A Phylogenetic Analysis of the Plastid matK Gene with Emphasis on Melanthiaceae sensu lato

Abstract

The presented matK tree primarily agrees well with the previously presented rbcL tree and combined rbcL + atpB + 18SrDNA tree. According to the matK tree, the monocotyledons are monophyletic with 100 % bootstrap support. Acorus diverges first from all other monocotyledons (90 % bootstrap support) in which two major clades are recognized: one (89 %) consisting of Alismatanae and Tofieldia (Nartheciaceae), and the other (< 50 %) comprising Lilianae, Commelinanae and Nartheciaceae other than Tofieldia. Within the latter major clade, Petrosavia and Japonolirion (Nartheciaceae) (82 %) diverge first from the remaining taxa (< 50 %) in which two clades are formed: one (81 %) consisting of Pandanales, Dioscoreales and Nartheciaceae-Narthecioideae, and the other (< 50 %) comprising Liliales, Asparagales and Commelinanae. In the former clade, Dioscoreales and Narthecioideae are grouped together (88 %). In the latter clade, Asparagales and Commelinanae are grouped together (< 50 %). Differences between the matK and rbcL tree topologies appear in the positions of Tricyrtis (Calochortaceae) and Dracaenaceae. Differences between the matK and combined rbcL + atpB + 18SrDNA tree topologies exist in the positions of the Petrosavia-Japonolirion pair (Nartheciaceae) and Pandanales. The stop codon position of the matK gene appears to be highly variable among the monocotyledons, especially in the Liliales.

Key words

Japonolirion - matK gene - Melanthiaceae - molecular phylogeny - monocotyledons - Petrosavia - stop codon

