2015.  

Evolutionary Developmental Biology - Graduate course

This is a class of seminar for the plant Evo-devo papers

ANNOUNCEMENTS

1. All students have to read two papers per a class and will present them as a format of symposium talk. And students have to prepare 1 page of handout and submit them to professor and other students (Direct translate of abstract is NOT allowed).

2. About 70 core papers for the plant Evo-Devo studies are prepared.

    Download CORE PAPERS for plant Evo-Devo studies

3. Grading: evaluate presentation (50%) and submitted handout (50%)

4. This class is resceduled to Wed. 3:00 PM.

 

Presentation Schedule

Sep. 1 (Week 1) Introduction

 

Sep. 9 (Week 2)

Coen ES, Meyerowitz EM (1991) The war of thewhorls: genetic interactions controlling flower development. Nature 353, 31-37.

Sommer H, Beltran J-P, Huijser P, et al. (1990) Deficiens, a homeoticgene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. The EMBO Journal 9, 605.

Bowman JL, Alvarez J, Weigel D, Meyerowitz EM, Smyth DR (1993) Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. Development 119, 721-743.

 

Sep. 16 (Week 3)

Weigel D, Meyerowitz EM (1994) The ABCs of floral homeotic genes. Cell 78, 203-209.

KramerEM, Dorit RL, Irish VF (1998) Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages. Genetics 149, 765-783.

Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes & Development 8, 1548-1560

 

Sep. 23 (Week 4)

     No class: students will attend the annual meeting of the Korean Society of Celluar and Molecular Biology.

 

Sep. 30 (Week 5)

Cacharr n J, Saedler H, Theissen G (1999) Expression of MADS box genes ZMM8 and ZMM14 during inflorescence development of Zea mays discriminates between the upper and the lower floret of each spikelet. Dev Genes Evol 209, 411-420.

Kramer EM, Irish VF (1999) Evolution of genetic mechanisms controlling petal development. Nature 399, 144-148.

Winter KU, Becker A, Munster T, et al. (1999) MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants. Proc Natl Acad Sci U S A 96, 7342-7347.

 

Oct. 7 (Week  6)

Pelaz S, Tapia-López R, Alvarez-Buylla ER, Yanofsky MF (2001) Conversion of leaves into petals in Arabidopsis. Current Biology 11, 182-184.

Theißen G, Saedler H (2001) Plant biology: floral quartets. Nature 409, 469-471.

Alvarez-Buylla ER, Pelaz S, Liljegren SJ, et al. (2000) An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci U S A 97, 5328-5333.

 

Oct. 14 (Week  7)

Ambrose BA, Lerner DR, Ciceri P, et al. (2000) Molecular and Genetic Analyses of the Silky1 Gene Reveal Conservation in Floral Organ Specification between Eudicots and Monocots. Mol Cell 5, 569-579.

Winter K-U, Weiser C, Kaufmann K, et al. (2002a) Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization. Molecular Biology and Evolution 19, 587-596.

Soltis DE, Soltis PS, Albert VA, et al. (2002) Missing links: the genetic architecture of flower and floral diversification. Trends in Plant Science 7, 22-31.

 

Oct. 21 (Week  8)

Irish VF (2009) Evolution of petal identity. J Exp Bot 60, 2517-2527.

Melzer R, Theissen G (2009) Reconstitution of 'floral quartets' in vitro involving class B and class E floral homeotic proteins. Nucleic Acids Res 37, 2723-2736.

Cui R, Han J, Zhao S, et al. (2010) Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). The Plant Journal 61, 767-781.

 

Oct. 28 (Week  9)

Winter KU, Saedler H, Theißen G (2002b) On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum. The Plant Journal 31, 457-475.

Becker A, Kaufmann K, Freialdenhoven A, et al. (2002) A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Mol Genet Genomics 266, 942-950.

Becker A, Saedler H, Theissen G (2003) Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon. Dev Genes Evol 213, 567-572.

 

Nov. 4  (Week  10)

Kramer EM, Di Stilio VS, Schlüter PM (2003) Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. International Journal of Plant Sciences 164, 1-11.

