Sequence analyses of the ITS regions and the matK gene for determining phylogenetic relationships of Diospyros kaki (persimmon) with other wild Diospyros (Ebenaceae) species

Tree Genetics and Genomes

Volumn 4, Issue 2, 2008, Pages 149-158

  Yonemori, Keizo ^a   Honsho, Chitose ^b   Kanzaki, Shinya ^c   Ino, Hitofumi ^a   Ikegami, Ayako ^a   Kitajima, Akira ^a   Sugiura, Akira ^a   Parfitt, Dan E ^d  

^a KYOTO UNIVERSITY   (Japan)

^b UNIVERSITY OF MIYAZAKI   (Japan)

^c KINKI UNIVERSITY   (Japan)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Diospyros spp.; Genetic diversity

Indexed keywords

DIOSPYROS; DIOSPYROS EHRETIOIDES; DIOSPYROS GLANDULOSA; DIOSPYROS KAKI; DIOSPYROS LYCIOIDES; DIOSPYROS OLEIFERA; EBENACEAE;

EID: 38949144329     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-007-0096-y     Document Type: Article

References (40)

1. Bakhuizen van den Brink RC (1936) Revisio Ebenacearum Malayensium. Bull Jard Bot Buitenzorg Ser 3(15):205-216
2. Baldwin BG (1992) Phylogenetic utility of the internal transcribed spacers of nuclear ribosomal DNA in plant: an example from the Compositae. Mol Phylogenet Evol 1:3-16
3. Campbell CS, Wojciechowski MF, Baldwin BG, Alice LA, Donoghue MJ (1997) Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol Biol Evol 14:81-90
4. Carriere EA (1872) Diospyros roxburghii. Rev Hortic 44:253-258
5. Choi Y-A, Tao R, Yonemori K, Sugiura A (2003a) Genomic in situ hybridization between persimmon (Diospyros kaki) and several wild species of Diospyros. J Jpn Soc Hortic Sci 72:385-399
6. Choi Y-A, Tao R, Yonemori K, Sugiura A (2003b) Genomic distribution of three repetitive DNAs in cultivated hexaploid Diospyros spp. (D. kaki and D. virginiana) and their wild relatives. Genes Genet Syst 78:301-308
7. Choi Y-A, Tao R, Yonemori K, Sugiura A (2003c) Physical mapping of 45S rDNA by fluorescent in situ hybridization in persimmon (Diospyros kaki) and its wild relatives. J Hortic Sci Biotech 78:265-271
8. Choi Y-A, Tao R, Yonemori K, Sugiura A (2003d) Simultaneous visualization of 5S and 45S rDNAs in persimmon (Diospyros kaki) and several wild relatives (Diospyros spp.) by fluorescent in situ hybridization (FISH) and multicolor FISH (MCFISH). J Am Soc Hortic Sci 128:736-740
9. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11-15
10. Farris JS, Kallersio M, Kluge AG, Bult C (1995) Testing significance of incongruence. Cladistics 10:315-320
11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
12. Ferguson CJ, Jansen RK (2002) A chloroplast DNA phylogeny of eastern Phlox (Polemoniaceae): implications of congruence and incongruence with the ITS phylogeny. Am J Bot 89:1321-1335
13. Food and Agriculture Organization (FAO) (2006) FAOSTAT. http://faostat.fao.org/
14. Grubov VI (1967) Family Ebenaceae. In: Shishkin BK, Bobrov EG (eds) Flora of the U.S.S.R. Israel Program for Scientific Translations, Jerusalem 18:349-355
15. Hardig TM, Soltis PS, Soltis DE (2000) Diversification of the North American shrub genus Ceanothus (Rhamnaceae): conflicting phylogenies from nuclear ribosomal DNA and chloroplast DNA. Am J Bot 87:108-123
16. Hemsley WB (1911) Persimmons. Kew Bull 234-245
17. Hiern WP (1873) A monograph of Ebenaceae. Trans Camb Phil Soc 12:227-230
18. Johnson LA, Soltis DE (1995) Phylogenetic inference in Saxifrogaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann Mo Bot Gard 82:371-382
19. Kikuchi A (1948) Pomology. Part I. Yokendo, Tokyo, Japan, pp 347-400
20. Kollipara KP, Singh RJ, Hymowitz T (1997) Phylogenetic and genomic relationships in the genus Glycine Willd. based on sequences from the ITS region of nuclear rDNA. Genome 40:57-68
21. Lashermes P, Combes MC, Trouslot P, Charrier A (1997) Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet 94:947-955
22. Maddison DR (1991) The discovery and importance of multiple islands of most-parsimonious trees. Syst Zool 40:315-328
23. Namikawa I, Higashi M (1928) On the number of chromosomes in Diospyros kaki L. f. and Diospyros lotus L. Bot Mag 42:436-438
24. Ng FSP (1978) Diospyros roxburghii and the origin of Diospyros kaki. Malays For 41:43-50
25. Phengklai C (1978) Ebenaceae of Thailand. Thai For Bull 11:1-103
26. Posada D, Crandall KA (1998) ModelTest: testing the model of DNA substitution. Bioinformatics 14:817-818
27. Sang T, Crawford DJ, Stuessy TF (1995) Documentation of retuculate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: implications for biogeography and concerted evolution. Proc Nat Acad Sci USA 92:6813-6817
28. Sang T, Crawford DJ, Stuessy TF (1997) Chloroplast DNA phylogeny, reticulate evolution, and Biogeography of Paeonia (Paeoniaceae). Am J Bot 84:1120-1136
29. Soltis DE, Kuzoff RK (1995) Discordance between molecular and chloroplast phylogenies in the Heuchera group (Saxifragaceae). Evolution 49:727-742
30. Soltis DE, Soltis PS, Collier TG, Edgerton ML (1991) Variation within and among genera of the Heuchera group: evidence of chloroplast capture and paraphyly. Am J Bot 78:1091-1112
31. Soltis DE, Johnson LA, Looney C (1996) Discordance between ITS and chloroplast topologies in the Boykinia group (Saxifragaceae). Syst Bot 21:169-176
32. Somego M (1978) Chromosome number of Diospyros roxburghii. Malays For 41:51-52
33. *: phylogenetic analysis using parsimony. Ver. 4. Sinauer Associates, Sunderland, MA, USA
34. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
35. Wendel JF, Schnabel A, Seelanan T (1995) An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol Phylogenet Evol 4:298-313
36. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Sninsky J, White T (eds) PCR protocols: A guide to methods and applications. Academic, San Diego, CA, USA
37. Wilson EH (1929) China-mother of gardens. The Stradford Company, Boston, MA, p 357
38. Yonemori K, Kanzaki S, Parfitt DE, Utsunomiya N, Subhadrabandhu S, and Sugiura A (1998) Phylogenetic relationship of Diospyros kaki (persimmon) to Diospyros spp. (Ebenaceae) of Thailand and four temperate zone Diospyros spp. from an analysis of RFLP variation in amplified cpDNA. Genome 41:173-182
39. Yonemori K, Sugiura A, Yamada M (2000) Persimmon genetics and breeding. pp 191-225. In : Janick J (ed) Plant Breeding Reviews 19. Wiley, New York
40. Zhuang D, Kitajima A, Ishida M, Sobajima Y (1990) Chromosome number of Diospyros kaki cultivars. J Jpn Soc Hortic Sci 59:289-297