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3 Department of Biology, Faculty of Science, Kyushu University, Ropponmatsu, Fukuoka 810-8560, Japan; and 2 Bio-resources Technology Division, Forestry and Forest Products Research Institute, Kukizaki, Ibaraki 305-8687, Japan
Received for publication June 15, 1999. Accepted for publication December 7, 1999.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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Key Words: chlL • Cupressaceae • lineage effect • matK • phylogeny • Taxodiaceae • trnL intron • trnL-trnF IGS region
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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, for a preliminary result). In conjunction with this, we thought it necessary to determine the phylogenetic position of C. japonica, which belongs to Taxodiaceae. Also of interest is its relationship with Cupressaceae whose close relationship to Taxodiaceae is indicated by recent studies (see below).
The family Taxodiaceae as traditionally defined includes ten genera and 
16 species, widely distributed in north-temperate to subtropical regions of both the Old and New Worlds, and one genus present in the Southern Hemisphere (Page, 1990
). Taxodium (from the northeastern United States to Florida and Mexico), Cunninghamia (northern China to Taiwan), Taiwania (southern China to Taiwan and northern Myanmar), and Cryptomeria (China and Japan) are widely ranging. The remainder are local, with Sequoia and Sequoiadendron in western North America, Glyptostrobus and Metasequoia in southern and central China, and Athrotaxis in Tasmania. All the genera of this family are either monotypic or consist of small and closely related species groups (e.g., Athrotaxis), and the geographic spread of genera is one of considerable general disjunction. On the basis of fossil records, mainly in late Cretaceous and Tertiary ages, there were wider occurrences of species of several genera. These aspects strongly indicated relict nature of the living genera (Page, 1990
).
The Cupressaceae, in contrast, are widely spread in both hemispheres and include 20 genera and 125 species (Page, 1990
). Half of the genera and almost three-fourths of the species occur in the Northern Hemisphere, with the widely ranging genera Juniperus, Cupressus, Chamaecyparis, and Thuja comprising most of the species. The remaining genera are either distributed exclusively in the northern or southern hemisphere. Hart and Price (1990)
presented a more exhaustive synopsis of Cupressaceae.
Taxodiaceae and Cupressaceae were traditionally recognized as separate families, but this separation has been recently questioned on the basis of morphology and some aspects of secondary product chemistry (Eckenwalder, 1976
; Hart, 1987
) and immunological data (Price and Lowenstein, 1989
). The genus Sciadopitys, traditionally associated with Taxodiaceae, is highly divergent in its leaf and short shoot morphology and differs from all Taxodiaceae and Cupressaceae in many other traits including chromosome number and karyotype (Khoshoo, 1961
; Schlarbaum and Tsuchiya, 1984, 1985
) embryology (Doyle and Brennan, 1971
), wood anatomy (Phillips, 1941
), and immunological data (Price and Lowenstein, 1989
). Recently, molecular phylogenetic studies of Taxodiaceae and Cupressaceae using the data of rbcL sequences (Brunsfeld et al., 1994
), 28S rRNA sequences (Stefanovic et al., 1998
), and restriction endonuclease fragment length polymorphism (RFLP) based on polymerase chain reaction (PCR)-amplified fragments of chloroplast genes (Tsumura et al., 1995
) have been reported. These studies supported the above hypotheses that Sciadopitys represents a distinct family (Sciadopityaceae; Hayata, 1931
) and that Taxodiaceae and Cupressaceae form a monophyletic group. However, some questions still have remained.
Although the molecular phylogenetic trees using the rbcL sequences, 28S rRNA sequences and PCR-RFLP method are basically similar to each other, there is some discrepancy among them (Brunsfeld et al., 1994
; Tsumura et al., 1995
; Stefanovic et al., 1998
). For example, the results of Brunsfeld et al. (1994)
differ from the PCR-RFLP study in the placement of Taxodium. Two genera, Taxodium and Glyptostrobus, are ecologically unusual in conifers, and only genera of Taxodiaceae to be amphibious. In addition, only Taxodium normally develops peneumatophores from its roots under appropriate ecological conditions (Page, 1990
). In phylogenetic analysis of the rbcL data, Brunsfeld et al. (1994)
suggested that Cryptomeria and Glyptostrobus form a group, which is the sister -group of the Cupressaceae, but Taxodium lacks an affinity with this group. In contrast, the PCR-RFLP data placed Cryptomeria, Glyptostrobus and Taxodium together in a group with closer affinities to Athrotaxis than to Cupressaceae (Tsumura et al., 1995
). However, the bootstrap values for this or other clusterings of both studies were not high.