Kanno A, Saeki H, Kameya T, Saedler H, Theissen G (2003) Heterotopic expression of class B floral homeotic genes supports a modified ABC model for tulip (Tulipa gesneriana). Plant molecular biology 52, 831-841.

Litt A, Irish VF (2003) Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165, 821-833.

 

Nov. 11 (Week  11)

Pinyopich A, Ditta GS, Savidge B, et al. (2003) Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature 424, 85-88.

Parenicova L, de Folter S, Kieffer M, et al. (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15, 1538-1551.

Ditta G, Pinyopich A, Robles P, Pelaz S, Yanofsky MF (2004) The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol 14, 1935-1940.

 

Nov. 18 (Week  12)

Kim S, Yoo MJ, Albert VA, et al. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am J Bot 91, 2102-2118.

Nam J, Kim J, Lee S, et al. (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc Natl Acad Sci U S A 101, 1910-1915.

Malcomber ST, Kellogg EA (2004) Heterogeneous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE1 in grasses. The Plant Cell Online 16, 1692-1706.

 

Nov. 25 (Week  13)

Vandenbussche M, Zethof J, Royaert S, Weterings K, Gerats T (2004) The duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development. The Plant Cell Online 16, 741-754.

Buzgo M, Soltis PS, Kim S, Soltis DE (2005) The making of the flower-The evolution of flowers has long been a matter of intense debate. Recent hypotheses are changing the way we view their origins. Biologist-London 52, 149-154.

Tzeng T-Y, Liu H-C, Yang C-H (2004) The C-terminal sequence of LMADS1 is essential for the formation of homodimers for B function proteins. Journal of Biological Chemistry 279, 10747-10755.

 

Dec. 2 (Week  14)

de Folter S, Angenent GC (2006) trans meets cis in MADS science. Trends Plant Sci 11, 224-231.

Kim S, Koh J, Yoo MJ, et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant J 43, 724-744.

Malcomber ST, Kellogg EA (2005) SEPALLATA gene diversification: brave new whorls. Trends in Plant Science 10, 427-435.

 

Dec. 9 (Week  15)

Di Stilio VS (2011) Empowering plant evo-devo: virus induced gene silencing validates new and emerging model systems. Bioessays 33, 711-718.

Immink RG, Kaufmann K, Angenent GC (2010) The 'ABC' of MADS domain protein behaviour and interactions. Semin Cell Dev Biol 21, 87-93.

Becker A, Lange M (2010) VIGS--genomics goes functional. Trends Plant Sci 15, 1-4.

 

Dec. 16 (Week  16)

Lee HL, Irish VF (2011) Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol 28, 3367-3380.

Yoo MJ, Chanderbali AS, Altman NS, Soltis PS, Soltis DE (2010) Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae). Plant J 64, 687-698.

Kaufmann K, Pajoro A, Angenent GC (2010) Regulation of transcription in plants: mechanisms controlling developmental switches. Nature Reviews Genetics 11, 830-842.

 

 

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Complete list of Core Plant Evo-Devo papers

Ackerman CM, Yu Q, Kim S, et al. (2008) B-class MADS-box genes in trioecious papaya: two paleoAP3 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI. Planta 227, 741-753.

Alvarez-Buylla ER, Pelaz S, Liljegren SJ, et al. (2000) An ancestral MADS-box gene duplication occurred before the divergence of plants and animals. Proc Natl Acad Sci U S A 97, 5328-5333.

Ambrose BA, Lerner DR, Ciceri P, et al. (2000) Molecular and Genetic Analyses of the< i> Silky1</i> Gene Reveal Conservation in Floral Organ Specification between Eudicots and Monocots. Mol Cell 5, 569-579.

Angenent GC, Colombo L (1996) Molecular control of ovule development. Trends in Plant Science 1, 228-232.

Aoki S, Uehara K, Imafuku M, Hasebe M, Ito M (2004) Phylogeny and divergence of basal angiosperms inferred from APETALA3- and PISTILLATA-like MADS-box genes. J Plant Res 117, 229-244.

