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DISSERTATION Chromosomal evolution in Prospero autumnale complex Verfasser Tae-Soo Jang angestrebter akademischer Grad Doctor of Philosophy (PhD) Wien, 2013 Studienkennzahl lt. Studienblatt: A 094 437 Dissertationsgebiet lt. Studienblatt: Biologie Betreuerin: Ass.-Prof. Mag. Dr. Hanna Schneeweiss Priv. Doz. TABLE OF CONTENTS Acknowledgements ............................................................................................................................ 1 Description of the contribution to the individual manuscripts ....................................................... 3 Abstract ................................................................................................................................................ 5 Zusammenfassung............................................................................................................................... 6 General introduction .......................................................................................................................... 7 Aims of the study .................................................................................................................. 11 Chapter 1: Chromosomal diversification and karyotype evolution of diploids in the cytologically diverse genus Prospero (Hyacinthaceae) ........................................................................................................ 19 Chapter 2: Expansion of tandem repeat PaB6 coincides with chromosomal rearrangements in the chromosomally hyper-variable Prospero autumnale complex (Hyacinthaceae) ................................ 37 Chapter 3: More than meets the eye: numerical convergence, multiple cycles of hybridization, and contrasting evolutionary trajectories in polyploids of the Prospero autumnale complex (Hyacinthaceae) .......... 69 Chapter 4: B-chromosomes in Prospero autumnale complex (Hyacinthaceae): structural polymorphisms and distinct repeat composition suggest their recurrent origin and ongoing evolution ........................... 121 Appendix: Morphometric analysis of species and cytotypes in the genus Prospero (Hyacinthaceae)............... 145 Summary and Conclusions ............................................................................................................. 155 Curriculum Vitae ............................................................................................................................ 161 iii iv ACKNOWLEDGEMENTS I would like to express my deepest thanks to my supervisor and mentor, Ass. Prof. Dr. Hanna Schneeweiss, for her patience and excellent academic guidance, and for the opportunities she has provided me with to develop scientifically. She has always had an open door for me whenever numerous basic and complex questions arose. Because of her endless encouragement, I have enjoyed working on my thesis and genus Prospero very much. I am very grateful to Prof. Dr. Tod Stuessy, Prof. Dr. Josef Greimler, Prof. Dr. Rosabelle Samuel, and Ass. Prof. Dr. Gerald Schneeweiss, who provided very helpful comments as well as warm atmosphere at the department. Special thanks to Prof. Dr. John Parker for many discussions, encouragement, valuable comments concerning data and manuscripts and many suggestions, and last but not least for supplying numerous Prospero bulbs for my study. I would like to thank Prof. Dr. Andrew R Leitch, Prof. Dr. Franz Speta, Prof. Dr. Jiří Macas, Prof. Dr. Aleš Kovařík, and Ass. Prof. Dr. Jan Suda for their kind help and valuable suggestions concerning data interpretation. I am grateful to my colleagues Dr. Khatere Emadzade, Dr. Eva Temsch, and Jamie McCann for their kindness, valuable assistance and fruitful discussions. Thanks go also to all former and present members in Department of Systematic and Evolutionary Botany of the University of Vienna, especially Dr. Diego Hojsgaard, Dr. Koji Takayama, Dr. Michael H. J. Barfuss, Mag. Barbara Turner, Mag. Dieter Reich, Mag. Ruth Flatscher, Hibbah Auf, and Markus Hofbauer for their kind help. I would like to thank Prof. Suk-Pyo Hong for his encouragement and moral support, and Prof. Chang-Gee Jang and Dr. Jeong-Mi Park for their concerns and support. I also would like to express my gratitude towards my mother and brother in Korea and my deceased father for their endless love and support. This study has been financially supported by the Austrian Science Fund (FWF) project P21440-B03 to Ass. Prof. Dr. Hanna Schneeweiss. 1 2 DESCRIPTION OF THE CONTRIBUTION TO THE INDIVIDUAL MANUSCRIPTS This thesis is based on following four manuscripts, which are published (one) or prepared as papers for submition in international journals (three). Manuscript 1: Chromosomal diversification and karyotype evolution of diploids in the cytologically diverse genus Prospero (Hyacinthaceae) T.