Development of COS genes as universally amplifiable markers for phylogenetic reconstructions of closely related plant species

Cladistics

Volumn 24, Issue 5, 2008, Pages 727-745

  Li, Mingai ^a   Wunder, Jörg ^a   Bissoli, Gaetano ^a,b   Scarponi, Eliana ^a   Gazzani, Silvia ^a   Barbaro, Enrico ^a   Saedler, Heinz ^a,c   Varotto, Claudio ^a  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b Ciudad Politécnica de la Innovación   (Spain)

^c MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANGIOSPERM; COMPARATIVE STUDY; GENETIC MARKER; PHYLOGENY; RECONSTRUCTION; RELATEDNESS; TAXONOMY;

MAGNOLIOPHYTA; OROBANCHACEAE;

EID: 52949127350     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2008.00207.x     Document Type: Article

References (80)

1. Alvarez, I., Cronn, R., Wendel, J.F., 2005. Phylogeny of the New World diploid cottons (Gossypium L., Malvaceae) based on sequences of three low-copy nuclear genes. Plant Syst. Evol. 252, 199 214.
2. Angiosperm Phylogeny Group, II, 2003. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Bot. J. Linn. Soc. 141, 399 436.
3. Bailey, C.D., Doyle, J.J., 1999. Potential Phylogenetic Utility of the low-copy nuclear gene Pistillata in dicotyledonous plants: comparison to nrDNA ITS and trnL intron in Sphaerocardamum and other Brassicaceae. Mol. Phylogenet. Evol. 13, 20 30.
4. Bailey, C.D., Hughes, C.E., Harris, S.A., 2004. Using RAPDs to identify DNA sequence loci for species level phylogeny reconstruction: an example from Leucaena (Fabaceae). Syst. Bot. 29, 4 14.
5. Bailey, C.D., Koch, M.A., Mayer, M., Mummenhoff, K., O'Kane, S.L., Warwick, S.I., Windham, M.D., Al-Shehbaz, I.A., 2006. Toward a global phylogeny of the Brassicaceae. Mol. Biol. Evol. 23, 2142 2160.
6. Baldwin, B.G., Sanderson, M.J., Porter, J.M., Wojciechowski, M.F., Campbell, C.S., Donoghue, M.J., 1995. The ITS region of nuclear ribosomal DNA - a valuable source of evidence on angiosperm phylogeny. Ann. Mo. Bot. Gard. 82, 247 277.
7. Barten, R., Meyer, T.F., 1998. Cloning and characterisation of the Neisseria gonorrhoeae aroB gene. Mol. Gen. Genet, 258, 34 44.
8. Bennett, J.R., Mathews, S., 2006. Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. Am. J. Bot. 93, 1039 1051.
9. Bull., J.J., Huelsenbeck, J.P., Cunningham, C.W., Swofford, D.L., Waddell, P.J., 1993. Partitioning and combining data in phylogenetic analysis. Syst. Biol. 42, 384 397.
10. Cheng, Z., Sattler, S., Maeda, H., Sakuragi, Y., Bryant, D.A., DellaPenna, D., 2003. Highly divergent methyltransferases catalyze a conserved reaction in tocopherol and plastoquinone synthesis in cyanobacteria and photosynthetic eukaryotes. Plant Cell 15, 2343 2356.
11. Choi, H.K., Luckow, M.A., Doyle, J., Cook, D.R., 2006. Development of nuclear gene-derived molecular markers linked to legume genetic maps. Mol. Genet. Genom. 276, 56 70.
12. Cronn, R., Cedroni, M., Haselkorn, T., Grover, C., Wendel, J.F., 2002a. PCR-mediated recombination in amplification products derived from polyploid cotton. Theor. Appl. Genet. 104, 482 489.
13. Cronn, R.C., Small, R.L., Haselkorn, T., Wendel, J.F., 2002b. Rapid diversification of the cotton genus (Gossypium: Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes. Am. J. Bot. 89, 707 725.
14. Cui, L.Y., Wall, P.K., Leebens-Mack, J.H., Lindsay, B.G., Soltis, D.E., Doyle, J.J., Soltis, P.S., Carlson, J.E., Arumuganathan, K., Barakat, A., Albert, V.A., Ma, H., Depamphilis, C.W., 2006. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16, 738 749.
15. Denton, A.L., Mcconaughy, B.L., Hall, B.D., 1998. Usefulness of RNA polymerase II coding sequences for estimation of green plant phylogeny. Mol. Biol. Evol. 15, 1082 1085.
16. Despres, L., Gielly, L., Redoutet, W., Taberlet, P., 2003. Using AFLP to resolve phylogenetic relationships in a morphologically diversified plant species complex when nuclear and chloroplast sequences fail to reveal variability. Mol. Phylogenet. Evol. 27, 185 196.