The present study examines some of the taxonomic problems within Taxodiaceae and Cupressaceae sensu stricto (s.s.) using the nucleotide sequences of the matK gene, chlL (frxC) gene, trnL-trnF IGS region, and trnL intron of the cp DNA. The matK gene, trnL-trnF IGS region, and trnL intron evolved more rapidly in the chloroplast genome (Neuhaus and Link, 1987
; Gielly and Taberlet, 1994
; Hilu and Liang, 1997
), and often used to study relationships among genera (Johnson and Soltis, 1994
; Plunkett, Soltis, and Soltis, 1997
), among species (Gielly and Taberlet, 1994
; Kajita et al., 1998
), and also within species (Fujii et al., 1997
). Furthermore, Johnson and Soltis (1994, 1995)
showed that analysis of the matK sequence data provided fine-scale resolution of relationships within Saxifeagaceae s.str. comparable to that achieved via RFLP analysis of cpDNA. The immediate goal of this study was to obtain a more refined phylogeny among genera of Taxodiaceae and Cupressaceae. With these sequences, we could obtain a reliable phylogeny. In addition, higher rates of replacement substitutions were observed in the Cupressaceae s.s. lineage.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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The trnL-trnF IGS region, trnL intron, and chlL (frxC) gene were amplified by PCR using TaqI polymerase (Pharmasia, Toyobo, Takara, Japan) with universal primers for the trnL-trnF IGS region, and trnL intron ("e", "f", "c", and "d" of Taberlet et al., 1991
), and with primers for the frxC as reported in Tsumura et al. (1995)
. PCR amplification of the matK region was accomplished using the primers matK-F and matK-R (Table 2). Amplified products were purified by GeneClean II (Bio 101, Carlsbad, California, USA) following the manufacturer's specifications. DNA sequencing was performed using an Applied Biosystems 377 automated sequencer (PE Biosystems, Foster City, California, USA) with BigdyeTM Terminator Cycle Sequencing Ready Reaction Kit (Perkin-Elmer Biosystems, Foster City, California, USA) following the supplier's instruction. The sequences were determined in both directions. Sequencing primers for the trnL-trnF spacer region and trnL intron were the same ones as those used as PCR primers. The chlL gene and matK gene were sequenced using the internal sequencing primers (Table 2) IF1, IR1, IR3, and IF2, IR2, IF4, IR4, respectively, besides the PCR primers. All new sequences obtained in this study were submitted to DNA Data Bank of Japan (DDBJ).
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). The trnL-trnF IGS region and trnL intron contained numerous insertion/deletions (indels) among conifer species. Therefore, alignments were visually corrected. Phylogenetic analyses were performed by the maximum parsimony (MP) method and neighbor-joining (NJ) method (Saitou and Nei, 1987
). For the parsimony analyses, we performed the branch-and-bound search using PAUP version 3.11 (Swofford, 1993
). No differential weighting of the substitutions was used in the MP analyses. For the NJ method, we used Clustal X (Thompson et al., 1997
). The level of support for branches of the phylogenetic trees was evaluated with the bootstrap test based on 1000 resamplings (Felsenstein, 1985
).
In the chlL and matK genes, numbers of nucleotide substitutions were estimated using Kimura's two-parameter method (Kimura, 1980
), and numbers of synonymous and nonsynonymous substitution per site between sequences were computed separately using the method of Nei and Gojobori (1986)
. Estimates of the average numbers of substitutions within and between groups with their variance were obtained using the method of Nei and Jin (1989)
. For these analyses, computer programs ODEN (Ina, 1994
) and SEnj (kindly provided by Dr. Y. Ina) were used.
