“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)


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.


Neighbor-Joining ClustalW Fusarium Distance method concatenations 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Yli-Mattila, Y., Mach, R.L., Alekhina, I.A., Bulat, S.A., Koskinen, S., Kulling-Gtadigner, C.M., Kubicek, C.P., Klemsdal, S.S.: Phylogenetic Relationship of Fusarium langsethiae to Fusarium poae and Fusarium sporotrichioides as Inferred by IGS, ITS, β-tubulin Sequences and UP-PCR Hybridization Analysis. International Journal of Food Microbiology 95, 267–285 (2004)CrossRefGoogle Scholar
  2. 2.
    Stenglein, S.A., Rodriguero, M.S., Chandler, E., Jennings, P., Salerno, G.L., Nicholson, P.: Phylogenetic Relationship of Fusarium poae Based on EF-1α and mtSSu Sequences. Fungal Biology 114, 96–106 (2010)CrossRefGoogle Scholar
  3. 3.
    Shi, J., Blundell, T.M., Mizuguchi, K.: FUGUE: Sequence-structure Homology Recognition Using Environment-specific Substitution Tables and Structure-dependent Gap Penalties. J. Mol. Biol. 310, 243–257 (2001)CrossRefGoogle Scholar
  4. 4.
    Scott, J., Chakraborty, S.: Multilocus Sequence Analysis of Fusarium pseudograminearum Reveals a Single Phylogenetic Species. Mycological Research 110, 1413–1425 (2006)CrossRefGoogle Scholar
  5. 5.
    Glass, N., Donaldson, G.: Development of Primer Sets Designed for Use with the PCR to Amplify Conserved Genes from Filamentous Ascomycetes. Appl. Environ. Microbial. 61 (1995)Google Scholar
  6. 6.
    Kroon, L.P., Bakkler, F.T., Van den Bosch, G.B., Bonants, P.J., Flier, W.G.: Phylogenetic Analysis of Phytophtora Species Based on Mitochondrial and Nuclear DNA Sequences. Fungal. Genet. Biol. 41, 766–782 (2004)CrossRefGoogle Scholar
  7. 7.
    Gilmore, S., Grafenhan, T., Seifert, K.: Multiple Copies of Cox1 in Species of the Fungal Genus Fusarium Canada (2007)Google Scholar
  8. 8.
    White, T.J., Bruns, T., Lee, S., Taylor, J.: Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. Genetics and Evolution (1990)Google Scholar
  9. 9.
    Lemey, P., Salemi, M., Vandamme, A.M.: The Phylogenetic Handbook, A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd edn., pp. 196–388. Cambridge University Press (2009)Google Scholar
  10. 10.
    Thompson, J.D., Higgins, D.G., Gibson, T.: CLUSTALW: Improving the Sensitivity of Progressive Multiple Sequence Aligment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice. Nucleic Acid Research 22, 4673–4680 (1994)CrossRefGoogle Scholar
  11. 11.
    Schmidt, H.A., Strimmer, K., Vingron, M., Von Haeseler, A.: TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quaetets and Parallel Computing. Bioinformatics 18, 502–504 (2002)CrossRefGoogle Scholar
  12. 12.
    Saitou, N., Nei, M.: The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution 4, 406–425 (1987)Google Scholar
  13. 13.
    Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S.: MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Parsimony Methods. Molecular Biology and Evolution 28, 2731–2739 (2011)CrossRefGoogle Scholar
  14. 14.
    Felsenstein, J.: Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 39, 783–791 (1985)CrossRefGoogle Scholar
  15. 15.
    Strimmer, K., Von Haeseler, A.: Likelihood-mapping: A Simple Method to Visualize Phylogenetic Contents of a Sequence Aligment. Proc. Nat. Acad. Sci. 94, 6815–6819 (1997)MATHCrossRefGoogle Scholar
  16. 16.
    Watanabe, M., Yonezawa, T., Lee, K., Kumagai, S., Sugita-Konishi, Y., Goto, K., Hara, K.: Molecular Phylogeny of the Higher and Lower Taxonomy of the Fusarium Genus and Differences in the Evolutionary Histories of Multiple Genes. BMC Evolutionary Biology 11, 322–338 (2011)CrossRefGoogle Scholar
  17. 17.
    Sarver, B.A., Ward, T.J., Gale, L.R., Broz, K., Kistler, C., Aoki, T., Nicholson, P., Carter, J., O’Donnell, K.: Novel Fusarium Head Blight Pathogens from Nepal and Louisiana Reveled by Multilocus Genealogical Concordance. Fungal Genetics and Biology 48, 1096–1107 (2011)CrossRefGoogle Scholar

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

Personalised recommendations