parameter model of molecular evolution was used in the NJ method of the nucleotide sequences. Bootstrap analysis was performed for the NJ method with 100 replicates.


cp genome: 

chloroplast genome


inverted repeat


small single copy


large single copy


base pair


hypothetical chloroplast reading frame


intergenic spacer.



We thank Dr. Yasukazu Nakamura at Kazusa DNA Research Institute for helpful advice on the annotation of the cp genome, and Dr. Shohab Youssefian at Akita Prefectural University for helpful discussions, comments and advice.

Authors’ Affiliations

Institute of Wood Technology, Akita Prefectural University
Forestry and Forest Products Research Institute, Forest Tree Breeding Center


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