Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region

Abstract

Crop Breeding and Applied Biotechnology 8: [85][86][87][88][89][90][91][92][93][94][95] 2008 85 Phylogenetic relationships in Solanaceae and related species based on cpDNA sequence from plastid trnE-trnT region Crop Breeding and Applied Biotechnology 8: [85][86][87][88][89][90][91][92][93][94][95] 2008 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.

In silico analysis of Simple Sequence Repeats from chloroplast genomes of Solanaceae species

“…The members included are those that have changed little from the ancestral state; those that have changed more are excluded: a paraphyletic group contains the rump of conservative descendants from an ancestral species. Thus, the absorption of Lycopersicon by Solanum seems justifiable (Melotto-Passarin et al 2008). As was expected, our results indicated the high identity between tomato and Solanum species, which have the same types and amounts of SSRs (Table 3).…”

“…Studies of chloroplast sequences from Solanaceae species have shown that those sequences are highly conservative among related species (Melotto-Passarin et al 2008).…”

Complete chloroplast genome sequence of Magnolia kwangsiensis (Magnoliaceae): implication for DNA barcoding and population genetics

“…The trnE-trnT was employed to infer the phylogenetic relationships of Gesnerioideae based on nrITS and cpDNA trnL-trnF and trnE-trnT spacer regions . Other molecular studies, for instance, phylogenetic relationships in Solanaceae (Melotto-Passarin et al 2008) or in Descurainia (Brassicaceae) (Goodson et al 2006) also adopted this marker. However, those studies were based on a combination of multigenes rather than entirely on trnE-trnT.…”

Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)

“…Using the genome sequence of A. thaliana as a reference, widely used molecular markers from three different genomes were selected. In total, three noncoding regions of cpDNA, i.e., trnE-trnT, trnT-trnL spacers, and trnL intron (Baumel et al, 2002;Taberlet et al, 2007;Melotto-Passarin et al, 2008), nad intron of mtDNA (Soria-Hernanz et al, 2008), and fourteen regions of nuclear DNA (thirteen genes and one nrDNA spacer) were amplified and sequenced. Genes AGAMOUS (AG), gamma carbonic anhydrase (CA), chalcone isomerase (CHI), chalcone synthase (CHS), CONSTANS-LIKE 2 (CO2), cryptochrome 2 gene R (Cry2), dihydroflavonol 4-reductase (Dfr), ethylene forming enzyme (EFE), flavanone-3-hydroxylase (F3h), ferulic acid 5-hydroxylase (Fah), LEAFY, PISTILLATA (PIS), Feregulated transporter-like protein (ZIP) and nuclear ribosomal internal spacers (nrITS) (El-Assal et al, 2001;Olsen et al, 2004;Ramos-Onsins et al, 2004;Masuzaki et al, 2006;Flowers et al, 2009;Hung et al, 2009).…”