Plant mitochondrial genomes are extremely large and variably sized (200-2,400 kb) compared to other eukaryotes (typically 15-60 kb). Remarkably, most of the inordinate size range in plants is encompassed by a single family, the Cucurbitaceae, whose mitochondrial genomes vary in size from 330 to 2,400 kb. One common and frustrating theme in plant mitochondrial genomics is that the overwhelming majority of size variation is due to large amounts of intergenic DNA with no identifiable homology to known sequences. This is also true in cucurbits, where 65-87% of the mitochondrial DNA (mtDNA) is of unknown origin. Discovering the source of these enigmatic sequences is one of the major challenges in mitochondrial genomics and represents a primary goal of this project. Beyond identifying the source of these sequences, a further goal is to identify the general processes facilitating the growth of plant mitochondrial genomes. A recent study proposed that similar population genetic processes govern the evolution of nuclear and organellar genome size and concluded that the disparity in mitochondrial genome size between plants and animals reflects their drastically different mitochondriaI mutation rates. That is, the vast amounts of noncoding sequence in plant mitochondrial genomes owe to the near-universally low mutation rate observed in plant mtDNA. By extension, the largest cucurbit mitochondrial genomes are predicted to have the lowest nucleotide substitution rates. Data from this project will provide the first empirical test of this hypothesis. The Cucurbitaceae offer an exciting opportunity both to address longstanding problems in plant mitochondrial genomics and to test provocative new hypotheses on genome evolution in the broad sense. I propose to fully sequence the mitochondrial genomes for 6-10 cucurbit plants and use a complementary set of experimental and bioinformatic approaches to test explicit hypotheses about the expansion and contraction of these exceptional mitochondrial genomes. In addition to forwarding the NIH mission to foster creative scientific discovery and expand our basic scientific knowledge base, this project has broader significance to the field of mitochondrial genomics. In humans, mitochondrial DNA mutations retard energy production and contribute to a number of age-related diseases. These mtDNA mutations accumulate 50- 100 faster in animals than in plants! Therefore, a full understanding of this disparity could benefit our understanding of age-related disease and illness. Comparative genomic studies like this one provide a powerful and efficient way to characterize """"""""enviable"""""""" genomic properties (i.e., the extraordinarily low nucleotide substitution rate of plants) and identify the processes that underlie them. ? ? ?

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
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Special Emphasis Panel (ZRG1-F08-G (20))
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Portnoy, Matthew
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Indiana University Bloomington
Schools of Arts and Sciences
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Richardson, Aaron O; Rice, Danny W; Young, Gregory J et al. (2013) The ""fossilized"" mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate. BMC Biol 11:29
Samson, Thomas; van Buul, Jaap D; Kroon, Jeffrey et al. (2013) The guanine-nucleotide exchange factor SGEF plays a crucial role in the formation of atherosclerosis. PLoS One 8:e55202
Sloan, Daniel B; Alverson, Andrew J; Chuckalovcak, John P et al. (2012) Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates. PLoS Biol 10:e1001241
Alverson, Andrew J; Rice, Danny W; Dickinson, Stephanie et al. (2011) Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell 23:2499-513
Alverson, Andrew J; Beszteri, Bánk; Julius, Matthew L et al. (2011) The model marine diatom Thalassiosira pseudonana likely descended from a freshwater ancestor in the genus Cyclotella. BMC Evol Biol 11:125
Alverson, Andrew J; Zhuo, Shi; Rice, Danny W et al. (2011) The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 6:e16404
Wu, Chuanshen; Agrawal, Sudesh; Vasanji, Amit et al. (2011) Rab13-dependent trafficking of RhoA is required for directional migration and angiogenesis. J Biol Chem 286:23511-20
Borikova, Asya L; Dibble, Christopher F; Sciaky, Noah et al. (2010) Rho kinase inhibition rescues the endothelial cell cerebral cavernous malformation phenotype. J Biol Chem 285:11760-4
Samson, Thomas; Welch, Christopher; Monaghan-Benson, Elizabeth et al. (2010) Endogenous RhoG is rapidly activated after epidermal growth factor stimulation through multiple guanine-nucleotide exchange factors. Mol Biol Cell 21:1629-42
Dibble, Christopher F; Horst, Jeremy A; Malone, Michael H et al. (2010) Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate. PLoS One 5:e11740

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