17. Doyle, J.J., Doyle, J.L., 1987. A rapid DNA isolation procedure for small quantities of leaf tissue. Phytochem. Bull. 19, 11 15.
18. Doyle, J.J., Doyle, J.L., 1999. Nuclear protein-coding genes in phylogeny reconstruction and homology assessment: some examples from Leguminosae. In: Hollingsworth, P.M., Bateman, R.M., Gornall, R.J. (Eds Molecular Systematics and Plant Evolution, pp. 229 254. Taylor & Francis, London.
19. Doyle, J.J., Doyle, J.L., Harbison, C., 2003. Chloroplast-expressed glutamine synthetase in Glycine and related Leguminosae: phylogeny, gene duplication, and ancient polyploidy. Syst. Bot. 28, 567 577.
20. Doyle, J.J., Doyle, J.L., Rauscher, J.T., Brown, A.H.D., 2004. Evolution of the perennial soybean polyploid complex (Glycine subgenus Glycine): a study of contrasts. Biol. J. Linn. Soc. 82, 583 597.
21. Emshwiller, E., Doyle, J.J., 1999. Chloroplast-expressed glutamine synthetase (ncpGS): potential utility for phylogenetic studies with an example from Oxalis (Oxalidaceae). Mol. Phylogenet. Evol. 12, 310 319.
22. Essigmann, B., Hespenheide, B.M., Kuhn, L.A., Benning, C., 1999. Prediction of the active-site structure and NAD (+) binding in SQD1, a protein essential for sulfolipid biosynthesis in Arabidopsis. Arch. Biochem. Biophys. 369, 30 41.
23. Ford, V.S., Lee, J., Baldwin, B.G., Gottlieb, L.D., 2006. Species divergence and relationships in Stephanomeria (Compositae): PGIC phylogeny compared to prior biosystematic studies. Am. J. Bot. 93, 480 490.
24. Fredslund, J., Madsen, L.H., Hougaard, B.K., Sandal, N., Stougaard, J., Bertioli, D., Schauser, L., 2006. GEMprospector - online design of cross-species genetic marker candidates in legumes and grasses. Nucleic Acids Res. 34, W670 W675.
25. Fulton, T.M., Van der Hoeven, R., Eannetta, N.T., Tanksley, S.D., 2002. Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Pl. Cell 14, 1457 1467.
26. Gadberry, M.D., Malcomber, S.T., Doust, A.N., Kellogg, E.A., 2005. Primaclade - a flexible tool to find conserved PCR primers across multiple species. Bioinformatics 21, 1263 1264.
27. Hall, T.A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids. Symp. Ser. 41, 95 98.
28. Hilu, K.W., Borsch, T., Muller, K., Soltis, D.E., Soltis, P.S., Savolainen, V., Chase, M.W., Powell, M.P., Alice, L.A., Evans, R., Sauquet, H., Neinhuis, C., Slotta, T.A.B., Rohwer, J.G., Campbell, C.S., Chatrou, L.W., 2003. Angiosperm phylogeny based on matK sequence information. Am. J. Bot. 90, 1758 1776.
29. Hughes, C.E., Eastwood, R.J., Bailey, C.D., 2006. From famine to feast? Selecting nuclear DNA sequence loci for plant species-level phylogeny reconstruction. Philos. Trans. R. Soc. B Biol. Sci. 361, 211 225.
30. Keller, Y., Bouvier, F., d'Harlingue, A., Camara, B., 1998. Metabolic compartmentation of plastid prenyllipid biosynthesis - evidence for the involvement of a multifunctional geranylgeranyl reductase. Eur J. Biochem. 251, 413 417.
31. Kimura, M., 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide-sequences. J. Mol. Evol. 16, 111 120.
32. Kubatko, L.S., Degnan, J.H., 2007. Inconsistency of phylogenetic estimates from concatenated data under coalescence. Syst. Biol. 56, 17 24.
33. Kusumi, J., Tsumura, Y., Yoshimaru, H., Tachida, H., 2002. Molecular evolution of nuclear genes in Cupressaceae, a group of conifer trees. Mol. Biol. Evol. 19, 736 747.
34. Lewis, C.E., Doyle, J.J., 2002. A phylogenetic analysis of tribe Areceae (Arecaceae) using two low-copy nuclear genes. Plant Syst. Evol. 236, 1 17.
35. Liepman, A.H., Olsen, L.J., 2003. Alanine aminotransferase homologs catalyze the glutamate: glyoxylate aminotransferase reaction in peroxisomes of Arabidopsis. Plant Physiol. 131, 215 227.
36. Lihova, J., Shimizu, K.K., Marhold, K., 2006. Allopolyploid origin of Cardamine asarifolia (Brassicaceae): Incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene. Mol. Phylogenet. Evol. 39, 759 786.