-S. Jang, K. Emadzade, J. Parker, E.M. Temsch, A.R. Leitch, F. Speta, H. Weiss-Schneeweiss (TS-J carried out the cytogenetic studies, participated in the sequence alignment and drafted the manuscript. KE carried out sequencing of the ITS regions, sequence alignments and analyses, helped to draft the manuscript. JP provided plant material, participated in the design of the study and data interpretation, helped to draft the manuscript. EMT carried out genome size measurements. ARL participated in the design of the study and data interpretation, helped to draft the manuscript. FS provided plant material, helped to draft the manuscript. HW-S designed and coordinated the study, participated in data interpretation, helped to draft the manuscript). Manuscript 2: Expansion of tandem repeat PaB6 coincides with chromosomal rearrangements in the chromosomally hyper-variable Prospero autumnale complex (Hyacinthaceae) T.-S. Jang*, K. Emadzade*, J. Macas, P. Novák, A. Kovařík, J. Parker, H. Weiss-Schneeweiss (TS-J: carried out the cytogenetic studies, participated in slot blot analyses, drafted the manuscript, and prepared figures. KE: carried out Southern and slot blot analyses, DNA sequencing, drafted manuscript and prepared figures. JM and PN analyzed next generation sequencing data, participated in data interpretation and manuscript drafting. AK: participated in Southern blot analyses and data interpretation. JP: provided plant material, participated in data interpretation and manuscript drafting. HW-S: designed and coordinated the study, participated in data interpretation and manuscript drafting). *these authors contributed equally to the manuscript. Manuscript 3: More than meets the eye: numerical convergence, cycles of hybridization, and contrasting evolutionary trajectories in polyploids of the Prospero autumnale complex (Hyacinthaceae) T.-S. Jang, K. Emadzade, E.M. Temsch, J. Parker, J. Macas, A.R. Leitch, F. Speta, H. Weiss- Schneeweiss (TS-J: carried out cytogenetic analyses, participated in sequence analyses, drafted the manuscript, prepared figures. KE: carried out DNA sequencing and phylogenetic analyses, prepared figures. EMT: carried out genome size measurements. JP: provided plant material, participated in data interpretation and manuscript drafting. JM and ARL participated in data interpretation and drafted the manuscript. FS provided plant material. HW-S: designed and coordinated the study, participated in data interpretation and manuscript drafting). Manuscript 4: B-chromosomes in Prospero autumnale complex (Hyacinthaceae): structural polymorphisms and distinct repeat composition suggest their recurrent origin and ongoing evolution T.-S. Jang, J. Parker, H. Weiss-Schneeweiss (TS-J: carried out cytogenetic studies, prepared figures and drafted the manuscript. JP: provided plant material, participated in data interpretation and manuscript drafting. HW-S: designed and coordinated the study, participated in data interpretation and manuscript drafting). 3 4 ABSTRACT The circum-Mediterranean Prospero autumnale is exceptionally dynamic with respect to karyotype evolution, showing numerical (dysploidy, polyploidy, B-chromosomes) and structural variation. It comprises four evolutionarily distinct diploid cytotypes (AA, B7B7, B6B6, and B5B5), each characterized by a unique combination of basic chromosome number (x = 5, 6, and 7), genome size, karyotype structure, and rDNA and satDNA PaB6 locus distribution. Comparative cytogenetic analyses, interpreted in a phylogenetic context, allowed a model of chromosomal evolution for diploids of P. autumnale to be established, with descending dysploidy from x = 7 to x = 6 and independently from x = 7 to x = 5 via chromosomal fusions. All cytotypes except B5B5 participate in polyploidization, without or with hybridization resulting in auto- and allopolyploids. Autopolyploids (only found in genome B7) are genomically stable, while allopolyploids are more dynamic. Depending on the divergence of the parental genomes, allopolyploids are either stable with near-complete additivity (polyploids of A and B7 origin) or variable both numerically (subgenome compensating aneuploidy, 2n = 25–28) and structurally (polyploids of B6 and B7 origin). In allotetraploids of B6 and B7 origin, four types of genomically unique and restructured individuals were identified, varying in genome size, rDNA and satellite DNA loci numbers and localization, and copy number of satDNA, in chromosomes of B7 origin. These groups represent different cycles of hybridization of the two basic genomes involved: primary allotetraploids (involving B6 and B7), secondary allotetraploids (primary allotetraploids with B7 diploids) and backcrosses of the latter. B-chromosomes and supernumerary segments