The one-degree-of-freedom (1D) method of Tajima (1993)
was used to compare the accumulation of site changes between the Cupressaceae s.s. lineage and the Cryptomeria/Glyptostrobus/Taxodium group.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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1500 base pairs (bp) in length and is located within the trnK intron, on the large single-copy region adjacent to the inverted repeat. A homology search indicates that the carboxyl terminus portion of the translated protein is structurally related to portions of maturase-like polypeptides and might be involved in the splicing of Group II introns (Neuhaus and Link, 1987
; Mohr, Perkman, and Lambowitz 1993). The obtained matK sequences vary from 1580 to 1622 bp in length among the 23 members of Taxodiaceae, Cupressaceae s.s., Taxaceae, Cephalotaxaceae (the matK fragments of Sciadopitys verticillata and Taxus cupsidata could not be amplified by the matK-F and matK-R primers). The fragment length of Cryptomeria japonica was 1597-bp including 166 bp of the intergenic spacer region between one of the trnK exon and the matK gene. This fragment corresponds to 1–1431 of the matK gene (1548 bp) of the black pine (in the complete chloroplast genome: Wakasugi et al., 1994
). There were 4 indels (15 bp) between the matK fragments of C. japonica and the black pine and the sequence identity was 77.9 %. Six indels of 3–15 bp (the sum of length 33 bp) were also found among the sequences of the Taxodiaceae and Cupressaceae s.s. species. These indels are mostly found in multiples of three nucleotides and thus did not result in a frameshift. The average nucleotide compositions of the matK fragments were 0.36 (A) 0.31 (T) 0.16 (C) 0.17 (G). The transition:transversion ratio was 1.74.
The chlL gene codes for one of the subunits of protochlorophyllide reductase involved in the light-independent synthesis of chlorophyll (Suzuki and Bauer, 1992
). We obtained 738 bp of DNA sequence of the chlL gene for each taxon, corresponding to positions 27 through 764 in the black pine chlL sequence (Wakasugi et al., 1994
). The identity between the black pine and C. japonica was 90.8%. The average nucleotide compositions were 0.30 (A) 0.31 (T) 0.15 (C) 0.23 (G). The transition: transversion ratio was 1.63. All sequences were easily alignable by eye.
The trnL-trnF IGS region and trnL intron sequences determined in this study vary from 278 to 413 bp and 324 to 529 bp, respectively, in length for each taxon. In the spacer region, the nucleotide positions between approximately 100 and 170 were highly variable because of many indels. C. fortunei and C. japonica (Saga 3) had a variant sized (30 and 32 bp each) dinucleotide repeat [d(A - T)]n/[d(T - A)]n in this region (Table 3). Furthermore, we sequenced the trnL-trnF IGS region of other 4 samples from different localities of C. japonica, and detected additional 4 distinct variants (44, 40, 24, 34 bp long). The nucleotide sequences of the trnL intron contains a highly variable region at 200–400. Especially in Juniperus rigida, this entire region was deleted. After elimination of regions involving gaps and TA repeats, 199 sites of the spacer region and 225 sites of the intron are available for comparison. The average nucleotide compositions were 0.27 (A) 0.41 (T) 0.13 (C), 0.19 (G) in the spacer region; and 0.35 (A) 0.31 (T) 0.15 (C) 0.19 (G) in the intron. The transition:transversion ratio of the spacer region and the intron were 1.88 and 1.70.
