Michael J Sanderson1, Dario Copetti2, Alberto Búrquez3, Enriquena Bustamante3, Joseph L M Charboneau1, Luis E Eguiarte4, Sudhir Kumar5, Hyun Oh Lee6, Junki Lee7, Michelle McMahon8, Kelly Steele9, Rod Wing2, Tae-Jin Yang9, Derrick Zwickl1, Martin F Wojciechowski10. 1. Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA. 2. School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines. 3. Instituto de Ecologia, Unidad Hermosillo, UNAM, Hermosillo, Sonora, Mexico. 4. Instituto de Ecologia, UNAM Mexico D.F., Mexico. 5. Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania 19122 USA. 6. Phyzen Genomics Institute, 501-1, Gwanak Century Tower, Gwanak-gu, Seoul, 151-836, Republic of Korea. 7. Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. 8. School of Plant Sciences, University of Arizona, Tucson, Arizona 85721 USA. 9. Faculty of Science and Mathematics, College of Letters and Sciences, Arizona State University, Mesa, Arizona 85212 USA. 10. School of Life Sciences, Arizona State University, Tempe, Arizona 85287 USA.
Abstract
UNLABELLED: • PREMISE OF THE STUDY: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.• METHODS: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).• KEY RESULTS: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.• CONCLUSIONS: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
UNLABELLED: • PREMISE OF THE STUDY: Land-plant plastid genomes have only rarely undergone significant changes in gene content and order. Thus, discovery of additional examples adds power to tests for causes of such genome-scale structural changes.• METHODS: Using next-generation sequence data, we assembled the plastid genome of saguaro cactus and probed the nuclear genome for transferred plastid genes and functionally related nuclear genes. We combined these results with available data across Cactaceae and seed plants more broadly to infer the history of gene loss and to assess the strength of phylogenetic association between gene loss and loss of the inverted repeat (IR).• KEY RESULTS: The saguaro plastid genome is the smallest known for an obligately photosynthetic angiosperm (∼113 kb), having lost the IR and plastid ndh genes. This loss supports a statistically strong association across seed plants between the loss of ndh genes and the loss of the IR. Many nonplastid copies of plastid ndh genes were found in the nuclear genome, but none had intact reading frames; nor did three related nuclear-encoded subunits. However, nuclear pgr5, which functions in a partially redundant pathway, was intact.• CONCLUSIONS: The existence of an alternative pathway redundant with the function of the plastid NADH dehydrogenase-like complex (NDH) complex may permit loss of the plastid ndh gene suite in photoautotrophs like saguaro. Loss of these genes may be a recurring mechanism for overall plastid genome size reduction, especially in combination with loss of the IR.
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