Patrick Edger

Assistant Professor

Patrick Edger

PhD

1066 Bogue St, Room A334
East Lansing, MI 48824

Phone: 765-749-1496

Area of Expertise: Polyploid Genomics

Quick links: Teaching   Publications

The primary research interest of my lab lies in understanding how plant genomes have and continue to be shaped by the environment. My lab leverages a diverse array of tools and a strong multidisciplinary approach, including comparative genomics, transcriptomics, phylogenetics and systems biology, to investigate gene family dynamics, the evolution of novel gene functions, and gene-gene interactions. Our research spans multiple phylogenetic scales from the species-level to eudicot-wide comparisons, but are largely focused on the families Rosaceae and Ericaceae, due to availability of rich genomic resources that are being generated by us and others in the scientific community. We use this approach to also identify markers that can be selected or modified to improve fruit quality, a(biotic) resistances, and yield of strawberry and blueberry cultivars.

“Nothing in biology makes sense except in the light of evolution.” - T. Dobzhansky

 

Teaching

HRT 362: Applied Crop Improvement (1 credit): Co-taught with Dr. Cornelius Barry

HRT 821: Crop Evolution (1 credit)

This five week module is taught as a sequence following HRT 820 (Plant Reproductive Biology and Polyploidy; Dr. Amy Iezzoni) and prior to HRT 822 (Historical Georgraphy of Crop Plants; Dr. Bob VanBuren)

HRT 892: Plant Breeding and Genetics Seminar on “Polyploidy” (1 credit)

 

Publications

2016

  1. Golicz, A.A., P.E. Bayer, G.C. Barker, P.P. Edger, H. Kim, P.A. Martinez, C.K.K. Chan, A. Severn-Ellis, W.R. McCombie, I.A.P. Parkin, A.H. Paterson, J.C. Pires, A.G. Sharpe, H. Tang, G.R. Teakle,C.D. Town, J. Batley and D. Edwards. 2016. The pangenome of an agronomically important cropplant Brassica oleracea. Nature Communications. Accepted.
  2. Bourque, S., V. Grandperret, S. Jeandroz, N. Lehotai, S. Aimé, D.E. Soltis, N.W. Miles, M. Melkonian, B. Surek, M.K. Deyholos, J.H. Leebens-Mack, M.W. Chase, C.J. Rothfels, D.W. Stevenson, S.W. Graham, X. Wang, S. Wu, J.C. Pires, P.P. Edger, Z. Yan, Y. Xie, E.J. Carpenter, G.K.S. Wong, D. Wendehenne and V. Nicolas-Francès. 2016. Type-2 HDACs: their evolution through the plant kingdom. Trends in Plant Sciences. Accepted.
  3. Nakano, R.T., M. Piƛlewska-Bednarek, K. Yamada, P.P. Edger, M. Miyahara, M. Kondo, C. Böttcher, M. Mori, M. Nishimura, P. Schulze-Lefert, I. Hara-Nishimura, and P. Bednarek. 2016. PYK10 Myrosinase Reveals a Functional Coordination between ER Bodies and Glucosinolates in Arabidopsis thaliana. The Plant Journal. Accepted. Published Online. http://onlinelibrary.wiley.com/doi/10.1111/tpj.13377/full
  4. Burke, S.V., W.P. Wysocki, F.O. Zuloaga, J.M. Craine, J.C. Pires, P.P. Edger, D. Mayfield-Jones, L.G. Clark, S.A. Kelchner, and M.R. Duvall. 2016. Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae). BMC Plant Biology. 16(1): 140. http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-016-0823-3
  5. Lane, T.S., C.S. Rempe, J. Davitt, M.E. Staton, Y. Peng, D.E. Soltis, M. Melkonian, M. Deyholos, J.H. Leebens-Mack, M. Chase, C.J. Rothfels, D. Stevenson, S.W. Graham, J. Yu, T. Liu, J.C. Pires, P.P. Edger, Y. Zhang, Y. Xie, Y. Zhu, E. Carpenter, G.K. Wong, and C.N. Stewart. 2016. Diversity of ABC transporter genes across the plant kingdom and their potential utility in biotechnology. BMC Biotechnology. 16(47): 1. https://bmcbiotechnol.biomedcentral.com/articles/10.1186/s12896-016-0277-6
  6. VanBuren, R., D. Bryant, J.M. Bushakra, K.J. Vining, P.P. Edger, E.R. Rowley, H.D. Priest, T.P. Michael, E. Lyons, S.A. Filichkin, M. Dossett, C.E. Finn, N.V. Bassil, and T.C. Mockler. 2016. The genome of black raspberry (Rubus occidentalis). The Plant Journal. 87(6): 535-547. http://onlinelibrary.wiley.com/doi/10.1111/tpj.13215/full
  7. Davin, N., P.P. Edger, C.A. Hefer, E. Mizrachi, M. Schuetz, E. Smets, A.A. Myburg, C.J. Douglas, M.E. Schranz, and F. Lens. 2016. Functional network analysis of genes differentially expressed during xylogenesis in soc1ful woody Arabidopsis plants. The Plant Journal. 86(5): 376-390 http://onlinelibrary.wiley.com/doi/10.1111/tpj.13157/full
  8. Honaas, L.A., E.K. Wafula, N.J. Wickett, J.P. Der, Y. Zhang, P.P. Edger, N.S. Altman, J.C. Pires, J.H. Leebens-Mack, and C.W. dePamphilis. 2016. Selecting superior de novo transcriptome assemblies: Lessons learned by leveraging the best plant genome. PloS One. 11(1): e0146062 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0146062
  9. Huang, C., R. Sun, Y. Hu, L. Zeng, N. Zhang, L. Cai, Q. Zhang, M.A. Koch, I. Al-Shehbaz, P.P. Edger, J.C. Pires, D. Tan, Y. Zhong, and H. Ma. 2016. Resolution of Brassicaceae phylogeny using nuclear genes uncovers nested radiations and supports convergent morphological evolution. Molecular Biology Evolution. 33 (2), 394-412. http://mbe.oxfordjournals.org/content/early/2015/10/28/molbev.msv22