Becker A, Kaufmann K, Freialdenhoven A, et al. (2002) A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes. Mol Genet Genomics 266, 942-950.

Becker A, Lange M (2010) VIGS--genomics goes functional. Trends Plant Sci 15, 1-4.

Becker A, Saedler H, Theissen G (2003) Distinct MADS-box gene expression patterns in the reproductive cones of the gymnosperm Gnetum gnemon. Dev Genes Evol 213, 567-572.

Becker A, Theissen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29, 464-489.

Bemer M, Gordon J, Weterings K, Angenent GC (2010a) Divergence of recently duplicated M{gamma}-type MADS-box genes in Petunia. Mol Biol Evol 27, 481-495.

Bemer M, Heijmans K, Airoldi C, Davies B, Angenent GC (2010b) An atlas of type I MADS box gene expression during female gametophyte and seed development in Arabidopsis. Plant Physiol 154, 287-300.

Bemer M, Wolters-Arts M, Grossniklaus U, Angenent GC (2008) The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules. Plant Cell 20, 2088-2101.

Bowman JL, Alvarez J, Weigel D, Meyerowitz EM, Smyth DR (1993) Control of flower development in Arabidopsis thaliana by APETALA1 and interacting genes. Development 119, 721-743.

Buzgo M, Soltis PS, Kim S, Soltis DE (2005) The making of the flower-The evolution of flowers has long been a matter of intense debate. Recent hypotheses are changing the way we view their origins. Biologist-London 52, 149-154.

Buzgo M, Soltis PS, Soltis DE (2004) Floral developmental morphology of Amborella trichopoda (Amborellaceae). International Journal of Plant Sciences 165, 925-947.

Cacharr n J, Saedler H, Theissen G (1999) Expression of MADS box genes ZMM8 and ZMM14 during inflorescence development of Zea mays discriminates between the upper and the lower floret of each spikelet. Dev Genes Evol 209, 411-420.

Causier B, Schwarz-Sommer Z, Davies B (2010) Floral organ identity: 20 years of ABCs. Semin Cell Dev Biol 21, 73-79.

Chang Y-Y, Kao N-H, Li J-Y, et al. (2010) Characterization of the possible roles for B class MADS box genes in regulation of perianth formation in orchid. Plant Physiology 152, 837-853.

Coen ES, Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353, 31-37.

Colombo L, Franken J, Koetje E, et al. (1995) The petunia MADS box gene FBP11 determines ovule identity. Plant Cell 7, 1859-1868.

Colombo M, Brambilla V, Marcheselli R, et al. (2010) A new role for the SHATTERPROOF genes during Arabidopsis gynoecium development. Developmental biology 337, 294-302.

Colombo M, Masiero S, Vanzulli S, et al. (2008) AGL23, a type I MADS-box gene that controls female gametophyte and embryo development in Arabidopsis. Plant J 54, 1037-1048.

Cui R, Han J, Zhao S, et al. (2010) Functional conservation and diversification of class E floral homeotic genes in rice (Oryza sativa). The Plant Journal 61, 767-781.

de Folter S, Angenent GC (2006) trans meets cis in MADS science. Trends Plant Sci 11, 224-231.

de Folter S, Shchennikova AV, Franken J, et al. (2006) A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis. Plant J 47, 934-946.

Di Stilio VS (2011) Empowering plant evo-devo: virus induced gene silencing validates new and emerging model systems. Bioessays 33, 711-718.

Di Stilio VS, Kramer EM, Baum DA (2005) Floral MADS box genes and homeotic gender dimorphism in Thalictrum dioicum (Ranunculaceae) - a new model for the study of dioecy. Plant J 41, 755-766.

Ditta G, Pinyopich A, Robles P, Pelaz S, Yanofsky MF (2004) The SEP4 gene of Arabidopsis thaliana functions in floral organ and meristem identity. Curr Biol 14, 1935-1940.

Ferrandiz C, Liljegren SJ, Yanofsky MF (2000) Negative regulation of the SHATTERPROOF genes by FRUITFULL during Arabidopsis fruit development. Science 289, 436-438.

