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

Content Provider	Springer Nature Link
Author	Orton, Lauren M. Burke, Sean V. Wysocki, William P. Duvall, Melvin R.
Copyright Year	2016
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.
Starting Page	311
Ending Page	323
Page Count	13
File Format	PDF
ISSN	01728083
Journal	Current Genetics
Volume Number	63
Issue Number	2
e-ISSN	14320983
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2016-08-03
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Zea Phylogeny Microstructural changes Evolutionary divergence Grasses Plastid Microbial Genetics and Genomics Microbiology Biochemistry Cell Biology Plant Sciences Proteomics
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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