2015

  1. VanBuren, R., D. Bryant, P.P. Edger, et al. 2015. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeumNature. Published online Nov 11th.. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature15714.html
  2. Ming, R., R. VanBuren, C.M. Wai, et al. 2015. The Pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47: 1435-1442.  http://www.nature.com/ng/journal/v47/n12/full/ng.3435.html* Cover art and highlighted article
  3. Mohammadin, S., P.P. Edger, J.C. Pires, and M.E. Schranz. 2015. Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. BMC Plant Biology.15(1): 217. http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-015-0603-5
  4. Cotton, J.L., W.P. Wysocki., L.G. Clark, et al. 2015. Resolving deep relationships of PACMAD grasses; a phylogenomic approach. BMC Plant Biology. 15(1), 178. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4498559/
  5. Edger, P.P., H. M. Heidel-Fischer, M. Bekaert, et al. 2015. The Butterfly Plant Arms-Race Escalated by Gene and Genome Duplications. PNAS 112(27), 8362-8366. http://www.pnas.org/content/112/27/8362.long 
  6. Saarela, J.M., W.P. Wysocki, C. Barrett, et al. 2015. Plastid phylogenomics of the cool-season grass subfamily Pooideae (Poaceae). AoB Plants Plv046.  http://aobpla.oxfordjournals.org/content/7/plv046.long
  7. Augustin, M.M., D. Ruzicka, A.K. Shukla, et al. 2015. Accelerating biochemical pathway elucidation in non-model systems: Formation of the antineoplastic cyclopamine in Veratrum californicumThe Plant Journal. 82(6): 991-1003. http://onlinelibrary.wiley.com/doi/10.1111/tpj.12871/abstract

