Abstract
We investigated the molecular phylogeny of conifers using restriction endonuclease fragment length polymorphism of six polymerase chain reaction-amplified chloroplast genes — frxC, rbcL, psbA, psbD, trnK, and 16S. We detected 227 total site changes among species, representing 23, 26, 38, 48, 67, and 25 site changes in frxC, psbA, psbD, rbcL, trnK and 16S, respectively. The mean nucleotide substitution was 10.75% (SD 0.573) among species in five families. Forty maximally parsimonious trees were obtained using the Wagner parsimony method, and a 50% majority-rule consensus tree was obtained from them. Data analysis produced similar basic patterns when both the Wagner parsimony and the neighbor-joining methods were applied, and the main lineages were clearly separated. Taxaceae and Cephalotaxaceae species were used as the out-groups when applying Wagner parsimony methods. With the Wagner method, the consistency index was 0.510, the retention index was 0.879, and tree length was 435 steps. Our results indicated that Cupressaceae and Taxodiaceae are closely related families and that Sciadopitys verticillata is the basal lineage of Cupressaceae and Taxodiaceae. The neighbor-joining tree is similar to the 50% majority-rule consensus of the 40 Wagner parsimony trees except for the position of Keteleeria daversifolia, the Picea and Cedrus group, and the divergence within Cupressaceae.
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References
Bousquet J, Strauss SH, Doerksen AH, Price RA (1992) Extensive variation in evolutionary of rbcL gene sequences among seed plant. Proc Natl Acad Sci USA 89:7844–7848
Brunsfeld SJ, Soltis PS, Soltis DE, Gadek PA, Quinn CJ, Strenge DD, Ranker TA (1994) Phylogenetic relationships among the genera of Taxodiaceae and Cupressaceae: evidence from rbcL sequences. Syst Bot 19:253–262
Chase MW, Soltis DE, Olmstead RG, Morgan D, Les DH, Mishler BD, Duvall MR, Price RA, Hills RA, Qiu Y-L, Kron KA, Retting KA, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim K-J, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang Q, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH, Graham SW, Barrett SCH, Dayanandan S, Albert VA (1993) Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Ann Mo Bot Gard 80:528–550
Chaw S-M, Long H, Wang B-S, Zharkikh A, Li W-H (1993) The phylogenetic position of Taxaceae based on 18S rRNA sequences. J Mol Evol 37:624–630
Cullen PJ, Kirkpatrick JB (1988) The ecology of Athrotaxis D. Don (Taxodiaceae). II. The distributions and ecological differentiation of A. cupressoides and A. selaginoides. Aust J Bot 36:561–573
Doyle J, Brennan SJ (1971) Cleavage polyembryony in conifers and taxads — a survey. I. Podocarps, taxads, and taxodioids. Sci Proc R Dublin Soc 4A:57–88
Eckenwalder JE (1976) Re-evaluation of Cupressaceae and Taxodiaceae: a proposed merger. Madrono 23:237–256
Govindaraju D, Lewis P, Cullis C (1992) Phylogenetic analysis of pine using ribosomal DNA restriction fragment length polymorphisms. Plant Syst Evol 179:141–153
Greenwood MS, Hopper CA, Hutchison KW (1989) Maturation in larch. I. Effect of age on shoot growth, foliar characteristics, and DNA methylation. Plant Physiol 90:406–412
Hart JA (1987) A cladistic analysis of conifers: preliminary results. J Arnold Arboretum 68:269–307
Hart JA, Price RA (1990) The genera of Cupressaceae (including Taxodiaceae) in the southeastern United States. J Arnold Arbor Harv Univ 71:275–322
Hayata B (1931) The Sciadopityaceae represented by Sciadopitys verticillata Sieb. et Zucc., an endemic species of Japan. Bot Mag 45:567–569
Hipkins VD, Tsai CH, Strauss SH (1990) Sequence of the gene forlarge subunit of ribulose 1,5-bisphosphate carboxylase from a gymnosperm, Douglas fir. Plant Mol Biol 15:505–507
Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of cereals. Mol Gen Genet 217:185–194
Khoshoo TN (1961) Chromosome numbers in gymnosperms. Silvae Genet 10:1–9
Kumar S, Tamura K, Nei M (1993) MEGA: molecular evolutionary genetics analysis, version 1.0. The Pennsylvania State University, University Park, Pa.
