Abstract
1 Laboratorio de Biotecnologia Agricola, Departamento de Ciencias Biologicas, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), Universidade de Sao Paulo (USP), Avenida Padua Dias, 11, 13.418-900, Piracicaba, SP, Brasil. *E-mail: hecarrer@esalq.usp.br 2 Companhia de Cigarros Souza Cruz, Av. Gal Pinto Tourinho, 3200, 83.880-000, Bom Jesus, Rio Negro, PR, Brasil 3 Departamento de Genetica, ESALQ, USP 4 Max Planck Institute of Molecular Plant Physiology, Am Muhlenberg 1, D-14476, Potsdam, Golm, Germany ABSTRACT Intergenic spacers of chloroplast DNA (cpDNA) are very useful in phylogenetic and population genetic studies of plant species, to study their potential integration in phylogenetic analysis. The non-coding trnE-trnT intergenic spacer of cpDNA was analyzed to assess the nucleotide sequence polymorphism of 16 Solanaceae species and to estimate its ability to contribute to the resolution of phylogenetic studies of this group. Multiple alignments of DNA sequences of trnE-trnT intergenic spacer made the identification of nucleotide variability in this region possible and the phylogeny was estimated by maximum parsimony and rooted with Convolvulaceae Ipomoea batatas, the most closely related family. Besides, this intergenic spacer was tested for the phylogenetic ability to differentiate taxonomic levels. For this purpose, species from four other families were analyzed and compared with Solanaceae species. Results confirmed polymorphism in the trnE-trnT region at different taxonomic levels.
Highlights
Chloroplast genes have been extensively used to reconstruct the phylogeny of related species
Moneymaker), peruvianum tomato (L. peruvianum), potato (Solanum tuberosum), aubergine (S. melongena), “jiló” (S. gilo), bittersweet nightshade (S. dulcamara), glossy nightshade (S. americanum), chinese lantern (Physalis alkekengi), sweet pepper (Capsicum annuum), pepper (C. frutescens), belladonna (Atropa belladonna), petunia (Petunia sp. obtained at the local market), garden petunia (Petunia hybrida), scopolia (Scopolia carniolica) and Physochlaina orientalis; the tobacco (Nicotiana tabacum) sequence was taken from the GenBank database (GenBank/EMBL/ DDBJ#Z00044); (b) 1 species of Convolvulaceae: sweet potato (Ipomoea batatas); (c) 1 species of Plantaginaceae: Plantago major; (d) 1 species of Buddlejaceae: Buddleja davidii; and (e) 3 species of Scrophulariaceae: Antirrhinum majus, Lathraea squamaria and Scrophularia nodosa
The length of the spacers ranged from 392 bp (L. esculentum) to 849 bp (Scopolia carniolica) with an average length of 653 bp (Table 1)
Summary
Chloroplast genes have been extensively used to reconstruct the phylogeny of related species. The sequences of the chloroplast rbcL gene (coding the large subunit of Rubisco) as well as a few other genes (i.e. matK, ndhF, psaB and trnL-trnF) have been widely used for inferring phylogeny in plants (Chiang and Schaal 2000, Oxelman et al 1999, Soltis et al 2000, Miz et al 2008). Sequences such as the intergenic spacer between the trnL (UUA) 3 ́ exon and the trnF (GAA) gene (Neves et al 2005, Miz et al 2008), the atpB-rbcL spacer (Chiang and Schaal 2000, Soltis et al 2000) and trnC-trnD spacer (Lee and Wen 2004) have been used to address questions concerning relationships among related species or related genera.
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