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Intraspecific sequence variation of chloroplast DNA among the component species of evergreen broad-leaved forests in Japan

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Abstract

For the purpose of phylogeographic study of lucidophyllous (evergreen broad-leaved) forests in Japan, we surveyed intraspecific chloroplast DNA (cpDNA) variation in 41 component species of such forests. Intraspecific cpDNA variations were detected in 14 species. In 15 species and one species group, 16 non-coding cpDNA regions were examined to find intraspecific sequence variation. The extent of variation in these regions was compared. The largest amount of intraspecific variation was detected in the rps16 region. A relatively large amount of intraspecific variation was detected in the petD-rpoA, rpl16, and trnL-F regions. It is suggested that these regions of cpDNA would be useful for detecting intraspecific variation in plant species, and could provide valuable information for various research purposes.

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References

  • Chiang TY, Schaal BA, Peng CI (1998) Universal primers for amplification and sequencing a noncoding spacer between the atpB and rbcL genes of chloroplast DNA. Bot Bull Acad Sin (Taiwan) 39:245–250

    Google Scholar 

  • Denda T, Tomiyama H, Yokota M (2001) An intersectional hybrid in the genus Pteris (Pteridaceae) on Okinawa Island: evidence from nuclear and chloroplast DNA. Acta Phytotax Geobot 52:159–165

    Google Scholar 

  • Downie SR, Plunkett GM, Watson MF, Spalik K, Katz-Downie DS, Valiejo-Roman CM, Terentieva EI, Troitsky AV, Lee B-Y, Lahham J, El-Oqlah A (2001) Tribes and clades within Apiaceae subfamily Apioideae: the contribution of molecular data. Edinb J Bot 58:301–330

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem Bull 19:11–15

    Google Scholar 

  • Dumolin-Lapègue S, Kremer A, Petit RJ (1999) Are chloroplast and mitochondrial DNA variation species independent in oaks? Evolution 53:1406–1413

    Google Scholar 

  • Fujii N, Ueda K, Shimizu T (1996) Intraspecific sequence variation of chloroplast DNA in Japanese alpine plants. J Phytogeogr Taxon 44:72–81

    Google Scholar 

  • Fujii N, Ueda K, Watano Y, Shimizu T (1997) Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese "alpine" plants. J Plant Res 110:195–207

    CAS  Google Scholar 

  • Fujii N, Tomaru N, Okuyama K, Koike T, Mikami T, Ueda K (2002) Chloroplast DNA phylogeography of Fagus crenata (Fagaceae) in Japan. Plant Syst Evol 232:21–33

    Article  CAS  Google Scholar 

  • Hattori T, Minamiyama N (2001) Flora of the lucidophyllous forest in Kyusyu and northward in Japan (in Japanese with English abstract). Humans Nature 12:91–104

    Google Scholar 

  • Kelchner SA (2002) Group II introns as phylogenetic tools: structure, function, and evolutionary constraints. Am J Bot 89:1651–1669

    CAS  Google Scholar 

  • Maki M, Oiki S, Morita H, Takahashi H (1999) The effect of geographic range and dichogamy on genetic variability and population genetic structure in Trycyrtis section Flavae (Liliaceae). Am J Bot 86:287–292

    Google Scholar 

  • Nishizawa T, Watano Y (2000) Primer pairs suitable for PCR-SSCP analysis of chloroplast DNA in angiosperms. J Phytogeogr Taxon 48:63–66

    Google Scholar 

  • Noguchi J, Tasaka M, Iwabuchi M (1995) The historical differentiation process in Hemerocallis middendorfii (Liliaeae) of Japan based on restriction site variations of chloroplast DNA. J Plant Res 108:41–45

    CAS  Google Scholar 

  • Ohi T, Murata J (2000) Geographical variations in chloroplast DNA of Stachyurus macrocarpus Koidz. and Stachyurus praecox Sieb. et Zucc. (Stachyuraceae). Ogasawara Res 25:1–24

    Google Scholar 

  • Okaura T, Harada K (2002) Phylogeographical structure revealed by chloroplast DNA variation in Japanese Beech (Fagus crenata Blume). Heredity 88:322–329

