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Innovations for investigating the plant tree of life

April 19, 2018

Advances in genome sequencing have resulted in vast amounts of genetic information being produced for ever-increasing numbers of species, but we are still just scratching the surface. The cutting-edge practices used to generate new types of data for exploring the plant family tree are highlighted in "Methods for Exploring the Plant Tree of Life," a special issue of Applications in Plant Sciences (APPS).

"New sequencing technologies and other advances in fields such as natural language processing and image analysis have rapidly changed what we can learn about the tree of life," says Dr. Matt Gitzendanner, Scientist at the University of Florida and co-editor of the special issue. The featured articles showcase an array of these techniques, which provide novel solutions to some of the biggest challenges in the study of the evolution of species, known as phylogenetics.

Newly developed phylogenetic approaches often allow these challenges to be tackled in unique ways. Co-editor Michael McKain, Assistant Professor at The University of Alabama and curator of the University of Alabama Herbarium, enthused about a paper by Tovar et al. outlining a method for collecting data from images of plants using the affordable Raspberry Pi computers, which he plans to try with his undergraduate students. In another article, Endara et al. describe an unusual approach for automatically extracting data from written descriptions of plants, allowing researchers to use information in the scientific literature without painstakingly trawling through decades of articles and books to find it.

Although a variety of techniques are covered in the APPS special issue, in their review article, authors Fay-Wei Li and Alex Harkess ask whether whole-genome sequencing will eventually remove the need for other types of phylogenetic information. In their introduction to the issue, the co-editors argue that other approaches are still vital; the major bottleneck when using whole-genome sequencing is the availability of too much data, which can be difficult or impossible to analyze when working with large numbers of species or complicated genomes. McKain explains, "Sequencing complex and large genomes has very real methodological challenges, and there will absolutely be a place for building phylogenies out of other types of data." Gitzendanner adds, "For most fossils, DNA sequencing will never be possible, so we will continue to see developments beyond sequencing when incorporating fossil species into phylogenetic studies."

The special issue was produced to benefit both researchers entering the field as well as long-standing experts, says Gitzendanner: "We hope that these articles will not only provide a good overview of these techniques, but also spark the reader's imagination about how these methods could be applied to solve new problems." These innovative technologies provide new insights into how communities of species interact, how genomes evolve, and how plants hybridize with other species, subjects featured in the forthcoming companion special issue on the use of plant phylogenies published in APPS's sister journal, the American Journal of Botany.

These special issues are particularly timely because phylogenetics has itself evolved to adapt to the massive changes in genome sequencing technologies. In the future, McKain concludes, we can expect more data for lower costs, leading to new insights: "These cutting-edge techniques continue to push the boundaries of the questions we can ask and answer, many of which have never been considered before. This is a really exciting time to be a plant biologist!"
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The Applications in Plant Sciences special issue "Methods for Exploring the Plant Tree of Life" is available online at: https://onlinelibrary.wiley.com/toc/21680450/6/3

Gitzendanner, M. A., Y. Yang, N. J. Wickett, M. McKain, and J. M. Beaulieu. 2018. Methods for exploring the plant tree of life. Applications in Plant Sciences 6(3): e1039. https://doi.org/10.1002/aps3.1039

Articles in the issue:

Chau, J. H., W. A. Rahfeldt, and R. G. Olmstead. 2018. Comparison of taxon-specific versus general locus sets for targeted sequence capture in plant phylogenomics. Applications in Plant Sciences 6(3): e1032. https://doi.org/10.1002/aps3.1032

Endara, L., H. Cui, and J. G. Burleigh. 2018. Extraction of phenotypic traits from taxonomic descriptions for the tree of life using natural language processing. Applications in Plant Sciences 6(3): e1035. https://doi.org/10.1002/aps3.1035

Harbert, R. S. 2018. Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. Applications in Plant Sciences 6(3): e1034. https://doi.org/10.1002/aps3.1034

Li, F.-W., and A. Harkess. 2018. A guide to sequence your favorite plant genomes. Applications in Plant Sciences 6(3): e1030. https://doi.org/10.1002/aps3.1030

McKain, M. R., M. G. Johnson, S. Uribe-Convers, D. Eaton, and Y. Yang. 2018. Practical considerations for plant phylogenomics. Applications in Plant Sciences 6(3): e1038. https://doi.org/10.1002/aps3.1038

Sedio, B. E., C. A. Boya P., and J. C. Rojas Echeverri. 2018. A protocol for high-throughput, untargeted forest community metabolomics using mass spectrometry molecular networks. Applications in Plant Sciences 6(3): e1033. https://doi.org/10.1002/aps3.1033

Tovar, J. C., J. S. Hoyer, A. Lin, A. Tielking, S. T. Callen, S. E. Castillo, M. Miller, et al. 2018. Raspberry Pi-powered imaging for plant phenotyping. Applications in Plant Sciences 6(3): e1031. https://doi.org/10.1002/aps3.1031

Vatanparast, M., A. Powell, J. J. Doyle, and A. N. Egan. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. Applications in Plant Sciences 6(3): e1036. https://doi.org/10.1002/aps3.1036

Zenil-Ferguson, R., J. G. Burleigh, and J. M. Ponciano. 2018. chromploid: An R package for chromosome number evolution across the plant tree of life. Applications in Plant Sciences 6(3): e1037. https://doi.org/10.1002/aps3.1037

Applications in Plant Sciences (APPS) is a monthly, peer-reviewed, open access journal focusing on new tools, technologies, and protocols in all areas of the plant sciences. It is published by the >Botanical Society of America, a nonprofit membership society with a mission to promote botany, the field of basic science dealing with the study and inquiry into the form, function, development, diversity, reproduction, evolution, and uses of plants and their interactions within the biosphere. APPS is available as part of the Wiley Online Library.

For further information, please contact the APPS staff at apps@botany.org.

Botanical Society of America

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