References

• 01 Ambrose,  J. D.. (1980) A re-evolution of the Melanthioideae (Liliaceae) using numerical analyses. Petaloid Monocotyledons, Linnean Society Symposium Series no. 8. Brickell, C. D., Cutler, D. F., and Gregory, M., eds. London; Academic Press pp. 65-81
• 02 Cameron,  K. M.. (1998) Systematics of heteromycotrophic Petrosaviaceae. Monocots II and Grasses III Conference. Sydney; Abstracts p. 64
• 03 Chase,  M. W.,, Duvall,  M. R.,, Hills,  H. G.,, Conran,  J. G.,, Cox,  A. V.,, Eguiarte,  L. E.,, Hartwell,  J.,, Fay,  M. F.,, Caddick,  L. R.,, Cameron,  K. M.,, and Hoot,  S.. (1995) Molecular systematics of Lilianae. Monocotyledons: Systematics and Evolution. Rudall, P. J., Cribb, P. J., Cutler, D. F., and Humphries, C. J., eds. Kew; Royal Botanic Gardens pp. 109-137
• 04 Chase,  M. W.,, Soltis,  D. E.,, Olmstead,  R. G.,, Morgan,  D.,, Les,  D. H.,, Mishler,  B. D.,, Duvall,  M. R.,, Price,  R. A.,, Hills,  H. G.,, Qiu,  Y-L.,, Kron,  K. A.,, Rettig,  J. H.,, Conti,  E.,, Palmer,  J. D.,, Manhart,  J. R.,, Sytsma,  K. J.,, Michaels,  H. J.,, Kress,  W. J.,, Karol,  K. G.,, Clark,  W. D.,, Hedrén,  M.,, Gaut,  B. S.,, Jansen,  R. K.,, Kim,  K.-J.,, Wimpee,  C. F.,, Smith,  J. F.,, Furnier,  G. R.,, Strauss,  S. H.,, Xiang,  Q.-Y.,, Plunkett,  G. M.,, Soltis,  P. S.,, Swensen,  S. M.,, Williams,  S. E.,, Gadek,  P. A.,, Quinn,  C. J.,, Eguiarte,  L. E.,, Golenberg,  E.,, Learn,  G. H., Jr.,, Graham,  S. W.,, Barrett,  S. C. H.,, Dayanandan,  S.,, and Albert,  V. A.. (1993);  Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL.  Ann. Missouri Bot. Gard.. 80 528-580
• 05 Chase,  M. W.,, Soltis,  D. E.,, Soltis,  P. S.,, Rudall,  P. J.,, Fay,  M. F.,, Hahn,  W. H.,, Sullivan,  S.,, Joseph,  J.,, Molvray,  M.,, Kores,  P. J.,, Givnish,  T. J.,, Sytsma,  K. J.,, and Chris Pires,  J.. (2000) Higher-level systematics of the monocotyledons: an assessment of current knowledge and a new classification. Monocots: systematics and evolution. Wilson, K. L. and Morrison, D. A., eds. Melbourne; CSIRO pp. 3-16
• 06 Cronquist,  A.. (1988) The Evolution and Classification of Flowering Plants, 2nd ed. The New York Botanical Garden pp. 555
• 07 Dahlgren,  R. M. T.,, Clifford,  H. T.,, and Yeo,  P. F.. (1985) The Families of the Monocotyledons. Berlin; Springer-Verlag pp. 520
• 08 Deyl,  M.. (1955);  The evolution of the plants and the taxonomy of the monocotyledons.  Acta Musei Nationalis Pragae, Botanica, no. 3,. 11 B 1-143
• 09 Ems,  S. C.,, Morden,  C. W.,, Dixon,  C. K.,, Wolfe,  K. H.,, Depamphilis,  C. W.,, and Palmer,  J. D.. (1995);  Transcription, splicing and editing of plastid RNAs in the nonphotosynthetic plant Epifagus virginiana. .  Pl. Mol. Biol.. 29 721-733
• 10 Goldblatt,  P.. (1995) The Status of Dahlgren's orders Liliales and Melanthiales. Monocotyledons: systematics and evolution. Rudall, P. J., Cribb, P. J., Cutler, D. F., and Humphries, C. J., eds. Kew; Royal Botanic Gardens pp. 181-200
• 11 Hatusima,  S.. (1971) Flora of the Ryukyus (including Amami Islands, Okinawa Islands, and Sakishima Archipelago). Naha; Okinawa-Seibutsukyoiku-Kenkyukai pp. 940 [in Japanese]
• 12 Huber,  H.. (1996);  Die Samenmerkmale und Verwandtschaftsverhältnisse der Liliifloren.  Mitt. Bot. München. 8 219-538
• 13 Johnson,  L. A., and Soltis,  D. E.. (1995);  Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences.  Ann. Missouri Bot. Gard.. 82 149-175
• 14 Kawahara,  T.,, Murakami,  N.,, Setoguchi,  H.,, and Tsuyama,  Y.. (1995);  Procedures of plant DNA extraction for phylogenetic analysis.  Proc. Jap. Soc. Pl. Tax.. 11 13-32
• 15 Kazempour Osaloo,  S., and Kawano,  S.. (1999);  Molecular systematics of Trilliaceae II. Phylogenetic analyses of Trillium and its allies using sequences of rbcL and matK gene of cpDNA and internal transcribed spacers (ITS) of 18S-26S nuclear ribosomal DNA.  Plant Species Biol.. 14 75-94
• 16 Kazempour Osaloo,  S.,, Utech,  F. H.,, Ohara,  M.,, and Kawano,  S.. (1999);  Molecular systematics of Trilliaceae I. Phylogenetic analyses of Trillium using matK gene sequences.  J. Plant Res.. 112 35-49
• 17 Kubitzki,  K.. (1998 a) Conspectus of Families Treated in this Volume. The Families and Genera of Vascular Plants, Vol. III. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 49-52
• 18 Kubitzki,  K.. (1998 b) Conspectus of Families Treated in this Volume. The Families and Genera of Vascular Plants, Vol. IV. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 1-4
• 19 Liston,  A., and Kadereit,  J. W.. (1995);  Chloroplast DNA evidence for introgression and long distance dispersal in the desert annual Senecio flavus (Asteraceae).  Pl. Syst. Evol.. 197 33-41
• 20 Ooi,  K.,, Endo,  Y.,, Yokoyama,  J.,, and Murakami,  N.. (1995);  Useful primer designs to amplify DNA fragments of the plastid gene matK from angiosperm plants.  J. Jap. Bot.. 70 328-331
• 21 Stant,  M. Y.. (1970) Anatomy of Petrosavia stellaris Becc., a saprophytic monocotyledon. New Research in Plant Anatomy. Robson, N. K. B., Cutler, D. F., and Gregory, M., eds. London; Academic Press pp. 147-161
• 22 Steele,  K. P., and Vilgalys,  R.. (1994);  Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK.  Syst. Bot.. 19 126-142
• 23 Sugita,  M.,, Shinozaki,  K.,, and Sugiura,  M.. (1985);  Tabacco chloroplast tRNA^Lys(UUU) gene contains a 2.5-kilobase-pair intron: an open reading frame and a conserved boundary sequence in the intron.  Proc. Natl. Acad. Sci. U.S.A.. 82 3557-3561
• 24 Swofford,  D. L.. (1998) PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sunderland; Sinauer
• 25 Takhtajan,  A.. (1997) Diversity and Classification of Flowering Plants. New York; Columbia Univ. Press pp. 643
• 26 Tamura,  M. N.. (1995);  A karyological review of the orders Asparagales and Liliales (Monocotyledonae).  Feddes Repert.. 106 83-111
• 27 Tamura,  M. N.. (1998 a) Liliaceae. The Families and Genera of Vascular Plants, Vol. III. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 343-353
• 28 Tamura,  M. N.. (1998 b) Melanthiaceae. The Families and Genera of Vascular Plants, Vol. III. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 369-380
• 29 Tamura,  M. N.. (1998 c) Nartheciaceae. The Families and Genera of Vascular Plants, Vol. III. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 381-392
• 30 Tamura,  M. N.. (1998 d) Trilliaceae. The Families and Genera of Vascular Plants, Vol. III. Kubitzki, K., ed. Berlin; Springer-Verlag pp. 444-452
• 31 Tamura,  M. N.,, Schwarzbach,  A. E.,, Kruse,  S.,, and Reski,  R.. (1997);  Biosystematic studies on the genus Polygonatum (Convallariaceae) IV. Molecular phylogenetic analysis based on restriction site mapping of the chloroplast gene trnK.  Feddes Repert.. 108 159-168
• 32 Tanaka,  N. Y.. (1998);  Phylogenetic and taxonomic studies on Helonias, Ypsilandra and Heloniopsis III. Taxonomic revision.  J. Jap. Bot.. 73 102-115
• 33 The Angiosperm Phylogeny Group. (1998);  An ordinal classification for the families of flowering plants.  Ann. Missouri Bot. Gard.. 85 531-553
• 34 Thorne,  R. F.. (1992);  Classification and geography of the flowering plants.  Bot. Rev.. 58 225-348
• 35 Tomlinson,  P. B.. (1982) Helobiae (Alismatidae). Anatomy of the Monocotyledons, Vol. 7. Metcalfe, C. R., ed. Oxford; Clarendon Press p. 559
• 36 Walker,  J. W.. (1986);  Classification and evolution of the monocotyledons.  Amer. J. Bot.. 73 (6) 746 (Abstract)
• 37 Yamashita,  J., and Tamura,  M. N.. (2000) Molecular phylogeny of the Convallariaceae (Asparagales). Monocots: systematics and evolution. Wilson, K. L. and Morrison, D. A., eds. Melbourne; CSIRO pp. 387-400

Section Editor: M. Hasebe