Phylogeny, duplication, and intraspecific variation of Adh sequences in new world diploid cottons (Gossypium L., Malvaceae)

Molecular Phylogenetics and Evolution

Volumn 16, Issue 1, 2000, Pages 73-84

  Small, Randall L ^a   Wendel, Jonathan F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; CHLOROPLAST DNA; GENE DUPLICATION; GENETIC POLYMORPHISM; GENETIC VARIANCE; GOSSYPIUM GOSSYPIOIDES; INTERNAL TRANSCRIBED SPACER; MEXICO; MONOPHYLY; MORPHOLOGY; PERU; PHYLOGENY; PLANT GENOME; UNITED STATES;

GOSSYPIOIDES; GOSSYPIUM; GOSSYPIUM GOSSYPIOIDES; GOSSYPIUM HIRSUTUM; MALVACEAE;

EID: 0033927114     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0750     Document Type: Article

References (60)

1. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution. 42:1988;795-803.
2. Brubaker C. L., Koontz J. A., Wendel J. F. Bidirectional cytoplasmic and nuclear introgression in the New World cottons, Gossypium barbadense and G. hirsutum (Malvaceae). Am. J. Bot. 80:1993;1203-1208.
3. Brubaker C. L., Paterson A. H., Wendel J. F. Comparative genetic mapping of allotetraploid cotton and its diploid progenitors. Genome. 42:1999;184-203.
4. Brubaker C. L., Wendel J. F. Reevaluating the origin of domesticated cotton (Gossypium hirsutum; Malvaceae) using nuclear restriction fragment length polymorphisms (RFLPs). Am. J. Bot. 81:1994;1309-1326.
5. Buckler E. S., Holtsford T. P. Zea systematics: Ribosomal ITS evidence. Mol. Biol. Evol. 13:1996a;612-622.
6. Buckler E. S., Holtsford T. P. Zea ribosomal repeat evolution and substitution patterns. Mol. Biol. Evol. 13:1996b;623-632.
7. Chang C., Meyerowitz E. M. Molecular cloning and DNA sequence of the Arabidopsis thaliana alcohol dehydrogenase gene. Proc. Natl. Acad. Sci. USA. 83:1986;1408-1412.
8. Charlesworth D., Liu F.-L., Zhang L. The evolution of the alcohol dehydrogenase gene family by loss of introns in plants of the genus Leavenworthia (Brassicaceae). Mol. Biol. Evol. 15:1998;552-559.
9. Clegg M. T., Cummings M. P., Durbin M. L. The evolution of plant nuclear genes. Proc. Natl. Acad. Sci. USA. 94:1997;7791-7798.
10. Cronn R. C., Zhao X., Paterson A. H., Wendel J. F. Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. J. Mol. Evol. 42:1996;685-705.
11. DeJoode D. R. Molecular Insights into Speciation in the Genus Gossypium L. (Malvaceae). 1992;Iowa State Univ. Ames.
12. Dennis E. S., Gerlach W. L., Pryor A. J., Bennetsen J. L., Inglis A., Llewellyn D., Sachs M. M., Ferl R. J., Peacock W. J. Molecular analysis of the alcohol dehydrogenase (Adh1) gene of maize. Nucleic Acids Res. 12:1984;3983-4000.
13. Dennis E. S., Sachs M. M., Gerlach W. L., Finnegan E. J., Peacock W. J. Molecular analysis of the alcohol dehydrogenase 2 (Adh2) gene of maize. Nucleic Acids Res. 13:1985;727-743.
14. Doyle J. J., Doyle J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19:1987;11-15.
15. Drouin G., Moniz de Sá M. Loss of introns in the pollen-specific actin gene subfamily members of potato and tomato. J. Mol. Evol. 45:1997;509-513.
16. Endrizzi J. E., Turcotte E. L., Kohel R. J. Genetics, cytology, and evolution of Gossypium. Adv. Genet. 23:1985;271-375.
17. Ford V. S., Thomas B. R., Gottlieb L. D. The same duplication accounts for the PgiC genes in Clarkia xantiana and C. lewisii (Onagraceae). Syst. Bot. 20:1995;147-160.
18. Fryxell P. A. Malvaceae of Mexico. Syst. Bot. Monographs. 25:1988;1-522.
