Multiple Divergent ITS1 Copies Were Identified in Single Tomato Genome Using DGGE Analysis
- 197 Downloads
The intra-genomic variation in the internal transcribed spacer (ITS) region has led to misleading conclusions in the evolutionary analysis of plants; understanding this variation is critical for correct evolutionary analysis based on ITS sequences. To reveal the ITS variation in tomato, entire copies of ITS1 sequences within tomato species were separated using denaturing gradient gel electrophoresis (DGGE) and DNA sequence analysis. ITS1 copies varied significantly in sequence composition, but not in sequence length within the same tomato cultivar. DNA sequence similarity of the ITS1 copies was 77–100 %. Moreover, AT and GC contents in ITS1 copies from each tomato cultivar were significantly different, ranging from 50.4 to 64.3 % for GC and from 35.7 to 49.6 % for AT. However, the length variation of ITS1 was insignificant, ranging from 279 to 282 bp. Multiple copies of divergent ITS1 present in the tomato genome indicate that some copies may be paralogues. In conclusion, DGGE technique is a reliable and novel approach to reveal the entire ITS copy variation and the possible evolutionary relationship of tomato.
KeywordsDivergent ITS copy DGGE GC content Solanum Tomato
This research was supported in part by grants from the USDA Sustainable Agriculture Research and Education (SARE) Program and in part by the North Carolina State University Agricultural Research Service. We would like to express our appreciation to Jinping Sun and Cary Rivard for their technical assistance and Stella Chang for editing the early version of the manuscript. We also would like to thank Dr. Bruce Baldwin for his suggestion through e-mail communication.
- Bortiri ES, Oh H, Jiang J, Baggett S, Granger A, Weeks C, Buckingham M, Potter D, Parfitt DE (2001) Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Syst Bot 26:797–807Google Scholar
- Li WH, Graur D (1991) Fundamentals of molecular evolution. Sinauer Associates, Sunderland, pp 1–284Google Scholar
- Muyzer G, De Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction amplified genes for 16S rRNA. Appl Environ Microb 59:695–700Google Scholar
- O’Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol Biol Evol 7:103–116Google Scholar
- Rivard C, Louws FJ (2008) Grafting to manage soilborns diseases in heirloom tomato production. Hortic Sci 43:2104–2111Google Scholar
- Sanderson MJ, Doyle JJ (1992) Reconstruction of organismal and gene phylogenies from data on multigene families: concerted evolution, homoplasy, and confidence. Syst Biol 41:4–17Google Scholar
- Thompson JD, Higgins DG, Gibson TJ (1997) ClustalX 1.5, software for Power PC. European Molecular Biology Organization, HeidelbergGoogle Scholar
- Tuddenham EGD, Schwaab R, Seehafer J, Millar DS, Gitschier J, Higuchi M, Bidichandani S, Connor JM, Hoyer LW, Yoshioka A, Peake IR, Oiek K, Kazazian HH, Lavergne JM, Giannelli F, Antonarakis SE, Cooper DN (1994) Haemophilia A: database of nucleotide substitutions, deletions, insertions and rearrangements of the factor VIII gene, second edition. Nucleic Acids Res 22:4851–4868PubMedCrossRefGoogle Scholar
- Zeze A, Sulistyowati E, Ophel-Keller K, Barker S, Smith S (1997) Intersporal genetic variation of Gigaspora margarita, a vesicular arbuscular mycorrhizal fungus, revealed by M13 minisatellite-primed PCR. Appl Environ Microb 63:676–678Google Scholar