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Practical considerations for plant phylogenomics

The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes an...

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Autores principales: McKain, Michael R., Johnson, Matthew G., Uribe‐Convers, Simon, Eaton, Deren, Yang, Ya
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895195/
https://www.ncbi.nlm.nih.gov/pubmed/29732268
http://dx.doi.org/10.1002/aps3.1038
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author McKain, Michael R.
Johnson, Matthew G.
Uribe‐Convers, Simon
Eaton, Deren
Yang, Ya
author_facet McKain, Michael R.
Johnson, Matthew G.
Uribe‐Convers, Simon
Eaton, Deren
Yang, Ya
author_sort McKain, Michael R.
collection PubMed
description The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further.
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spelling pubmed-58951952018-05-04 Practical considerations for plant phylogenomics McKain, Michael R. Johnson, Matthew G. Uribe‐Convers, Simon Eaton, Deren Yang, Ya Appl Plant Sci Review Articles The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. The development of high‐throughput sequencing and long‐read technologies has ushered in the era of phylogenomics, where hundreds to thousands of nuclear genes and whole organellar genomes are routinely used to reconstruct evolutionary relationships. As a result, understanding which options are best suited for a particular set of questions can be difficult, especially for those just starting in the field. Here, we review the most recent advances in plant phylogenomic methods and make recommendations for project‐dependent best practices and considerations. We focus on the costs and benefits of different approaches in regard to the information they provide researchers and the questions they can address. We also highlight unique challenges and opportunities in plant systems, such as polyploidy, reticulate evolution, and the use of herbarium materials, identifying optimal methodologies for each. Finally, we draw attention to lingering challenges in the field of plant phylogenomics, such as reusability of data sets, and look at some up‐and‐coming technologies that may help propel the field even further. John Wiley and Sons Inc. 2018-04-02 /pmc/articles/PMC5895195/ /pubmed/29732268 http://dx.doi.org/10.1002/aps3.1038 Text en Applications in Plant Sciences is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Review Articles
McKain, Michael R.
Johnson, Matthew G.
Uribe‐Convers, Simon
Eaton, Deren
Yang, Ya
Practical considerations for plant phylogenomics
title Practical considerations for plant phylogenomics
title_full Practical considerations for plant phylogenomics
title_fullStr Practical considerations for plant phylogenomics
title_full_unstemmed Practical considerations for plant phylogenomics
title_short Practical considerations for plant phylogenomics
title_sort practical considerations for plant phylogenomics
topic Review Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895195/
https://www.ncbi.nlm.nih.gov/pubmed/29732268
http://dx.doi.org/10.1002/aps3.1038
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