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Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes

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Abstract

This project examines the relationships within the genus Zea using complete plastid genomes (plastomes). While Zea mays has been well studied, congeneric species have yet to be as thoroughly examined. For this study four complete plastomes and a fifth nearly complete plastome were sequenced in the five species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis) by Sanger or next-generation methods. An analysis of the microstructural changes, such as inversions, insertion or deletion mutations (indels) and determination of their frequencies were performed for the complete plastomes. It was determined that 193 indels and 15 inversions occurred across the examined plastomes of Zea. Tandem repeat indels were the most common type of microstructural change observed. Divergence times were estimated using a noncorrelated relaxed clock method. Divergence dates for specific nodes relative to Zea were calculated to fall between 38,000 years before present (YBP) for the subspecies included in this study and 23,000 YBP for section Luxuriantes included in this study. The stem lineage of all Zea species was calculated to have diverged at 176,000 YBP. The calculated mutation rates for the genus fell within the range of 1.7E−8 to 3.5E−8 microstructural changes per site per year. These rates of change are not uniform, despite the close relationships of taxa in this study. Phylogenomic analyses using full plastome alignments were also conducted to compare tree topologies from different types of mutations. In most cases, the previous work examining Zea mitochondrial and nuclear data was confirmed.

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Acknowledgments

We thank the Iowa State University Seed Science Center and Seed Lab under the direction of Mr. Mike Stahr, the Small Seed Department Head, Ms. Kim North, and Mr. Mark Millard of the USDA/ARS Plant Introduction Station at Iowa State University for providing the seed accessions used within this study. We also extend our gratitude to Dr. Scot Kelchner for providing a review of an earlier draft of this manuscript. We acknowledge the support of the National Science Foundation (NSF Grants DEB-1120761 and DEB-1342782 to MRD). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. Finally, we thank the Department of Biological Sciences and the Plant Molecular and Bioinformatics Center at Northern Illinois University for financial assistance.

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  1. William P. Wysocki

    Present address: University of Chicago, Center for Data Intensive Sciences, 5454 S. Shore Dr., Chicago, IL, 60615, USA

Authors and Affiliations

  1. Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, Dekalb, IL, 60115-2861, USA

    Lauren M. Orton, Sean V. Burke, William P. Wysocki & Melvin R. Duvall

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  1. Lauren M. Orton
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Correspondence to Lauren M. Orton.

Additional information

Communicated by M. Kupiec.

Sean V. Burke, William P. Wysocki, and Melvin R. Duvall contributed equally to this work.

Nucleotide sequence data reported are available in the GenBank database under the accession numbers: KR873421, KR873422, KR873423, KR873424, and KU291447.

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Orton, L.M., Burke, S.V., Wysocki, W.P. et al. Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes. Curr Genet 63, 311–323 (2017). https://doi.org/10.1007/s00294-016-0637-8

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