37. Linder, C.R., Rieseberg, L.H., 2004. Reconstructing patterns of reticulate evolution in plants. Am. J. Bot. 91, 1700 1708.
38. Londo, J.P., Chiang, Y.C., Hung, K.H., Chiang, T.Y., Schaal, B.A., 2006. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proc. Natl Acad. Sci. USA 103, 9578 9583.
39. Lyons, L.A., Laughlin, T.F., Copeland, N.G., Jenkins, N.A., Womack, J.E., Obrien, S.J., 1997. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nature Genet. 15, 47 56.
40. Maddison, W.P., 1997. Gene trees in species trees. Syst. Biol. 46, 523 536.
41. Malcomber, S.T., 2002. Phylogeny of Gaertnera Lam. (Rubiaceae) based on multiple DNA markers: evidence of a rapid radiation in a widespread, morphologically diverse genus. Evol. Int. J. Org. Evol, 2002, 42 57.
42. Marhold, K., Lihova, J., 2006. Polyploidy, hybridization and reticulate evolution: lessons from the Brassicaceae. Plant Syst. Evol. 259, 143 174.
43. Mason-Gamer, R.J., Weil, C.F., Kellogg, E.A., 1998. Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15, 1658 1673.
44. Mast, A.R., Jones, E.H., Havery, S.P., 2005. An assessment of old and new DNA sequence evidence for the paraphyly of Banksia with respect to Dryandra (Proteaceae). Aust. Syst. Bot. 18, 75 88.
45. Mathews, S., Donoghue, M.J., 2000. Basal angiosperm phylogeny inferred from duplicate phytochromes a and c. Int. J. Plant Sci. 161, S41 S55.
46. Montamat, F., Guilloton, M., Karst, F., Delrot, S., 1995. Isolation and characterization of a cDNA encoding Arabidopsis thaliana 3-hydroxy-3- methylglutaryl-coenzyme A synthase. Gene 167, 197 201.
47. Oliverio, K.A., Crepy, M., Martin-Tryon, E.L., Milich, R., Harmer, S.L., Putterill, J., Yanovsky, M.J., Casal, J.J., 2007. GIGANTEA regulates phytochrome A-mediated photomorphogenesis independently of its role in the circadian clock. Plant Physiol. 144, 495 502.
48. Olmstead, R.G., dePamphilis, C.W., Wolfe, A.D., Young, N.D., Elisons, W.J., Reeves, P.A., 2001. Disintegration of the Scrophulariaceae. Am. J. Bot. 88, 348 361.
49. Oxelman, B., Yoshikawa, N., Mcconaughy, B.L., Luo, J., Denton, A.L., Hall, B.D., 2004. Rpb2 gene phylogeny in flowering plants, with particular emphasis on Asterids. Mol. Phylogenet. Evol. 32, 462 479.
50. Pelser, P.B., Gravendeel, B., Van Der Meijden, R., 2003. Phylogeny reconstruction in the gap between too little and too much divergence: the closest relatives of Senecio jacobaea (Asteraceae) according to DNA sequences and AFLPs. Mol. Phylogenet. Evol. 29, 613 628.
51. Poke, F.S., Martin, D.P., Steane, D.A., Vaillancourt, R.E., Reid, J.B., 2006. The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase). Mol. Phylogenet. Evol. 39, 160 170.
52. Posada, D., Crandall, K.A., 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14, 817 818.
53. Ronquist, F., Huelsenbeck, J.P., 2003. MrBayes 3: bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572 1574.
54. Rose, T.M., Schultz, E.R., Henikoff, J.G., Pietrokovski, S., Mccallum, C.M., Henikoff, S., 1998. Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res. 26, 1628 1635.
55. Rozas, J., Sanchez-Delbarrio, J.C., Messeguer, X., Rozas, R., 2003. Dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496 2497.
56. Rudd, S., Schoof, H., Mayer, K., 2005. Plantmarkers - a database of predicted molecular markers from plants. Nucleic Acids Res. 33, D628 D632.
57. Rzeznicka, K., Walker, C.J., Westergren, T., Kannangara, C.G., von Wettstein, D., Merchant, S., Gough, S.P., Hansson, M., 2005. Xantha-1 encodes a membrane subunit of the aerobic Mg-protoporphyrin IX monomethyl ester cyclase involved in chlorophyll biosynthesis. Proc. Natl Acad. Sci. USA 102, 5886 5891.
58. Sang, T., 2002. Utility of low-copy nuclear gene sequences in plant phylogenetics. Crit. Rev. Biochem. Mol. Biol. 37, 121 147.
59. Scherson, R.A., Choi, H.K., Cook, D.R., Sanderson, M.J., 2005. Phylogenetics of New World Astragalus: screening of novel nuclear loci for the reconstruction of phylogenies at low taxonomic levels. Brittonia 57, 354 366.
