Developmental and Genetic Mechanisms
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Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2016 INDEPENDENT ORIGINATION OF FLORAL ZYGOMORPHY, A PREDICTED ADAPTIVE RESPONSE TO POLLINATORS: DEVELOPMENTAL AND GENETIC MECHANISMS Ghadeer Bukhari Wenheng Zhang Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Biology Commons, Evolution Commons, and the Molecular Genetics Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/4482 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. i © Ghadeer Bukhari, 2016 All Rights Reserved i INDEPENDENT ORIGINATION OF FLORAL ZYGOMORPHY, A PREDICTED ADAPTIVE RESPONSE TO POLLINATORS: DEVELOPMENTAL AND GENETIC MECHANISMS A Thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by GHADEER BUKHARI BACHELOR OF SCIENCE, KING ABDULAZIZ UNIVERSITY, 2009 MASTER OF SCIENCE, VIRGINIA COMMONWEALTH UNIVERSITY, 2016 Director: WENHENG ZHANG, PHD ASSISTANT PROFESSOR, DEPARTMENT OF BIOLOGY Codirector: BONNIE L. BROWN, PHD PROFESSOR AND ASSOCIATE DEPARTMENT CHAIR, DEPARTMENT OF BIOLOGY Virginia Commonwealth University Richmond, Virginia July, 2016 iii Acknowledgements It is a great opportunity and pleasure to express my profound gratitude to a number of people to whom I am greatly in debt and appreciate. To my advisor Dr. Wenheng Zhang, a very special thank you for the inspiration, priceless advice, constant guidance, friendship, mentorship, and continuing gifts of wisdom. Thank you for believing in me and for allowing me to grow as a research scientist. I am also very grateful to Dr. Bonnie L. Brown for presenting me with fascinating researches, continuing support, and for sharing the scientific knowledge and experience with me. To my dear parents and siblings, thank you for all of the endless support, encouragement, and caring love you provide for which none of this would have been possible to achieve. To my best friend, dear husband, and great father, Hamza Magsood who remains willing to practically and emotionally supports me as a wife and then a mother of our beloved Eleen, and consistently have faith in me that has been and will be the driving force behind all my achievements. In addition, a great thanks to my committee members: Dr. Wenheng Zhang, Dr. Bonnie L. Brown, Dr. Karen M. Kester, and Dr. Edward L. Boone whom have guided me, supported me, and continue to motivate me to be the best version of myself. In addition, my special appreciation to my great labmates: Dr. Jingbo Zhang, Farahnoz Khojayori, Joon Kim, and Ao Gao for their friendship and support in providing assistance to complete my study. iii iv Table of Contents Page Acknowledgements………………………………………………………………………...iii List of Tables ……………………………………………………………………………....vi List of Figures……………………………………………………………………………..vii List of Abbreviations……………………………………………………………………..viii Chapter One 1 Introduction ……………………………………………………………..…….12 2 Materials and Methods ………………………………………………….…….17 Characterizing traits from floral diagram.......................................................17 Phylogenetic reconstruction of pentapetalous angiosperms...........................21 Reconstructing ancestral states for floral traits..............................................22 3 Results and Discussion………………………………………………………...28 Diversity of pentapetalous angiosperms…………………….……………..28 Evolution of MAB and MAD petal initiation………………………….......30 Distinct developmental processes to give rise to floral zygomorphy……...30 Development constrains process to give rise to floral zygomorphy, phylogenetic distance diverges constraints………………………..35 v Developmental process and genetic mechanisms underlying floral symmetry evolution………………………………………………..36 Displays of floral zygomorphy and pollinator selection…………………….37 Conclusion…………………………………………………………………..39 Chapter Two 4 Introduction ……………………………………………………………..…….40 5 Materials and Methods ………………………………………………….…….43 Plant materials................................................................................................43 Sampling………………………………………………….............................43 Total RNA extraction and quality tests………..............................................43 6 Results and Discussion………………………………………………………...46 RNA-seq data analysis………………...…………………….……………..46 TCP gene expression in corolla………………………….............................47 Differential gene expression in corolla…….................................................49 7 Reference …...………………………………………………..