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Tree Genetics & Genomes

, Volume 2, Issue 3, pp 132–139 | Cite as

Phylogeny of Castanea (Fagaceae) based on chloroplast trnT-L-F sequence data

  • Ping Lang
  • Fenny DaneEmail author
  • Thomas L. Kubisiak
Original Paper

Abstract

Species in the genus Castanea are widely distributed in the deciduous forests of the Northern Hemisphere from Asia to Europe and North America. They show floristic similarity but differences in chestnut blight resistance especially among eastern Asian and eastern North American species. Phylogenetic analyses were conducted in this study using sequences of three chloroplast noncoding trnT-L-F regions. The trnT-L region was found to be the most variable and informative region. The highest proportion of parsimony informative sites, more and larger indels, and higher pairwise distances between taxa were obtained at trnT-L than at the other two regions. The high A+T values (74.5%) in the Castanea trnT-L region may explain the high proportion of transversions found in this region where as comparatively lower A+T values were found in the trnL intron (68.35%) and trnL-F spacer (70.07%) with relatively balanced numbers of transitions and transversions. The genus Castanea is supported as a monophyletic clade, while the section Eucastanon is paraphyletic. C. crenata is the most basal clade and sister to the remainder of the genus. The three Chinese species of Castanea are supported as a single monophyletic clade, whose sister group contains the North American and European species. There is consistent but weak support for a sister–group relationship between the North American species and European species.

Keywords

Fagaceae Castanea trnT-L-F Phylogenetics 

Notes

Acknowledgements

We thank Cliff Parks of the University of North Carolina, Sandra Anagnostakis of the Connecticut Agricultural Research Station, and Alexandru-Lucian Curtu for providing samples.