19. Fryxell P. A. A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea. 2:1992;108-165.
20. Gaut B. S., Clegg M. T. Molecular evolution of the Adh1 locus in the genus Zea. Proc. Natl. Acad. Sci. USA. 90:1993;5095-5099.
21. Goloubinoff P., Pääbo S., Wilson A. C. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc. Natl. Acad. Sci. USA. 90:1993;1997-2001.
22. Gottlieb L. D., Ford V. S. Phylogenetic relationships among the sections of Clarkia (Onagraceae) inferred from the nucleotide sequences of PgiC. Syst. Bot. 21:1996;45-62.
23. Gottlieb L. D., Ford V. S. A recently silenced, duplicate PgiC locus in Clarkia. Mol. Biol. Evol. 14:1997;125-132.
24. Häger K.-P., Müller B., Wind C., Erbach S., Fischer H. Evolution of legumin genes: Loss of an ancestral intron at the beginning of angiosperm diversification. FEBS Lett. 387:1996;94-98.
25. Hanson M. A., Gaut B. S., Stec A. O., Fuerstenberg S. I., Goodman M. M., Coe E. H., Doebley J. F. Evolution of anthocyanin biosynthesis in maize kernels: The role of regulatory and enzymatic loci. Genetics. 143:1996;1395-1407.
26. Hilton H., Gaut B. S. Speciation and domestication in maize and its wild relatives: Evidence from the globulin-1 gene. Genetics. 150:1998;863-872.
27. Howe G. T., Bucciaglia P. A., Hackett W. P., Furnier G. R., Cordonnier-Pratt M.-M., Gardner G. Evidence that the phytochrome gene family in Black Cottonwood has one PHYA locus and two PHYB loci but lacks members of the PHYC/F and PHYE subfamilies. Mol. Biol. Evol. 15:1998;160-175.
28. Jukes T. H., Cantor C. R. Evolution of protein molecules. Munro H. N. Mammalian Protein Metabolism. 1969;21-132 Academic Press, New York.
29. Klein J., Sato A., Nagl S., O'huigin C. Molecular trans-species polymorphism. Annu. Rev. Ecol. Syst. 29:1998;1-21.
30. Liu F., Charlesworth D., Kreitman M. The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase locus in the plant genus Leavenworthia. Genetics. 151:1999;343-357.
31. Loguercio L. L., Wilkins T. A. Structural analysis of a hmg-coA-reductase pseudogene: Insights into evolutionary processes affecting the hmgr gene family in allotetraploid cotton (Gossypium hirsutum L.). Curr. Genet. 34:1998;241-249.
32. Miyashita N. T., Innan H., Terauchi R. Intra- and interspecific variation of the alcohol dehydrogenase locus region in wild plants Arabis gemmifera and Arabidopsis thaliana. Mol. Biol. Evol. 13:1996;433-436.
33. Nagl S., Tichy H., Mayer W. E., Takahata N., Klein J. Persistence of neutral polymorphisms in Lake Victoria cichlid fish. Proc. Natl. Acad. Sci. USA. 95:1998;14238-14243.
34. Ohta T. Further examples of evolution by gene duplication revealed through DNA sequence comparisons. Genetics. 138:1994;1331-1337.
35. Paterson A. H., Brubaker C. L., Wendel J. F. A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Pl. Mol. Biol. Rep. 11:1993;122-127.
36. Perry D. J., Furnier G. R. Pinus banksiana has at least seven expressed alcohol dehydrogenase genes in two linked groups. Proc. Natl. Acad. Sci. USA. 93:1996;13020-13023.
37. Richman A. D., Kohn J. R. Self-incompatibility alleles from Physalis: Implications for historical inference from balanced genetic polymorphisms. Proc. Natl. Acad. Sci. USA. 96:1999;168-172.
38. Rieseberg L. H., Wendel J. F. Introgression and its consequences. Harrison R. Hybrid Zones and the Evolutionary Process. 1993;70-109 Oxford Univ. Press, New York.
39. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:1987;406-425.
40. Sambrook J., Fritsch E. F., Maniatis T. Molecular Cloning, A Laboratory Manual. 1989;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
41. Sanderson M. J., Doyle J. J. Reconstruction of organismal and gene phylogenies from data on multigene families: Concerted evolution, homoplasy, and confidence. Syst. Biol. 41:1992;4-17.
42. Sang T., Donoghue M. J., Zhang D. Evolution of the alcohol dehydrogenase genes in Peonies (Paeonia): Phylogenetic relationships of putative nonhybrid species. Mol. Biol. Evol. 14:1997;994-1007.
43. Seelanan T., Schnabel A., Wendel J. F. Congruence and consensus in the cotton tribe (Malvaceae). Syst. Bot. 22:1997;259-290.
44. Seelanan T., Brubaker C. L., Stewart J. McD., Craven L. A., Wendel J. F. Molecular systematics of Australian Gossypium section Grandicalyx (Malvaceae). Syst. Bot. 24:1999;183-208.
45. Small R. L. Evolution of the Alcohol Dehydrogenase Gene Family in Diploid and Tetraploid Gossypium L. 1999;Iowa State Univ. Ames.
46. Small R. L., Ryburn J. A., Cronn R. C., Seelanan T., Wendel J. F. 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. 85:1998;1301-1315.
47. Small R. L., Ryburn J. A., Wendel J. F. Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Mol. Biol. Evol. 16:1999;491-501.
48. Stewart J. McD. Potential for crop improvement with exotic germplasm and genetic engineering. Constable G. A., Forrester N. W. Challenging the Future: Proceedings of the World Cotton Research Conference-1. 1995;313-327 CSIRO, Melbourne.
49. Swofford, D. L. 1999, PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4.0b2, Sinauer, Sunderland, MA.
50. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
51. Trick M., Dennis E. S., Edwards K. J. R., Peacock W. J. Molecular analysis of the alcohol dehydrogenase gene family of barley. Pl. Mol. Biol. 11:1988;147-160.
52. Wendel J. F. Cotton. Smartt J., Simmonds N. W. Evolution of Crop Plants. 1995;358-366 Longman Scientific, Essex.
53. Wendel J. F., Brubaker C. L., Percival A. E. Genetic diversity in Gossypium hirsutum and the origin of upland cotton. Am. J. Bot. 79:1992;1291-1310.
54. Wendel J. F., Doyle J. J. Phylogenetic incongruence: Window into genome history and molecular evolution. Soltis D., Soltis P., Doyle J. Molecular Systematics of Plants. 1998;Chapman & Hall, New York.
55. Wendel J. F., Olson P. D., Stewart J. McD. Genetic diversity, introgression, and independent domestication of Old World cultivated cottons. Am. J. Bot. 76:1989;1795-1806.
56. Wendel J. F., Percy R. G. Allozyme diversity and introgression in the Galapagos Islands endemic Gossypium darwinii and its relationship to continental G. barbadense. Biochem. Syst. Ecol. 18:1990;517-528.
57. Wendel J. F., Albert V. A. Phylogenetics of the cotton genus (Gossypium): Character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Syst. Bot. 17:1992;115-143.
58. Wendel J. F., Schnabel A., Seelanan T. An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, intergenomic introgression. Mol. Phylogenet. Evol. 4:1995a;298-313.
59. Wendel J. F., Schnabel A., Seelanan T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA. 92:1995b;280-284.
60. Zhao X.-P., Si Y., Hanson R. E., Crane C. F., Price H. J., Stelly D. M., Wendel J. F., Paterson A. H. Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton. Genome Res. 8:1998;479-492.