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“Head to Tail” Tool Analysis through ClustalW Alignment Algorithms and Construction of Distance Method Neighbor-Joining Trees Based on Genus Fusarium Genomic Distances

  • Juan David Henao
  • S. Melissa Rincón
  • D. Juan Jose Filgueira
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 232)

Abstract

The genomic sequences concatenations are the most used tool for phylogenetic studies; such arrangements are characterized by eliminating all gaps arising in the process of alignment to improve phylogenetic constructions. However, no studies dedicated to the analysis of the concatenations with gaps, as these regions represent genetic transformation events that are crucial evolutionary events. For the concatenation analysis, nucleotide sequences of 11 species of the genus Fusarium, were experimentally obtained. For each species we used sequences of 10 amplicons, corresponding to 10 genic regions. Later several permutations were generated, concerning the order of the sequences, to observe topologies changes on the resulting trees with minimal changes in the “Head to Tail” arrangements. Multiple alignment of the DNA sequences, were performed using the ClustalW algorithm. Subsequently a feasibility analysis of sequences for phylogenetic analysis method was generated based on the likelihood-mapping tool using the Tree-puzzle-5.2 program. From this analysis, molecular inferences from trees were made using MEGA5 software, through a Neighbor-Joining distance method with 1000 bootstrap replicates, to support the resulting trees. We observed that there is variation level in the trees using “Head to Tail” arrays, which prevents showing the uniformity of the resulting cluster, keeping alignment gaps regardless of the order of the array. So far, the results obtained indicate that the “Head to Tail” arrangements are subject to the order of the genomic sequences that comprise it, and they are susceptible to possessing a sequence difference relative to another; i.e., the input of a single species whose “Head to Tail” arrangement possesses a range of major change, in comparison to the others in terms of concatenated with gaps included, generates a considerable change in the output of the resulting tree.

Keywords

Neighbor-Joining ClustalW Fusarium Distance method concatenations 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Juan David Henao
    • 1
  • S. Melissa Rincón
    • 2
  • D. Juan Jose Filgueira
    • 3
  1. 1.Student of Applied Biology of Nueva Granada Military UniversityUMNGBogotáColombia
  2. 2.Research Assistant Faculty of Basic and Applied SciencesUMNGBogotáColombia
  3. 3.Director of Molecular phytopathology Research Group, Faculty of Basic and Applied SciencesUMNGBogotáColombia

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