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; Tsumura et al., 1995
; Stefanovic et al., 1998
). However, some clusterings had low support. In order to obtain a more refined phylogeny among genera of Taxodiaceae and Cupressaceae s.s., we used Cunninghamia as an outgroup for the subsequent analysis. The MP analysis resulted in one parsimonious tree with a consistency index (CI) of 0.860 (0.821 excluding uninformative characters), a retention index (RI) of 0.908 and a tree length of 645 (Fig. 1). In this parsimonious tree, the relationships among genera are further resolved, with Taiwania diverging first, Athrotaxis second, the Metasequoia, Sequoia and Sequoiadendron group third and the remaining genera last. The Cryptomeria fortunei and C. japonica share almost the same sequence excepting TA-repeats in the trnL-trnF IGS region (Table 3) and Cryptomeria forms a clade with the Glyptostrobus and Taxodium group. This clade is the sister lineage to the Cupressaceae s.s. species. Genera in Cupressaceae s.s. consist of two major lineages of the Thujopsis dolabrata and Thuja standishii group and Juniperus rigida and Chamaecyparis group. The topology of the NJ tree was consistent with the parsimony tree (Fig. 2). These trees have the same topology as that obtained by the second analysis including two outgroup species (see above).
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) was applied to test the homogeneity of the substitution rate between the two lineages. We analyzed the matK and chlL sequences from five taxa within Cupressaceae s.s. lineage and three representative taxa within the Cryptomeria/Glyptostrobus/Taxodium group (Cryptomeria japonica (Saga 3), Glyptostrobus pensilis, and Taxodium mucronatum). Sequoia sempervirens was used as an outgroup. Among the 30 tests, 12 comparisons gave significant results. Some results showing typical patterns are presented (Table 5). In the matK gene, almost all tests rejected the null hypothesis of homogeneity of the rates (P values < 0.05) and revealed higher rates of accumulation of nucleotide substitutions in the Cupressaceae s.s. lineage. In the chlL gene, although most comparisons of pair were not significant at the 0.05 level, we observed larger numbers of different sites (Tajima's m in the method) in taxa of the Cupressaceae s.s. lineage in all pairs. These results indicated that the Cupressaceae s.s. lineage evolved more rapidly compared to the Cryptomeria/Glyptostrobus/Taxodium lineage.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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; Tsumura et al., 1995
). However, relationships among these subclades were not fully resolved. In this study, we could obtain one most parsimonious tree based on the matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequence data (Fig. 1). Bootstrap supports for all of theseo subclades in this tree are mostly strong (80–100%). This tree is compatible with these suggested by the rbcL data and the PCR-RFLP data. Differences among the present analysis and these previous analyses are in the relationship of Taiwania and Athrotaxis to other taxa and the placement of Taxodium.
The analysis of the matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequence data obviously indicates that Taiwania segregated next to Cunninghamia and then Athrotaxis followed it (Figs. 1, 2). Previous workers have not suggested these relationships, but these clades are well supported (>79%). The strict consensus tree based on the rbcL sequences suggested that Taiwania and Athrotaxis were a part of tetrachotomy along with Taxodium and the remaining genera, but their placements in the rbcL phylogeny were equivocal (Brunsfeld et al., 1994
). The result of the PCR-RFLP differs from that of our data in the placing of Athrotaxis (Tsumura et al., 1995
). In that study, Athrotaxis had a closer affinity to the Cryptomeria, Glyptostrobus, and Taxodium group, although the support was low than to Taiwania. Perhaps because these genera are modern representatives of long lines of specialization, the evolutionary relationships among them are a matter of controversy (Miller, 1977). Furthermore, the NJ tree indicates that the divergence between Taiwania and Athrotaxis and other genera occurred during a short time (Fig. 2). Thus, more definitive resolution of this problem may require a comparison of results from additional studies using was examining nuclear genes or more informative data.
Taxodium and Glyptostrobus have often been treated as closest relatives of each other based on similarities in their ecology (both are deciduous trees of swampy habitats), and morphological aspects (possession of knees, patterns of cone-scale development, number of cotyledons), and immunological characteristics (Eckenwalder, 1976
; Price and Lowenstein, 1989
; Hart and Price, 1990
). An alternative placement in which Taxodium lacks a strong affinity with Glyptostrobus was suggested by the rbcL data, but with little support. Our results and those of the PCR-RFLP analysis both support the former conclusion that Taxodium is closest to Glyptostrobus (Figs. 1, 2). Taxodium, Glyptostrobus, and Metasequoia are only genera among Taxodiaceae and Cupressaceae s.s. to be annual deciduous. Stebbins (1948)
hypothesized the independent origin of the deciduous habit in Metasequoia. Thus, such habit may have evolved at least twice in these lineages, once in Metasequoia and once in the ancestor of Taxodium and Glyptostrobus.
