Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences

Genetic Resources and Crop Evolution

Volumn 56, Issue 5, 2009, Pages 663-678

  Zuriaga, Elena ^a   Blanca, Jose ^a   Nuez, Fernando ^a  

^a UNIVERSITAT POLITÈCNICA DE VALÈNCIA   (Spain)

Author keywords

Classification; Lycopersicon; Phylogeny; Solanum; Taxonomy

Indexed keywords

CLASSIFICATION; DATA SET; DIVERGENCE; FRUIT; GENE EXPRESSION; GENETIC ANALYSIS; HYBRIDIZATION; INTERSPECIFIC VARIATION; INTRASPECIFIC VARIATION; MOLECULAR ANALYSIS; PHYLOGENETICS; PHYLOGENY; SPECIES DIVERSITY; TAXONOMY;

LYCOPERSICON; LYCOPERSICON PENNELLII; SOLANUM; SOLANUM LYCOPERSICOIDES;

EID: 70349869428     PISSN: 09259864     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10722-008-9392-0     Document Type: Article

References (53)

1. Alvarez AE, van De Wiel CCM, Smulders MJM, Vosman B (2001) Use of microsatellites to evaluate genetic diversity and species relationships in the genus Lycopersicon. Theor Appl Genet 103:1283-1292. doi:10.1007/s001220100662.
2. Arunyawat U (2007) Population structure and speciation history of two closely related wild tomato species. Ph.D. dissertation, Ludwig-Maximilians-Universität München, Germany.
3. Benham J, Jeung JU, Jasieniuk M, Kanazin V, Blake T (1999) Genographer: a graphical tool for automated fluorescent AFLP and microsatellite analysis. Department of Plant Science, Montana State University, Bozeman.
4. Blanca JM, Prohens J, Anderson GJ, Zuriaga E, Cañizares J, Nuez F (2007) AFLP and DNA sequence variation in an Andean domesticate, pepino (Solanum muricatum, Solanaceae): implications for evolution and domestication. Am J Bot 94:1219-1229. doi:10.3732/ajb.94.7.1219.
5. Bohs L (2007) Phylogeny of the cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data. Taxon 56:1012-1026.
6. Bohs L, Olmstead RG (1997) Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences. Syst Bot 22:5-17. doi:10.2307/2419674.
7. Bonfield J (2004) Staden package, version 1.4. Available at http://staden.sourceforge.net. Accessed 28 July 2008.
8. Child A (1990) A synopsis of Solanum subgenus Potatoe (G. Don) (D'Arcy) (Tuberarium (Dun.) Bitter (s.l.)). Feddes Repert 101:209-235.
9. Clark AG (1990) Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 7:111-122.
10. Darwin SC, Knapp S, Peralta IE (2003) Taxonomy of tomatoes in the Galapagos Islands: native and introduced species of Solanum section Lycopersicon (Solanaceae). Syst Biodivers 1:29-53. doi:10.1017/S1477200003001026.
11. Esquinas-Alcazar J, Nuez F (2001) Situación taxonómica, domesticación y difusión del tomate. In: Nuez F (ed) El cultivo del tomate. Mundi-Prensa, Madrid, pp 13-42.
12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
13. Hodkinson TR, Renvoize SA, Chonghaile GN, Stapleton CMA, Chase MW (2000) A comparison of ITS nuclear rDNA sequence data and AFLP markers for phylogenetic studies in Phyllostachys (Bambusoideae, Poaceae). J Plant Res 113:259-269. doi:10.1007/PL00013936.
14. Knapp SL, Bohs MN, Spooner DM (2004) Solanaceae: a model for linking genomics and biodiversity. Comp Funct Genomics 5:285-291. doi:10.1002/cfg.393.
15. Kosakovsky Pond SL, Frost SDW, Muse SV (2005) HyPhy: hypothesis testing using phylogenies. Bioinformatics 21:676-679. doi:10.1093/bioinformatics/bti079.
16. Luckwill LC (1943) The genus Lycopersicon: an historical, biological, and taxonomical survey of the wild and cultivated tomatoes. PhD dissertation, Aberdeen University Studies 120:1-44.
17. Marshall JA, Knapp S, Davey MR, Power JB, Cocking EC, Bennett MD, Cox AV (2001) Molecular systematics of Solanum section Lycopersicum (Lycopersicon) using the nuclear ITS rDNA region. Theor Appl Genet 103:1216-1222. doi:10.1007/s001220100671.
18. McClean PE, Hanson MR (1986) Mitochondrial DNA sequence divergence among Lycopersicon and related Solanum species. Genetics 112:649-667.
19. Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437-448.
20. Miller P (1754) The gardeners dictionary abridged, 4th edn. John and James Rivington, London.
21. Müller CH (1940) The taxonomy and distribution of the genus Lycopersicon. Natl Hortic Mag 19:157-160.
22. Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162:365-379.
23. Nuez F, Prohens J, Blanca JM (2004) Relationships, origin, and diversity of Galápagos tomatoes: implications for the conservation of natural populations. Am J Bot 91:86-99. doi:10.3732/ajb.91.1.86.
24. Nuez F, Díez MJ, Valcárcel JV, Cebolla-Cornejo J, Pérez A, Soler S, Roselló S, Adalid A, Galiana L, Sifres A, Picó B, Blanca JM, Frutos R (2008) Genetic resources of Lycopersicon at the Institute for the Conservation and Improvement of the Agrodiversity. Acta Hortic 789:293-297.
25. Olmstead RG, Palmer JD (1997) Implications for phylogeny, classification, and biogeography of Solanum from cpDNA restriction site variation. Syst Bot 22:19-29. doi:10.2307/2419675.
