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A plant biologists’ guide to phylogenetic analysis of biological macromolecule sequences

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Biologia Plantarum

Abstract

Phylogenetic analysis has become a common step in characterization of gene and protein sequences. However, despite the availability of numerous affordable and more-or-less intuitive software tools, construction of biologically relevant, informative phylogenetic trees remains a process involving several critical steps that are inherently non-algorithmic, i.e., dependent on decisions made by the user. These steps involve, but are not limited to, setting the aims of the phylogenetic study, choosing sequences to be analyzed, and selecting methods employed in sequence alignment construction, as well as algorithms and parameters used to construct the actual phylogenetic tree. This review aims towards providing guidance for these decisions, as well as illustrating common pitfalls and problems occurring during phylogenetic analysis of plant gene sequences.

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Abbreviations

BLAST :

basic local alignment search tool

CD-search:

conserved domain search

COBALT :

constraint-based multiple protein alignment tool

DDBJ :

DNA data bank of Japan

ENA :

European nucleotide archive

INSDC :

international nucleotide sequence database collaboration

MACAW :

multiple alignment construction and analysis workbench

MAFFT :

multiple alignment using fast Fourier transform

MEGA :

molecular evolutionary genetics analysis

ML:

maximum likelihood

MUSCLE :

multiple sequence comparison by log-expectation

NCBI :

National Centre for Biotechnology Information

NJ:

neighbor-joining

PAUP :

phylogenetic analysis using parsimony

PHYLIP :

phylogeny inference package

SMART :

simple modular architecture research tool

T-REX :

tree and reticulogram reconstruction

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  1. Department of Experimental Plant Biology, Faculty of Sciences, Charles University, Viničná 5, CZ 128 43, Prague, Czech Republic

    F. Cvrčková

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  1. F. Cvrčková
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Correspondence to F. Cvrčková.

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Acknowledgments: I thank the many generations of students of my Introduction to Bioinformatics undergraduate course for providing continuous feedback that helped to shape the ideas presented here, Anton Markoš, Vojtěch Žárský and Shigehiro Kuraku for critical reading of this manuscript, and the Ministry of Education of the Czech Republic for financial support from the NPUI LO1417 project.

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Cvrčková, F. A plant biologists’ guide to phylogenetic analysis of biological macromolecule sequences. Biol Plant 60, 619–627 (2016). https://doi.org/10.1007/s10535-016-0649-8

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  • DOI: https://doi.org/10.1007/s10535-016-0649-8

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