    Article  CAS  PubMed  Google Scholar 

  • Okutsu K, Kuramoto N (1999) Analysis of genetic variability of Castanopsis sieboldii (Makino) Hatusima for transplant to Mt. Atago in Izu Oshima (in Japanese with English abstract). J JILA 62:533–538

    Google Scholar 

  • Seo A, Watanabe M, Hotta M, Murakami N (2001) Allozyme variation of the three varieties of Peucedanum japonicum Thunb. in Japan. Acta Phytotax Geobot 52:135–148

    Google Scholar 

  • Suzuki T, Murayama K, Kadono Y, Nagayoshi T (1997) Allozyme variation of Nuphar subintegerrimmum (Nymphaeaceae) at Kita-Nagaike pond, Kakogawa City, Hyogo Prefecture, Japan. Nat Hum Activities 2:47–52

    Google Scholar 

  • Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109

    CAS  PubMed  Google Scholar 

  • Tomaru N, Tsumura Y, Ohba K (1994) Genetic variation and population differentiation in natural populations of Cryptomeria japonica. Plant Species Biol 9:191–199

    Google Scholar 

  • Tomaru N, Mitsutsuji T, Takahashi M, Tsumura Y, Uchida K, Ohba K (1997) Genetic diversity in Fagus crenata (Japanese beech): influence of the distributional shift during the late-Quaternary. Heredity 78:241–251

    Article  Google Scholar 

  • Tsumura Y, Taguchi H, Suyama Y, Ohba K (1994) Geographical cline of chloroplast DNA variation in Abies mariesii. Theor Appl Genet 89:922–926

    Google Scholar 

  • Watanabe M, Serizawa S, Suganuma T (1996) Can we allow the alien Picea jezoensis var. hondoensis (Pinaceae) in Mt. Odaigahara? (in Japanese with English abstract). Veg Sci 13:107–110

    Google Scholar 

  • Whittemore AT, Schaal BA (1991) Interspecific gene flow in sympatric oaks. Proc Natl Acad Sci USA 88:2540–2544

    CAS  PubMed  Google Scholar 

  • Yatabe Y, Takamiya M, Murakami N (1998) Variation in the rbcL sequence of Stegnogramma pozoi subsp. Mollissima (Thelypteridaceae) in Japan. J Plant Res 111:557–564

    CAS  Google Scholar 

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Acknowledgements

We would like to thank Dr. Tamotsu Hattori for his generous support and valuable suggestions, especially his information on the collection sites for lucidophyllous forests. We would also like to thank Mr. Seiya Morinaga, Dr. Tsuguo Sakura, Dr. Nobuyuki Tanaka, Mr. Noritoshi Inagaki, Mr. Shungo Kariyama, Dr. Akihiro Seo, Ms. Miho Imada, Ms. Utami Makino, Ms. Yukimi Yoshida, Ms. Rika Takeuchi, Ms. Akemi Nakagoshi, and Ms. Keiko Aoki for their assistance in our collection of plant materials in Japan. We are grateful to Dr. Tzen-Yuh Chiang, Mr. Tsai-Wen Hsu, Mr. Shann-Jye Moore, Mr. Ho-Ming Chang, Dr. Chang-Fu Hsieh, Ms. I-Ling Lai in Taiwan, and to Dr. Do-Soon Cho in Jeju Island for their assistance with our fieldwork outside Japan. We would like to thank Mr. Hidenobu Funakoshi, Mr. Taku Fujita, Dr. Kayo Asami, Mr. Hiroaki Ishida, Mr. Yoshihiro Sawada, and Mr. Hiroji Akamatsu for sending plant materials. Finally, we would like to acknowledge Dr. Masayuki Takamiya for his identification of Arachniodes aristata.

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Authors and Affiliations

  1. Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan

    Kyoko Aoki & Noriaki Murakami

  2. Division of Biological Resources, Museum of Nature and Human Activities, Sanda, Japan

    Takeshi Suzuki

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  1. Kyoko Aoki
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  2. Takeshi Suzuki
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  3. Noriaki Murakami
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Correspondence to Kyoko Aoki.

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Aoki, K., Suzuki, T. & Murakami, N. Intraspecific sequence variation of chloroplast DNA among the component species of evergreen broad-leaved forests in Japan. J Plant Res 116, 337–344 (2003). https://doi.org/10.1007/s10265-003-0103-9

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  • DOI: https://doi.org/10.1007/s10265-003-0103-9

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