References

  1. Applequist WL, Wallace RS (2002) Deletions in the plastid trnT-trnL intergenic spacer define clades within Cactaceae subfamily Cactoideae. Plant Syst Evol 231:153–162CrossRefGoogle Scholar
  2. Bakker FT, Culham A, Gomez-Martinez R, Carvalho J, Compton J, Dawtrey R, Gibby M (2000) Patterns of nucleotide substitution in angiosperm cpDNA trnL (UAA)-trnF (GAA) regions. Mol Biol Evol 17:1146–1155PubMedGoogle Scholar
  3. Clegg MT, Zurawaki G (1992) Chloroplast DNA and the study of plant phylogeny: present status and future prospects. In: Doyle JJ (ed) Molecular systematics of plants. Chapman & Hall, New York, pp 275–294Google Scholar
  4. Cummings M, King L, Kellogg E (1994) Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol Biol Evol 11:1–8PubMedGoogle Scholar
  5. Dane F, Hawkins LK, Huang H (1999) Genetic variation and population structure of Castanea pumila var. ozarkensis. J Am Soc Hortic Sci 124:666–670Google Scholar
  6. Dane F, Lang P, Huang H, Fu Y (2003) Intercontinental genetic divergence of Castanea species in eastern Asia and eastern North America. Heredity 91:314–321CrossRefPubMedGoogle Scholar
  7. Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  8. Fineschi S, Taurchini D, Villani F, Vendramin GG (2000) Chloroplast DNA polymorphism reveals little geographical structure in Castanea sativa mill. (Fagaceae) throughout southern European countries. Mol Ecol 9:1495–1503CrossRefPubMedGoogle Scholar
  9. Fukuda T, Yokoyama J, Ohashi H (2001) Phylogeny and biogeography of the genus Lycium (Solanaceae): inferences from chloroplast DNA sequences. Mol Phylogenet Evol 19:246–258CrossRefPubMedGoogle Scholar
  10. Graham SW, Patrick A Reeves, Analiese CE Burns, Olmstead RG (2000) Microstructural changes in noncoding chloroplast DNA: interpretation, evolution, and utility of indels and inversions in basal angiosperm phylogenetic inference. Int J Plant Sci 161:S83–S96CrossRefGoogle Scholar
  11. Graves AH (1950) Relative blight resistance in species and hybrids of Castanea. Phytopathology 49:1125–1131Google Scholar
  12. Huang H, Dane F, Norton JD (1994) Allozyme diversity in Chinese, Seguin and American chestnut (Castanea spp.). Theor Appl Genet 88:981–985CrossRefGoogle Scholar
  13. Huang H, Carey WA, Dane F, Norton JD (1996) Evaluation of Chinese chestnut cultivars for resistance to Cryphonectria parasitica. Plant Dis 80:45–47Google Scholar
  14. Huang H, Dane F, Kubisiak TL (1998) Allozyme and RAPD analysis of the genetic diversity and geographic variation in wild populations of the American chestnut (Fagaceae). Am J Bot 85:1013–1021CrossRefGoogle Scholar
  15. Jaynes R (1975) Chestnut. In: Moore J (ed) Advances in fruit breeding. Purdue Univ. Press, West Lafayette, pp 490–503Google Scholar
  16. Johnson GP (1988) Revision of Castanea sect. Balanocastanon (Fagaceae). J Arnold Arbor 69:25–49Google Scholar
  17. Kelchner SA (2000) The evolution of non-coding chloroplast DNA and its application in plant systematics. Ann Mo Bot Gard 87:482–498CrossRefGoogle Scholar
  18. Kelchner SA, Wendel JF (1996) Hairpins create minute inversions in non-coding regions of chloroplast DNA. Curr Genet 30:259–262CrossRefPubMedGoogle Scholar
  19. Kelchner SA, Clark LG (1997) Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Mol Phylogenet Evol 8:385–397CrossRefPubMedGoogle Scholar
  20. Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120CrossRefPubMedGoogle Scholar
  21. Lang P, Huang H (1999) Genetic diversity and geographic variation in natural populations of the endemic Castanea species in China. Acta Bot Sin 41:651–657 (in Chinese)Google Scholar
  22. Levinson G, Gutman G (1987) Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol 4:203–221PubMedGoogle Scholar
  23. Manos PS, Stanford AM (2001) The historical biogeography of Fagaceae: tracking the tertiary history of temperate and subtropical forests of the Northern Hemisphere. Int J Plant Sci 162:S77–S93CrossRefGoogle Scholar
  24. Manos PS, Zhou ZK, Cannon CH (2001) Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. Int J Plant Sci 162:1361–1379CrossRefGoogle Scholar
  25. McDade LA, Moody ML (1999) Phylogenetic relationships among Acanthaceae: evidence from noncoding trnL-trnF chloroplast DNA sequences. Am J Bot 86:70–80CrossRefGoogle Scholar
  26. Morton BR (1995) Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc Natl Acad Sci USA 92:9717–9721PubMedCrossRefGoogle Scholar
  27. Nixon KC, Crepet WL (1989) Trigonobalanus (Fagaceae): taxonomic status and phylogenetic relationships. Am J Bot 6:828–841CrossRefGoogle Scholar
  28. Olmstead R, Palmer JD (1994) Chloroplast DNA systematics: a review of methods and data analysis. Am J Bot 81:1205–1224CrossRefGoogle Scholar
  29. Qui Y, Chase MW, Parks CR (1995) A chloroplast DNA phylogenetic study of the eastern Asia-eastern North America disjunct section Rytidospermum of Magnolia (Magnoliaceae). Am J Bot 82:1582–1588CrossRefGoogle Scholar
  30. Shaw J, Lickey EB, Beck JT, Farmer SB, Liu W, Miller J, Siripun KC, Winder CT, Schilling EE, Small RL (2005) The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot 92:142–166CrossRefGoogle Scholar
  31. Simmons MP, Ochotreana H (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst Biol 49:369–381CrossRefPubMedGoogle Scholar
  32. Small RL, Ryburn JA, Cronn RC, Seelanan T, Wendel JF (1998) The tortoise and the hare: choosing between noncoding plastome and nuclear Adh sequences for phylogeny reconstruction in a recently diverged plant group. Am J Bot 85:1301–1315CrossRefGoogle Scholar
  33. Soltis DE, Kuzoff RK (1995) Discordance between nuclear and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49:727–742CrossRefGoogle Scholar
  34. Stanford A (1998) The biogeography and phylogeny of Castanea, Fagus, and Juglans based on matK and ITS sequence data. UNC, Chapel HillGoogle Scholar
  35. Swofford DL (2000) PAUP. Phylogenetic Analysis Using Parsimony. Version 4. Sinauer Associates, Sunderland, MassachusettsGoogle Scholar
  36. Taberlet P, Gielly L, Pautou G, Bouvet J (1991) Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol 17:1105–1109PubMedCrossRefGoogle Scholar
  37. Vijverberg K, Bachmann K (1999) Molecular evolution of a tandemly repeated trnF(GAA) gene in the chloroplast genomes of Microseris (Asteraceae) and the use of structural mutations in phylogenetic analyses. Mol Biol Evol 16:1329–1340PubMedGoogle Scholar
  38. Villani F, Pigliucci M, Benedettelli S, Cherubini M (1991) Genetic differentiation among Turkish chestnut (Castanea sativa Mill) populations. Heredity 66:131–136CrossRefGoogle Scholar
  39. Wen J (1999) Evolution of eastern Asian and eastern North American disjunct distributions in flowering plants. Annu Rev Ecol Syst 30:421–455CrossRefGoogle Scholar
  40. Zuker M, Mathews DH, Turner DH (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide in RNA biochemistry and biotechnology. NATO ASI Series, Kluwer, BostonGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  1. 1.Department of HorticultureAuburn UniversityAuburnUSA
  2. 2.USDA-Forest ServiceSouthern Institute of Forest GeneticsSaucierUSA

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