Recently, a survey of cp DNA of the B-genome group of Glycine subgenus Glycine revealed that its haplotype polymorphisms transgressed species boundaries in several cases. Thus, phylogenetic trees inferred from cp DNA haplotypes show much less correspondence with taxonomic and apparent morphological boundaries in the Glycine group of taxa (Doyle, Doyle, and Brown, 1990
). In addition, incongruence between the tree of a nuclear gene and the cp DNA data set have been reported (Doyle, Doyle, and Brown, 1999
). These data suggested that lineage sorting and hybridization or a combination of these phenomena in a group of closely related taxa likely affected the distribution of cp DNA haplotypes. Since our analysis used only the cp DNA data, it is possible that such phenomena also affected the tree of Taxodiaceae and Cupressaceae s.s. However, the distribution among genera of the cp DNA haplotypes agrees with the several morphological groupings and the immunological analysis (Hida, 1957
; Price and Lowenstein, 1989
) in our case. Thus, the lineage sorting and hybridization seem unlikely to have affected our tree with regard to the relationship among genera, although we need nuclear data for confirmation. On the other hand, Athrotaxis laxifolia is said to be a hybrid between A. selaginoides and A. cupressoides based on the morphological traits (Cullen and Kirkpatrick, 1988
). In our study, there is no difference between sequences of A. laxifolia and A. selaginoides. In addition, we detected only a few differences within each of two Cunninghamia species, two Taiwania species, two Cryptomeria species and two Taxodium species. Some of them may be of hybrid origin, although a lack of differences does not in itself evidence for hybridization.
Our phylogenetic analyses reinforce the view that Cupressaceae s.s. and Taxodiaceae form a monophyletic conifer lineage. Cupressaceae s.s. form a clade with the Cryptomeria/Glyptostrobus/Taxodium group of which the bootstrap value is high (Figs. 1, 2). Our results are consistent with other recent interpretations (Eckenwalder, 1976
; Hart, 1987
; Price and Lowenstein, 1989
; Brunsfeld et al., 1994
; Stefanovic et al., 1998
). We have used only five taxa of Cupressaceae s.s from the Northern Hemisphere, which are divided into two clades. Thujopsis dolabrata and Thuja standishii form a clade and the other clade consists of the remaining genera, Juniperus rigida and Chamaecyparis (Fig. 1, 2). This result is consistent with the rbcL analysis (Brunsfeld et al., 1994
).
Comparison of substitution rates of the chlL and matK genes among lineages
The branch lengths shown in Fig. 2 clearly reveal that the Cupressaceae s.s. lineages tend to have higher substitution rates than do the Cryptomeria/Glyptostrobus/Taxodium lineages. In the matK and chlL genes, average numbers of nucleotide substitutions within the Cupressaceae s.s. were higher than those within the Cryptomeria/Glyptostrobus/Taxodium group (Table 4). Furthermore, we compared the accumulation of site changes between taxa from these two different lineages using the 1D method for testing the molecular evolutionary clock hypothesis (Tajima, 1993
). The results indicated that evolutionary rates in the Cupressaceae s.s. lineage are higher than those in the Cryptomeria/Glyptostrobus/Taxodium lineages (Table 5). We also applied this method to the 28S rRNA and rbcL gene data (Brunsfeld et al., 1994
; Stefanovic et al., 1998
) obtained from GeneBank. We used those sequences from the same taxa or the same genera used in the analyses of the matK and chlL gene (data not shown). The placement of Taxodium based on the rbcL data is different from ours, so we excluded the sequence of Taxodium from the analysis of the rbcL gene. The heterogeneity of the rate was also observed in the rbcL and 28S rRNA genes in the same direction, and these results indicated that the Cupressaceae s.s. lineage evolved more rapidly compared to the Cryptomeria/Glyptostrobus/Taxodium lineage. Thus, the change in substitution rate is likely to have occurred across multiple loci (lineage effects; Muse and Gaut, 1997
). Several factors could be invoked to explain this heterogeneity of substitution rates. For one thing, it should be notable that Cupressaceae s.s. includes much larger number of species than Taxodiaceae does (Page, 1990
). This suggests that the change of substitution rate might be result of lineage effects produced by changes in population size (Moran, 1996
) and speciation rate (DeSalle and Templeton, 1988
; Bousquet et al., 1992
). Ohta (1972)
predicted that rates of substitution for mildly deleterious mutation were greater in small populations (see also Ohta, 1992
). In the Cupressaceae s.s. lineage, the rate heterogeneity was more extensive at nonsynonymous site than synonymous sites (Table 4). This observation supports the hypothesis that accelerated evolution involves accumulation of deleterious mutations.
