Genetic Relationships Among Continental Cotton Species Based On ITS1 Gene Region Aligned With Different Alignment Tools

The molecular systematic studies that reveal the biodiversity have been rapidly evolving in the last 20 years. In this developing process sequence analysis and methods of phylogenetic analysis of molecular systematics have also started to contribute the phylogenetic studies In terms of phylogenetic information, morphological characters are insufficient for phylogenetic studies. In that situation DNA sequence analysis is very useful for phylogenetic studies. In this study, sequences of “Internal transcribed spacer1” (ITS1) rDNA regions were aligned with three different alignment tools (ClustalW, T-COFFEE, MAFFT) to infer the genetic relationship between forty-four woody, bushy and herbaceous cotton species originated from Africa, America, Australia. In the study maximum likelihood (ML), maximum parsimony (MP), and Bayesian-MCMC methods were utilized. Results revealed that MAFFT presented the best alignments while parsimony and Bayesian methods provided better tree topologies.