2014

  1. Floyd, S.K., J.G. Ryan, S.J. Conway, et al. 2014. Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Mol. Phylogenetics & Evolution 81: 159-73. http://www.sciencedirect.com/science/article/pii/S1055790314002309
  2. Chalhoub B., F. Denoeud, S. Liu, et al. 2014. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345 (6199): pg 950-953.  http://classic.sciencemag.org/content/345/6199/950.long
  3. Wysocki, W.P., L.G. Clark, S.A. Kelchner, et al. 2014. A multi-step comparison of short-read full plastome sequence assembly methods in grasses. Taxon 11: p20. http://www.ingentaconnect.com/content/iapt/tax/2014/00000063/00000004/art00015
  4. Delaux, P., K. Varala, P.P. Edger, et al. 2014. Comparative Phylogenomics Uncovers The Impact of Symbiotic Associations on Host Genome Evolution. PloS Genetics. 10 (7): e1004487. http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004487
  5. Kagale, S., S.J. Robinson, J. Nixon, et al. 2014. Polyploid Evolution of the Brassicaceae during the Cenozoic Era. The Plant Cell. 26 (7): 2777-2791. http://www.plantcell.org/content/26/7/2777.full
  6. Edger, P.P., M. Tang,  K.A. Bird, et al. 2014. Secondary Structure Analyses of the nuclear rRNA Internal Transcribed Spacers and Assessment of its Phylogenetic Utility across the Brassicaceae (Mustards). PloS ONE. 9: e101341. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101341
  7. Grewe, F., P.P. Edger, I. Keren, et al. 2014. Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleraceaMitochondrion. 19, 135-143. http://www.sciencedirect.com/science/article/pii/S1567724914000828

2013 and before

  1. Haudry, A., A.E. Platts, E. Vello et al. 2013. An Atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nature genetics 45 (8), 891-898. http://www.nature.com/ng/journal/v45/n8/abs/ng.2684.html
  2. Mayfield-Jones, D., J.D. Washburn, T. Arias, et al. 2013. Watching the grin fade: tracing the effects of polyploidy on different evolutionary time scales. Seminars in Cell & Developmental Biology 24 (4): 320-331. http://www.sciencedirect.com/science/article/pii/S1084952113000207
  3. Hofberger, J.A., E. Lyons, P.P. Edger, et al. 2013. Whole genome and tandem duplicate retention facilitated glucosinolate pathway diversification in the mustard family. Genome Biology and Evolution. 5 (11): 2155-2173. http://gbe.oxfordjournals.org/content/5/11/2155.full
  4. Johnson, M.T.J., E.J. Carpenter, Z. Tian, et al. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. Plos One. 7 (11) e50226. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0050226
  5. Bekaert, M., P.P. Edger, C.M. Hudson, J.C. Pires, and G.C. Conant. 2012 Metabolic and evolutionary costs of herbivory defense: systems biology of glucosinoalte biosynthesis. New Phytologist. 196 (2): 596-605. http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2012.04302.x/full
  6. Schranz, M.E., S. Mohammadin, and P.P. Edger. 2012. Ancient whole genome duplicaitons, novelty and diversification: the WGD Radiation Lag-Time Model. Current Opinion of Plant Biology. 15 (2): 147-153. http://www.sciencedirect.com/science/article/pii/S1369526612000465
  7. Bekaert, M., P.P. Edger, J.C. Pires, and G.C. Conant. 2011. Two-phase resolution of polyploidy in the Arabidopsis metabolic network gives rise to relative and absolute dosage constraints. The Plant Cell. 23 (5): 1719-1728.  http://www.plantcell.org/content/23/5/1719.full
  8. Duarte, J.M., P.K. Wall, P.P. Edger, et al. 2010. Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Orzya and their phylogenetic utility across various taxonomic levels. BMC Evolutionary Biology 10 (1): 61. http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-61
  9. P.P. Edger and J.C. Pires. 2009. Gene and Genome Duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Research. 17 (5): 699-717. http://link.springer.com/article/10.1007/s10577-009-9055-9

 

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