Nonsynonymous substitution rate of the chlL gene in the Cupressaceae s.s. lineage
The numbers of nonsynonymous substitution per site of the chlL gene within Cupressaceae s.s. is almost 10 times higher than that within the Cryptomeria/Glyptostrobus/Taxodium group (Table 4). Especially in the Thuja standishii lineage, nine nonsynonymous substitutions are observed, whereas only a few nonsynonymous substitutions are observed in the whole Taxodiaceae (data not shown). The chlL gene is currently considered to encode one of the structural subunits of a light-independent protochlorophilide reductase. Genes for the other subunits of this enzyme are predicted to be the chlN and chlB, which are also in cp DNA. These genes were shown to be required for light-independent chlorophyll accumulation (even in the dark) in Clamydomonas reinhardtii (Choquet et al., 1992
; Huang and Liu, 1992
; Suzuki and Bauer, 1992
; Liu, Xu, and Huang, 1993
; Li, Goldschmidt-Clermant, and Timko, 1993
), and Plectonema borianum (Fujita et al., 1991
). In fact, most but not all gymnosperms, pteridophytes, and algae which produce chlorophyll in the dark have all these three genes, but angiosperms and a few other eukaryotic organisms that do not green in the dark have, in most cases, lost these genes during evolution (Armstrong, 1998
). In the Thujopsis standishii, the relaxation of the functional constraint on the light-independent protochlorophilide reductase might have changed the substitution rate of the chlL gene. on its wayAlthough we could not detect any nonsense mutations within the chlL region we examined, there are possibilities that the chlN or chlB would have become a pseudogene.
Polymorphic simple sequence repeats in the trnL-trnF IGS region
In the trnL-trnF IGS region of Cryptomeria, we found simple sequence repeats, consisting of repeats of dinucleotide [d(A - T)]n/[d(T - A)]n motif in tandem. We compared the repeated regions from C. fortunei and five samples of C. japonica, and identified six length variants (Table 3). Powell et al. (1995)
examined the polymorphism of simple sequence repeats in the chloroplast genomes of plants using a PCR-based assay and identified nine length variants of the repeated region from 11 pine species. Furthermore, they analyzed 305 individuals from seven populations of Pinus leucodermis Ant., and found four variants with the intrapopulation diversity ranging from 0.000 to 0.629. In the present analysis, we have obtained only a limited data from six individuals, but the repeated sequence in the trnL-trnF IGS region would be useful to examine the population genetics problems in Cryptomeria species, and to perform paternity analyses.
In conclusion, our analyses of the four regions of cp DNA elucidated phylogenetic relationships among genera of Taxodiaceae and Cupressaceae s.s. The phylogenetic tree agrees with previous molecular phylogenic analyses except for the positions of Taxodium, Taiwania, and Athrotaxis, but we could get good resolution for these relationships. Our result is consistent with the several morphological groupings and the immunological analysis (Pierce, 1936; Hida, 1957
; Price and Lowenstein, 1989
). With the phylogenetic knowledge, we can choose appropriate species for contrasting variation within and between species and studying conservation of gene arrangements on chromosomes (synteny).
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FOOTNOTES |
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4 Author for correspondence (e-mail: htachscb{at}mbox.nc.kyushu-u.ac.jp
).
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