Bio 431 - Molecular Genetic Analysis of Plant Evolution

Sept 12

Horizontal gene transfer in plants

Wickell, DA & F-W Li.  2019.  On the evolutionary significance of horizontal gene transfers in plants.  The New Phytologist   doi: 10.1111/nph.16022

Li, F-W and 33 others. 2014. Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns. Proceedings of the National Academy of Sciences, USA 111: 6672-6677.

Sept 19

Genetics underlying establishment of arbuscular mycorrhizal symbioses

Choi, J, W Summers, and U Paszkowski.  2018.  Mechanisms underlying establishment of arbuscular mycorrhizal symbioses.  Annual Review of Phytopathology 56: 135-160.

Labbé, J, W Muchero,  O Czarnecki,  J Wang,  X Wang,  AC Bryan,  K Zheng,  Y Yang,  M Xie,  J.Zhang,  D Wang,  P Meidl,  H Wang,  JL Morrell-Falvey,  KR Cope,  LGS Maia,  J-M Ané,  R Mewalal,  SS Jawdy,  LE Gunter,  W Schackwitz,  J Martin,  F Le Tacon,  T Li, ,  Z Zhang, ,  P Ranjan, Priya,  E Lindquist, Erika,  X Yang,  DA Jacobson,  TJ Tschaplinski,  K Barry,  J Schmutz,  J-G Chen, &  GA Tuskan. 2019. Mediation of plant–mycorrhizal interaction by a lectin receptor-like kinase.  Nature Plants 5: 676–680.

Sept 26

Molecular genetics of herbivory

Kariñho-Betancourt, E. 2019. Coevolution: Plant-herbivore interactions and secondary metabolites of plants, in, Merillon JM., Ramawat K. (eds) Co-Evolution of Secondary Metabolites. Reference Series in Phytochemistry. Springer, Cham.

Nallu, S,  JA Hill, K Don, C Sahagun, W Zhang, C Meslin, E Snell-Rood, NL Clark, NI Morehouse, J Bergelson, CW Wheat, & MR Kronforst.  2018.  The molecular genetic basis of herbivory between butterflies and their host plants.  Nature Ecology & Evolution 2: 1418-1427.

Oct 3

Molecular genetics of whole genome duplication

Clark, JW, & PCJ Donoghue.  2018.  Whole-genome duplication and plant macroevolution. Trends in Plant Sciences 23: 933-945. 

Kagale, S, SJ Robinson, J Nixon, R Xiao, T Huebert, J Condie, D Kessler, WE Clarke, PP Edger, MG Links, AG Sharpe, & IAP Parkin.  2014. Polyploid evolution of the Brassicaceae during the Cenozoic era. Plant Cell 26: 2777–2791.

Oct 10

Molecular analysis of a living fossils

Royer, DL,  LJ Hickey & SL Wing. 2003.  Ecological conservatism in the ‘living fossil’ Ginkgo. Paleobiology 29: 84–104. 

Zhao, YP, G Fan, P-P Yin, S Sun, N Li, X Hong, G Hu, H Zhang, F-M Zhang, J-D Han, Y-J Hao, Q Xu, X Yang, W Xia, W Chen, H-Y Lin, R Zhang, J Chen, X-M Zheng, SM-Y Lee, J Lee, K Uehara, J Wang, H Yang, C-X Fu, X Liu, X Xu & S Ge. 2019.  Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil.  Nature Communications 10: 4201

Oct 17

Evolutionary genetics of photosynthesis

Heyduk, K, JJ  Moreno-Villena, IS Gilman, P-A Christin, and EJ Edwards. 2019. The genetics of convergent evolution: insights from plant photosynthesis. Nature Reviews Genetics 20: 485–493.

Goolsby, EW, AJ Moore, LP Hancock, JM De Vos, and EJ Edwards. 2018. Molecular evolution of key metabolic genes during transitions to C-4 and CAM Photosynthesis. American Journal of Botany 105: 602–613.

Oct 31

Comapring NGS approaches for plant genetics

Torkamaneh, D, B Boyle & F Belzile. 2018. Efficient genome-wide genotyping strategies and data integration in crop plants. Theoretical and Applied Genetics 131: 499.

Darrier, B, J Russell, SG Milner, PE Hedley, PD Shaw, M Macaulay, LD Ramsay, C Halpin, M Mascher, DL Fleury, P Langridge, N Stein & R Waugh. 2019. A comparison of mainstream genotyping platforms for the evaluation and use of barley genetic resources. Frontiers in Plant Science 10: 544.

Nov 7

Conservation genomics

Shafer, ABA, JBW Wolf, PC Alves, L Bergström, MW Bruford, I Brännström, G Colling, L Dalén, LD  Meester, R Ekblom, KD Fawcett, S Fior, M Hajibabaei, JA Hill, AR Hoezel, J Höglund, EL Jensen, J Krause, TN Kristensen, M Krützen, JK McKay, AJ Norman, R Ogden, EM Österling, NJ Ouborg, J Piccolo, D Popović, CR Primmer, FA Reed, M Roumet, J Salmona, T Schenekar, MK Schwartz, G Segelbacher, H Senn, J Thaulow, M Valtonen, A Veale, P Vergeer, N Vijay, C Vilà, M Weissensteiner, L Wennerström, CW Wheat, & P Zieliński. 2015.  Genomics and the challenging translation into conservation practice.  Trends in Ecology & Evolution 30:  78-87.

Cordeiro, EMG, CM Macrini, PS Sujii, KD Schwarcz, JB Pinheiro, RR Rodrigues, PHS Brancalion & MI  Zucchi.  2019.  Diversity, genetic structure, and population genomics of the tropical tree Centrolobium tomentosum in remnant and restored Atlantic forests.  Conservation Genetics 20: 1073.

Nov 14

Epigenetic dynamics in plants

Gehring, M.  2019.   Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming?  New Phytologist 224: 91-96.

Sijacic P, M Bajic, EC McKinne, RB Meagher, & RB Dea. 2018. Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks. The Plant Journal 94: 215–231.

Nov 21

The evolution of anthocyanin pathway enzymes

Bar-Even, A, E Noor, Y Savir, W Liebermeister, D Davidi, DS Tawfik , & R Milo. 2011. The moderately efficient enzyme:  evolutionary and physicochemical trends shaping enzyme parameters. Biochemistry 50: 4402–4410.

Wheeler, LC, & SD Smit. 2019.  Computational modeling of anthocyanin pathway evolution: biases, hotspots, and trade-offs.  Integrative and Comparative Biology 59: 585-598.

Dec 5

Evolutionary genetics of crop domestication & improvement

Purugganan, MD.  2019.  Evolutionary insights into the nature of plant domestication.  Current Biology 29: R705-R714.

Fang, H , X Fu, Y Wang, J  Xu, H Feng, W Li, J Xu, O Jittham, X Zhang, L Zhang, N Yang, G Xu, M Wang, X Li, J Li, J Yan, & X Yang.  2019.  Genetic basis of kernel nutritional traits during maize domestication and improvement. Plant Journal doi:10.1111/tpj.14539

Dec 10

The genetics of  crop arbuscular mycorrhizal symbioses

Lehnert, H, A Serfling, M Enders, W Friedt, & F Ordon.  2017.  Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum). New Phytologist 215: 779-791.

(for a review, you might reread from week 2:

Choi, J, W Summers, and U Paszkowski.  2018.  Mechanisms underlying establishment of arbuscular mycorrhizal symbioses.  Annual Review of Phytopathology 56: 135-160.)