Flanagan CA, Hu Y, Ma H (1996) Specific expression of the AGL1 MADS-box gene suggests regulatory functions in Arabidopsis gynoecium and ovule development. Plant J 10, 343-353.

Gao X, Liang W, Yin C, et al. (2010) The SEPALLATA-like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiology 153, 728-740.

Geuten K, Irish V (2010) Hidden variability of floral homeotic B genes in Solanaceae provides a molecular basis for the evolution of novel functions. The Plant Cell Online 22, 2562-2578.

Goto K, Meyerowitz EM (1994) Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes & Development 8, 1548-1560.

Gramzow L, Ritz MS, Theissen G (2010) On the origin of MADS-domain transcription factors. Trends Genet 26, 149-153.

Gramzow L, Theissen G (2010) A hitchhiker's guide to the MADS world of plants. Genome Biol 11, 214.

Hasebe M, Banks J (1997) Evolution of MADS Gene Family in Plants. In: Evolution and Diversification of Land Plants (eds. Iwatsuki K, Raven P), pp. 179-197. Springer Japan.

Hileman LC, Irish VF (2009) More is better: the uses of developmental genetic data to reconstruct perianth evolution. American Journal of Botany 96, 83-95.

Immink RG, Kaufmann K, Angenent GC (2010) The 'ABC' of MADS domain protein behaviour and interactions. Semin Cell Dev Biol 21, 87-93.

Irish VF (2009) Evolution of petal identity. J Exp Bot 60, 2517-2527.

Kanno A, Saeki H, Kameya T, Saedler H, Theissen G (2003) Heterotopic expression of class B floral homeotic genes supports a modified ABC model for tulip (Tulipa gesneriana). Plant molecular biology 52, 831-841.

Kaufmann K, Pajoro A, Angenent GC (2010) Regulation of transcription in plants: mechanisms controlling developmental switches. Nature Reviews Genetics 11, 830-842.

Kim S, Koh J, Yoo MJ, et al. (2005) Expression of floral MADS-box genes in basal angiosperms: implications for the evolution of floral regulators. Plant J 43, 724-744.

Kim S, Yoo MJ, Albert VA, et al. (2004) Phylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functional implications of a 260-million-year-old duplication. Am J Bot 91, 2102-2118.

Kofuji R, Sumikawa N, Yamasaki M, et al. (2003) Evolution and divergence of the MADS-box gene family based on genome-wide expression analyses. Mol Biol Evol 20, 1963-1977.

Kramer EM, Di Stilio VS, Schlüter PM (2003) Complex patterns of gene duplication in the APETALA3 and PISTILLATA lineages of the Ranunculaceae. International Journal of Plant Sciences 164, 1-11.

Kramer EM, Dorit RL, Irish VF (1998) Molecular evolution of genes controlling petal and stamen development: duplication and divergence within the APETALA3 and PISTILLATA MADS-box gene lineages. Genetics 149, 765-783.

Kramer EM, Irish VF (1999) Evolution of genetic mechanisms controlling petal development. Nature 399, 144-148.

Lee HL, Irish VF (2011) Gene duplication and loss in a MADS box gene transcription factor circuit. Mol Biol Evol 28, 3367-3380.

Litt A, Irish VF (2003) Duplication and diversification in the APETALA1/FRUITFULL floral homeotic gene lineage: implications for the evolution of floral development. Genetics 165, 821-833.

Malcomber ST, Kellogg EA (2004) Heterogeneous expression patterns and separate roles of the SEPALLATA gene LEAFY HULL STERILE1 in grasses. The Plant Cell Online 16, 1692-1706.

Malcomber ST, Kellogg EA (2005) SEPALLATA gene diversification: brave new whorls. Trends in Plant Science 10, 427-435.

Melzer R, Theissen G (2009) Reconstitution of 'floral quartets' in vitro involving class B and class E floral homeotic proteins. Nucleic Acids Res 37, 2723-2736.

Nam J, Kim J, Lee S, et al. (2004) Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc Natl Acad Sci U S A 101, 1910-1915.