26. Palmer JD, Zamir D (1982) Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci USA 79:5006-5010. doi:10.1073/pnas.79.16.5006.
27. Peralta IE, Spooner DM (2001) Granule-bound starch synthase (GBSSI) gene phylogeny of wild tomatoes (Solanum L. section Lycopersicon [Mill.] Wettst. subsection Lycopersicon). Am J Bot 88:1888-1902. doi:10.2307/3558365.
28. Peralta IE, Spooner DM (2005) Morphological characterization and relationships of wild tomatoes (Solanum L. section Lycopersicon). In: Keating RC, Hollowell VC, Croat TB (eds) A festschrift for William G. D'Arcy: the legacy of a taxonomist. Monogr Syst Bot Mo Bot Gard 104:227-257.
29. Peralta IE, Knapp S, Spooner DM (2005) New species of wild tomatoes (Solanum section Lycopersicon: Solanaceae) from northern Peru. Syst Bot 30(2):424-434. doi:10.1600/0363644054223657.
30. Peralta IE, Spooner DM, Knapp S (2008) Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Syst Bot Monogr:84.
31. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818. doi:10.1093/bioinformatics/14.9.817.
32. R Development Core Team (2007) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org. Accessed 28 July 2008.
33. Rick CM (1963) Barriers to interbreeding in Lycopersicon peruvianum. Evolution Int J Org Evolution 17:216-232. doi:10.2307/2406467.
34. Rick CM (1971) Lycopersicon. In: Wiggins IL, Porter DM (eds) Flora of the Galapagos Islands. Stanford University Press, Stanford, pp 468-471.
35. Rick CM (1979) Biosystematic studies in Lycopersicon and closely related species of Solanum. In: Hawkes JG, Lester RN, Skelding AD (eds) The biology and taxonomy of the Solanaceae. Academic Press, New York, pp 667-678.
36. Rick CM (1986) Reproductive isolation in the Lycopersicon peruvianum complex. In: D'Arcy WG (ed) Solanaceae: biology and systematics. Columbia University Press, New York, pp 477-495.
37. Rick CM, Lamm R (1955) Biosystematic studies on the status of Lycopersicon chilense. Am J Bot 42:663-675. doi:10.2307/2485327.
38. Rick CM, Kesicki E, Fobes JF, Holle M (1976) Genetic and biosystematic studies on two new sibling species of Lycopersicon from interandean Peru. Theor Appl Genet 47:55-68. doi:10.1007/BF00281917.
39. Rick CM, Fobes JF, Tanksley SD (1979) Evolution of mating systems in Lycopersicon hirsutum as deduced from genetic variation in electrophoretic and morphological characters. Plant Syst Evol 132:279-298. doi:10.1007/BF00982390.
40. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. doi:10.1093/bioinformatics/btg180.
41. Roselius K, Stephan W, Städler T (2005) The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics 171:753-763. doi:10.1534/genetics.105.043877.
42. Rozas J, Sanchez-Del Barrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19:2496-2497. doi:10.1093/bioinformatics/btg359.
43. Sifres A, Picó B, Blanca J, De Frutos R, Nuez F (2007) Genetic structure of Lycopersicon pimpinellifolium (Solanaceae) populations collected after the ENSO event 1997-1998. Genet Resour Crop Evol 54:359-377. doi:10.1007/s10722-005-5725-4.
44. Spooner DM, Anderson GJ, Jansen RK (1993) Chloroplast DNA evidence for the interrelationships of tomatoes, potatoes, and pepinos (Solanaceae). Am J Bot 80:676-688. doi:10.2307/2445438.
45. Spooner DM, Peralta IE, Knapp S (2005) Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes. Taxon 54:43-61. Solanum L. section Lycopersicon (Mill.) Wettst.
46. Städler T, Roselius K, Stephan W (2005) Genealogical footprints of speciation processes in wild tomatoes: demography and evidence for historical gene flow. Evolution Int J Org Evolution 59:1265-1270.
47. Städler T, Arunyawat U, Stephan W (2008) Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178:339-350. doi:10.1534/genetics.107.081810.
48. Taylor IB (1986) Biosystematics of the tomato. In: Atherton JG, Rudich J (eds) The tomato crop: a scientific basis for improvement. Chapman and Hall, London, pp 1-34.
49. Thompson JD, Higgins DG, Gibson TJ (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. doi:10.1093/nar/22.22.4673.
50. van Ee BW, Jelinski N, Berry PE, Hipp AL (2006) Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data. Mol Ecol 15:2735-2751.
51. Warnock SJ (1991) Natural habitats of Lycopersicon species. HortScience 26:466-471.
52. Xu F, Sun M (2001) Comparative analysis of phylogenetic relationships of grain amaranths and their wild relatives (Amaranthus; Amaranthaceae) using internal transcribed spacer, amplified fragment length polymorphism, and double-primer fluorescent intersimple sequence repeat markers. Mol Phylogenet Evol 21:372-387. doi:10.1006/mpev.2001.1016.
53. Zuriaga E, Blanca JM, Cordero L, Sifres A, Blas-Cerdán WG, Morales R, Nuez F (2008) Genetic and bioclimatic variation in Solanum pimpinellifolium. Genet Resour Crop Evol. doi:10.1007/s10722-008-9340-z.