Lidholm J, Gustafsson P (1991) The chloroplast genome of the gymnosperm Pinus conforta: a physical map and a complete collection of overlapping clones. Curr Genet 20:161–166
Liston A (1992) Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astaglus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. Am J Bot 79:953–961
Moran GF, Smith D, Bell JC, Apples R (1992) The 5S RNA genes in Pinus radiata and the spacer region as a probe for relationship between Pinus species. Plant Syst Evol 183:209–221
Murray M, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
Neale DB, Sederoff RR (1989) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in loblolly pine. Theor Appl Genet 77:212–216
Neale DB, Wheeler NC, Allard RW (1986) Paternal inheritance of chloroplast DNA in Douglas-fir. Can J For Res 16:1152–1154
Neale DB, Marberly KA, Sederoff RR (1989) Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl. Proc Natl Acad Sci USA 86:9347–9349
Neale DB, Marshall KA, Harry DE (1991) Inheritance of chloroplast and mitochondrial DNA in incense-cedar (Calocedrus decurrens). Can J For Res 21:717–720
Nei M, Tajima F (1983) Maximum likelihood estimation of the number of the nucleotide substitutions from restriction sites data. Genetics 105:207–217
Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T, Ohyama K (1992) Complete nucleotide sequence of the mitochondrial DNA from a liverwort, Marchantia polymorpha. Plant Mol Biol Rep 10:105–163
Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota H, Inokuchi H, Ozeki H (1986) Complete nucleotide sequence of liverwort Marchantia polymorpha chloroplast DNA. Plant Mol Biol Rep 4:148–175
Phillips EWJ (1941) The identification of coniferous woods by their microscopic structure. J Linn Soc Bot 52:259–320
Price RA, Lowenstein JM (1989) An immunological comparison of the Sciadopityaceae, Taxodiaceae, and Cupressaceae. Syst Bot 14:141–149
Price RA, Olsen-Stojkovich J, Lowenstein JM (1987) Relationship among the genera of Pinaceae: an immunological comparison. Syst Bot 12:91–97
Saitou N, Nei M (1987) The neighbor-joining method: a new method reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schlarbaum SE, Tsuchiya T (1984) Cytotaxonomy and phylogeny in certain species of Taxodiaceae. Plant Syst Evol 147:29–54
Schlarbaum SE, Tsuchiya T (1985) Karyological deviation of Sciadopitys verticillata Sieb, et Zucc. from a pro-Taxodiaceous ancestor. Bot Gaz 146:264–267
Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki K, Ohta C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide sequence of tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049
Soltis PS, Soltis DE, Smiley CJ (1992) An rbcL sequence from amiocene Taxodium (bald cypress). Proc Natl Acad Sci USA 89:449–451
Strauss SH, Doerksen AH (1990) Restriction fragment analysis of pine phylogeny. Evolution 44:1081–1096
Strauss SH, Palmer JD, Howe GT, Doerksen AH (1988) Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proc Natl Acad Sci USA 85:3898–3902
Strauss SH, Doerksen AH, Byrne JR (1990) Evolutionary relationship of Douglas-fir and its relatives (genus Pseudotsuga) from DNA restriction fragment analysis. Can J For Res 68:1502–1510
Stine M, Sears BB, Keathley DE (1989) Inheritance of plastids in interspecific hybrids of blue spruce and white spruce. Theor Appl Genet 78:768–774
Sutton BCS, Flanagan DJ, Gawley JR, Newton CH, Lester DT, El-Kassaby YA (1991) Inheritance of chloroplast and mitochondrial DNA in Picea and composition of hybrids from introgression zones. Theor Appl Genet 82:242–248
Swofford DL (1991) PAUP: phylogenetic analysis using parsimony, version 3.0s. Computer program distributed by the Illinois Natural History Survey, Champaign, Ill.
Szmidt AE, Alden T, Hallgren J-E (1987) Paternal inheritance of chloroplast DNA in Larix. Plant Mol Biol 9:59–64
Tsudzuki J, Nakashima K, Tsudzuki T, Hiratsuka J, Shibata M, Wakasugi T, Sugiura M (1992) Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK. psbA, trnI and trnH and the absence of rps16. Mol Gen Genet 232:206–214
Tsumura Y, Ogihara Y, Sasakuma T, Ohba K (1993) Physical map of chloroplast DNA in sugi, Cryptomeria japonica. Theor Appl Genet 86:166–172
Wakasugi T, Tsudzuki J, Ito S, Shibata M, Sugiura M (1994) A physical map and clone bank of the black pine (Pinus thunbergii) chloroplast genome. Plant Mol Biol Rep 12:227–241
Wang X-R, Szmidt A (1993) Chloroplast DNA-based phylogeny of Asian Pinus species (Pinaceae) Plant Syst Evol 188:197–211
Watson FD (1985) The nomenclature of pond cypress and bald cypress (Taxodiaceae). Taxon 34:506–509
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Communicated by P. M. A. Tigerstedt
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Tsumura, Y., Yoshimura, K., Tomaru, N. et al. Molecular phytogeny of conifers using RFLP analysis of PCR-amplified specific chloroplast genes. Theoret. Appl. Genetics 91, 1222–1236 (1995). https://doi.org/10.1007/BF00220933
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DOI: https://doi.org/10.1007/BF00220933