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Using Tobamoviruses for Phylogenetic Instruction in Undergraduate Biology Courses

    Authors: Kornelia Fillmer1, Scott Adkins2, Patchara Pongam1, Tom D’Elia1,*
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    Affiliations: 1: Biology Department, Indian River State College, Fort Pierce, FL 34981; 2: USDA, ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL 34945
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Received 03 November 2017 Accepted 14 February 2018 Published 25 May 2018
    • ©2018 Author(s). Published by the American Society for Microbiology.
    • [open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.

    • Supplemental materials available at http://asmscience.org/jmbe
    • *Corresponding author. Mailing address: Biology Department, Indian River State College, 3209 Virginia Ave., Fort Pierce, FL 34981. Phone: 772-462-7492. Fax: 772-462-7447. E-mail: [email protected].
    Source: J. Microbiol. Biol. Educ. May 2018 vol. 19 no. 2 doi:10.1128/jmbe.v19i2.1519
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    Abstract:

    Microbial diversity and taxonomy instruction provide an ideal opportunity to introduce students to basic bioinformatics skills. There are many ways to illustrate evolutionary relationships between microorganisms using phylogenetic trees. Thought must be given to the method of presentation used in class because interpreting complex trees can be quite challenging for students. Here we present a simple activity that teaches the fundamental bioinformatics skills of multiple sequence alignments and phylogenetics by using Tropical soda apple mosaic virus and other tobamoviruses that produce trees that are easy to interpret. Tobamoviruses are important agricultural pathogens and have well defined phylogenetic groupings that correspond to the phylogenetic groupings of host plant families. This clear pattern illustrates the coevolution of the virus and host, and makes interpreting relationships based on these trees very straightforward. The organization of the trees also indicates related plants that a given virus may potentially infect, making this type of analysis useful for developing measures to limit spread and minimize economic impacts. The simplicity of the analysis, coupled with the real-world application in agricultural science, helps actively engage students in a topic that is challenging to learn. This activity is broadly adaptable, and can be introduced as a learning module in courses covering topics in microbiology, molecular biology, genetics and evolution. Completion of this activity provides students with key foundational skills for phylogenetic analysis and the confidence to utilize bioinformatics software.

References & Citations

1. American Association for the Advancement of Science2011Vision and change in undergraduate biology education: a call to action: a summary of recommendations made at a national conference organized by the American Association for the Advancement of ScienceJuly 15–17, 2009Washington, DC
2. Merkel S, Reynolds J, Hung K, Siegesmund A, Smith A, Smith H2012ASM curriculum guidelines for undergraduate microbiology education. [Online.]http://www.asm.org/index.php/guidelines/curriculum-guidelines
3. White HB, Benore MA, Sumter TF, Caldwell BD, Bell E2013Special section: foundational concepts and assessment tools for biochemistry and molecular biology educators, part 1: essential concepts and skillsBiochem Mol Biol Educ41297301
4. Welch L, Lewitter F, Schwartz R, Brooksbank C, Radivojac P, Gaeta B, Schneider MV2014Bioinformatics curriculum guidelines: toward a definition of core competenciesPLOS Comput Biol103e100349610.1371/journal.pcbi.1003496 http://dx.doi.org/10.1371/journal.pcbi.1003496
5. Adams MJ, Heinze C, Jackson AO, Kreuze JF, Macfarlane SA, Torrance L2012Tobamovirus11531156 King AMQ, Adams MJ, Carstens EB, Lefkowitz EJVirus taxonomy: ninth report of the international committee on taxonomy of virusesElsevier/Academic PressLondon, United Kingdom
6. Gibbs A1999Evolution and origin of tobamovirusesPhilos Trans R Soc Lond B Biol Sci35459360210.1098/rstb.1999.0411 http://dx.doi.org/10.1098/rstb.1999.0411
7. Lewandowski DJ, Dawson WO2000Functions of the 126- and 183-kDa proteins of tobacco mosaic virusVirology271909810.1006/viro.2000.0313 http://dx.doi.org/10.1006/viro.2000.0313
8. Adkins S, Kamenova I, Rosskopf EN, Lewandowski DJ2007Identification and characterization of a novel tobamovirus from tropical soda apple in FloridaPlant Dis9128729310.1094/PDIS-91-3-0287 http://dx.doi.org/10.1094/PDIS-91-3-0287
9. Coile NC1993Tropical soda apple, Solanum viarum Dunal: the plant from hell. Florida Department of Agriculture and Consumer Services, Division of Plant IndustryBot Circ27
10. Fillmer K, Adkins S, Pongam P, D’Elia T2016The complete nucleotide sequence and genomic characterization of tropical soda apple mosaic virusArch Virol1612317232010.1007/s00705-016-2888-6 http://dx.doi.org/10.1007/s00705-016-2888-6
11. Kumar S, Stecher G, Tamura K2016MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasetsMol Biol Evol331870187410.1093/molbev/msw054 http://dx.doi.org/10.1093/molbev/msw054

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2018-05-25
2018-08-15

Abstract:

Microbial diversity and taxonomy instruction provide an ideal opportunity to introduce students to basic bioinformatics skills. There are many ways to illustrate evolutionary relationships between microorganisms using phylogenetic trees. Thought must be given to the method of presentation used in class because interpreting complex trees can be quite challenging for students. Here we present a simple activity that teaches the fundamental bioinformatics skills of multiple sequence alignments and phylogenetics by using Tropical soda apple mosaic virus and other tobamoviruses that produce trees that are easy to interpret. Tobamoviruses are important agricultural pathogens and have well defined phylogenetic groupings that correspond to the phylogenetic groupings of host plant families. This clear pattern illustrates the coevolution of the virus and host, and makes interpreting relationships based on these trees very straightforward. The organization of the trees also indicates related plants that a given virus may potentially infect, making this type of analysis useful for developing measures to limit spread and minimize economic impacts. The simplicity of the analysis, coupled with the real-world application in agricultural science, helps actively engage students in a topic that is challenging to learn. This activity is broadly adaptable, and can be introduced as a learning module in courses covering topics in microbiology, molecular biology, genetics and evolution. Completion of this activity provides students with key foundational skills for phylogenetic analysis and the confidence to utilize bioinformatics software.

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