Parenicova L, de Folter S, Kieffer M, et al. (2003) Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis: new openings to the MADS world. Plant Cell 15, 1538-1551.

Pelaz S, Tapia-López R, Alvarez-Buylla ER, Yanofsky MF (2001) Conversion of leaves into petals in Arabidopsis. Current Biology 11, 182-184.

Pinyopich A, Ditta GS, Savidge B, et al. (2003) Assessing the redundancy of MADS-box genes during carpel and ovule development. Nature 424, 85-88.

Prasad K, Parameswaran S, Vijayraghavan U (2005) OsMADS1, a riceMADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs. Plant J 43, 915-928.

Soltis DE, Soltis PS, Albert VA, et al. (2002) Missing links: the genetic architecture of flower and floral diversification. Trends in Plant Science 7, 22-31.

Sommer H, Beltran J-P, Huijser P, et al. (1990) Deficiens, a homeotic gene involved in the control of flower morphogenesis in Antirrhinum majus: the protein shows homology to transcription factors. The EMBO Journal 9, 605.

Stellari GM, Jaramillo MA, Kramer EM (2004) Evolution of the APETALA3 and PISTILLATA lineages of MADS-box-containing genes in the basal angiosperms. Mol Biol Evol 21, 506-519.

Su HY, Li QZ, Li XG, Zhang XS (2005) Characterization and expression analysis of a MADS box gene, HoMADS2, in Hyacinthus orientalis L. Yi Chuan Xue Bao 32, 1191-1198.

Tanabe Y, Uchida M, Hasebe M, Ito M (2003) Characterization of the Selaginella remotifolia MADS-box gene. J Plant Res 116, 71-75.

Theißen G, Saedler H (2001) Plant biology: floral quartets. Nature 409, 469-471.

Theissen G, Melzer R (2007) Molecular mechanisms underlying origin and diversification of the angiosperm flower. Annals of Botany 100, 603-619.

Trevaskis B, Bagnall DJ, Ellis MH, Peacock WJ, Dennis ES (2003) MADS box genes control vernalization-induced flowering in cereals. Proc Natl Acad Sci U S A 100, 13099-13104.

Tzeng T-Y, Liu H-C, Yang C-H (2004) The C-terminal sequence of LMADS1 is essential for the formation of homodimers for B function proteins. Journal of Biological Chemistry 279, 10747-10755.

Vandenbussche M, Theissen G, Van de Peer Y, Gerats T (2003) Structural diversification and neo-functionalization during floral MADS-box gene evolution by C-terminal frameshift mutations. Nucleic Acids Res 31, 4401-4409.

Vandenbussche M, Zethof J, Royaert S, Weterings K, Gerats T (2004) The duplicated B-class heterodimer model: whorl-specific effects and complex genetic interactions in Petunia hybrida flower development. The Plant Cell Online 16, 741-754.

Weigel D, Meyerowitz EM (1994) The ABCs of floral homeotic genes. Cell 78, 203-209.

Winter K-U, Weiser C, Kaufmann K, et al. (2002a) Evolution of class B floral homeotic proteins: obligate heterodimerization originated from homodimerization. Molecular Biology and Evolution 19, 587-596.

Winter KU, Becker A, Munster T, et al. (1999) MADS-box genes reveal that gnetophytes are more closely related to conifers than to flowering plants. Proc Natl Acad Sci U S A 96, 7342-7347.

Winter KU, Saedler H, Theißen G (2002b) On the origin of class B floral homeotic genes: functional substitution and dominant inhibition in Arabidopsis by expression of an orthologue from the gymnosperm Gnetum. The Plant Journal 31, 457-475.

Yang Y, Fanning L, Jack T (2003) The K domain mediates heterodimerization of the Arabidopsis floral organ identity proteins, APETALA3 and PISTILLATA. The Plant Journal 33, 47-59.

Yoo MJ, Chanderbali AS, Altman NS, Soltis PS, Soltis DE (2010) Evolutionary trends in the floral transcriptome: insights from one of the basalmost angiosperms, the water lily Nuphar advena (Nymphaeaceae). Plant J 64, 687-698.