………………..52 8 Appendix………………………………………………………………………60 9 Vita.....................................................................................................................88 vi List of Tables Page Appendix table 1. Floral characters describe the developmental mechanisms of floral symmetry………………………………………………………………………...60 Appendix table 2. The references to solve the relationships in the phylogenetic tree……………………………………………………………………………….73 Appendix table 3. Molecular markers from GenBank used to resolve the phylogenetic tree……………………………………………………………………………….75 Table 4. Developmental processes associated with clades of floral zygomorphy with CV patterns of symmetry……………………………………………………………33 Table 5. Developmental processe associated with clades of floral zygomorphy with CD patterns of symmetry…………………………………………………………….34 Table 6. GENEWIZ Quality Control (QC) report…………………………………………45 Table 7. The assembled transcript measurements………………………………………....47 Table 8. The mapping summary…………………………………………………………..47 Table 9. TCP loci identified from corolla of Schizanthus pinnatus………………………48 Table 10. Number of up-regulated and down-regulated genes in both biological replicates………………………………………………………………………..51 Table 11. The present/absent transcripts genes…………………………………………..51 vii List of Figures Page Figure 1. Floral initiation and petal arrangement of floral zygomorphy in pentapetalous angiosperms…………………………………………………………..................14 Figure 2. Data statistics……………………………………………………………………18 Figure 3. Distinct mechanisms to develop floral zygomorphy from MAB floral initiation………………………………………………………………………...10 Appendix figure 4. Phylogenetic reconstructions based on Bayesian and ML methods using molecular markers from Genebank………………………………………..88 Figure 5. Ancestral state reconstruction of floral initiate………………….........................23 Figure 6. Ancestral state reconstruction of floral symmetry………………........................24 Figure 7 . Ancestral state reconstruction of patterns of floral symmetry………………….25 Figure 8: Ancestral state reconstruction of development processes to establish floral zygomorphy……………………………………………………………………..26 Figure 9. Fully resolved phylogeny tree of angiosperms in the dataset…………………...29 Figure 10. Frequencies of floral zygomorphy with CV and CD patterns evolved from MAB and MAD floral initiations………………………………………………………32 Figure 11. Summary of the developmental processes giving arise to floral zygomorphy……………………………………………………………………...38 Figure 12. Floral morphology of Schizanthus pinnatus ………………………………….42 Figure 13. Codes using Python programming language…………………...……………..50 viii List of Abbreviations MAB: Medially abaxial petal initiation. MAD: Medially adaxial petal initiation. CV: Central ventral petal. CD: Central dorsal petal. ML: Maximum likelihood. MrBayers: Baysian bp: base pair Mbp: million base pairs RPKM: Reads per kilobase of transcript per million mapped reads viii Abstract INDEPENDENT ORIGINATION OF FLORAL ZYGOMORPHY, A PREDICTED ADAPTIVE RESPONSE TO POLLINATORS: DEVELOPMENTAL AND GENETIC MECHANISMS By Ghadeer Bukhari, B.S. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Biology at Virginia Commonwealth University. Virginia Commonwealth University, 2016 Major Advisor: Wenheng Zhang Assistant Professor, Department of Biology Coadvisor: Bonnie L. Brown Professor and Associate Department Chair, Department of Biology Observations of floral development indicate that floral organ initiation in pentapetalous flowers more commonly results in a medially positioned abaxial petal (MAB) than in a medially positioned adaxial petal (MAD), where the medial plane is defined by the stem and the bract during early floral development. It was proposed that the ix dominant MAB petal initiation might impose a developmental constraint that leads to the evolution of limited patterns of floral zygomorphy in Asteridae, a family in which the floral zygomorphy develops along the medial plane and results in a central ventral (CV) petal in mature flowers. Here, I investigate whether the pattern of floral organ initiation may limit patterns of floral zygomorphy to evolve in pentapetalous angiosperms. I analyzed floral diagrams representing 405 species in 330 genera of pentapetalous angiosperms to reconstruct the evolution of floral organ initiation and the evolution of developmental processes that give rise to floral zygomorphy on a phylogenetic framework. Results indicate that MAB petal initiation is the most common; it occupies 86.2% of diversity and represents the ancestral state of floral organ initiation in pentapetalous angiosperms. The MAD petal initiation evolved 28 times independently from the ancestral MAB petal initiation. Among the 34 independent originations of floral