60. Schlueter, P.M., Stuessy, T.F., Paulus, H.F., 2005. Making the first step: practical considerations for the isolation of low-copy nuclear sequence markers. Taxon 54, 766 770.
61. Senchina, D.S., Alvarez, I., Cronn, R.C., Liu, B., Rong, J.K., Noyes, R.D., Paterson, A.H., Wing, R.A., Wilkins, T.A., Wendel, J.F., 2003. Rate variation among nuclear genes and the age of polyploidy in Gossypium. Mol. Biol. Evol. 20, 633 643.
62. Small, R.L., Wendel, J.F., 2000. Copy number lability and evolutionary dynamics of the adh gene family in diploid and tetraploid cotton (Gossypium). Genetics 155, 1913 1926.
63. Small, R.L., Cronn, R.C., Wendel, J.F., 2004. Use of nuclear genes for phylogeny reconstruction in plants. Aust. Syst. Bot. 17, 145 170.
64. Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W., Swensen, S.M., Zimmer, E.A., Chaw, S.M., Gillespie, L.J., Kress, W.J., Sytsma, K.J., 1997. Angiosperm phylogeny inferred from 18s ribosomal DNA sequences. Ann. Mo. Bot. Gard. 84, 1 49.
65. Soltis, D.E., Soltis, P.S., Chase, M.W., Mort, M.E., Albach, D.C., Zanis, M., Savolainen, V., Hahn, W.H., Hoot, S.B., Fay, M.F., Axtell, M., Swensen, S.M., Prince, L.M., Kress, W.J., Nixon, K.C., Farris, J.S., 2000. Angiosperm phylogeny inferred from 18s rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133, 381 461.
66. Strand, A.E., Leebensmack, J., Milligan, B.G., 1997. Nuclear DNA-based markers for plant evolutionary biology. Mol. Ecol. 6, 113 118.
67. Swofford, D.L., 2003. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, MA.
68. Syring, J., Willyard, A., Cronn, R., Liston, A., 2005. Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. Am. J. Bot. 92, 2086 2100.
69. Thompson, J.D., Higgins, D.G., Gibson, T.J., 1994. 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, 4673 4680.
70. Van de Peer, Y., De Wachter, R., 1997. Construction of evolutionary distance trees with Treecon for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Appl. Biosci. 13, 227 230.
71. Vision, T.J., Brown, D.G., Tanksley, S.D., 2000. The origins of genomic duplications in Arabidopsis. Science 290, 2114 2117.
72. Walsh, B.M., Hoot, S.B., 2001. Phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two noncoding regions: the chloroplast atpB-rbcL spacer region and nuclear waxy introns. Int. J. Plant Sci. 162, 1409 1418.
73. Weese, T.L., Johnson, L.A., 2005. Utility of NADP-dependent isocitrate dehydrogenase for species-level evolutionary inference in angiosperm phylogeny: a case study in Saltugilia. Mol. Phylogenet. Evol. 36, 24 41.
74. Wendel, J.F., Schnabel, A., Seelanan, T., 1995. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl Acad. Sci. USA 92, 280 284.
75. Whittall, J.B., Medina-Marino, A., Zimmer, E.A., Hodges, S.A., 2006. Generating single-copy nuclear gene data for a recent adaptive radiation. Mol. Phylogenet. Evol. 39, 124 134.
76. Winkworth, R.C., Donoghue, M.J., 2004. Viburnum phylogeny: evidence from the duplicated nuclear gene GbssI. Mol. Phylogenet. Evol. 33, 109 126.
77. Wu, F., Mueller, L.A., Crouzillat, D., Petiard, V., Tanksley, S.D., 2006. Combining bioinformatics and phylogenetics to identify large sets of single copy, orthologous genes (COS II) for comparative, evolutionary and systematics studies: a test case in the euasterid plant clade. Genetics. 174, 1407 1420.
78. Xu, W., Briggs, W.J., Padolina, J., Timme, R.E., Liu, W., Linder, C.R., Miranker, D.P., 2004. Using MoBIoS' scalable genome join to find conserved primer pair candidates between two genomes. Bioinformatics 20, i355 362.
79. Yahalom, A., Kim, T.H., Winter, E., Karniol, B., von Arnim, A.G., Chamovitz, D.A., 2001. Arabidopsis eIF3e (INT-6) associates with both eIF3c and the COP9 signalosome subunit CSN7. J. Biol. Chem. 276, 334 340.
80. Young, N.D., Healy, J., 2003. Gapcoder automates the use of indel characters in phylogenetic analysis. Bmc Bioinformatics 4, 6.