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Analysis of the Olive Genome Irene Consuelo Julca Chávez

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Analysis of the Olive Genome Irene Consuelo Julca Chávez ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Analysis of the Olive genome Irene Consuelo Julca Chavez´ Universitat Autonoma` de Barcelona Faculty of Bioscience Department of Animal Biology, Plant Biology and Ecology TESI DOCTORAL UAB 2017 Analysis of the Olive genome A thesis submitted by Irene Consuelo Julca Chavez´ for the degree of Doctor in Plant Biology and Biotechnology under the direction of Dr. Toni Gabaldon,´ Dr. Pablo Vargas, and tutored by Dr. Josep Allue` This thesis has been inscribed in the Plant Biology and Biotechnology PhD program from the Universitat Autonoma` de Barcelona Director Codirector Dr. Toni Gabaldon´ Dr. Pablo Vargas Centre for Genomic Regulation Royal Botanical Garden of Madrid Tutor PhD student Dr. Josep Allue` Irene Julca Universitat Autonoma` de Barcelona Universitat Autonoma` de Barcelona Barcelona, September 2017 A mis padres Delia Ch´avezy Jos´eJulca. ”Discovery consists of seeing what everybody has seen, and thinking what nobody has thought.” Albert Szent-Gy¨orgyi Acknowledgments A veces pequenas˜ decisiones cambian el curso de nuestras vidas. Todo empezo´ cuando decid´ı dejar el laboratorio y las pipetas por bioinformatica.´ Que idea mas´ loca, iniciar todo de nuevo y encima trabajando en genomas de plantas! En esta historia hubo un poco de suerte porque encontre´ un grupo muy agradable, aqu´ı en Barcelona. En este pequeno˜ punto en la tierra muchas cosas de mi vida han cambiado, incluso algunas ideas. Aun´ recuerdo mi primera entrevista con Toni, que nervios y luego todo calma en un lugar que parec´ıa mas´ que un centro de investigacion´ un hotel con vista al mar. No puedo mentir, la ubicacion´ del centro fue una de las primeras cosas que me impresionaron. Desde esa primera entrevista, yo supe que Toni era una persona sencilla y amable y que yo quer´ıa trabajar con el.´ Muchas gracias Toni por toda la paciencia que has tenido conmigo durante todo este per´ıodo. Gracias por siempre ayudarme a ver el lado positivo de los resultados, una cosa importante en esta carrera. Luego conoc´ı a Pablo, una persona muy entusiasta, que a pesar de la distancia, siempre ha encontrado la manera de estar en constante comunicacion,´ sobre todo en los momentos claves. Gracias por guiarme cuando yo estaba perdida en taxonom´ıa y por incentivarme a estudiar filogenias. Gracias por las instructivas charlas durante nuestras largas llamadas telefonicas´ y por contestarme siempre, incluso cuando te he escrito tarde. Durante estos anos,˜ una persona ha estado guiandome´ desde el comienzo. Nada hubiera sido igual sin su apoyo. Estoy segura que he tenido mucha suerte, no todos inician con una guia como Marina. Muchas gracias por ensenarme˜ todas las herramientas que finalmente he utilizado, espero bien. ix x Gracias, por todo el tiempo que te has tomado para ayudarme durante este periodo y tambien´ por las fascinantes discusiones sobre los extranos˜ resultados que ´ıbamos encontrando a lo largo de estos anos.˜ Each day from the beginning to the end of this period I was surrounded by amazing people. I want to thank you all, for every moment that we’ve shared, even the ones that I can’t remember now. Miguel, always on time for the breakfast, the lunch, and the coffee break. Gracias por compartir tus ideas, a veces locas, pero siempre interesantes. Cinta, siempre amable y sonriente, gracias por todos los tips sobre el otro mundo de la genetica´ de poblaciones. Ernst, my ‘friendly’ neighbor, thanks for helping me to solve some problems with my computer and for your valuable advices about statistics. Laia, por la compan˜´ıa en la parte final de este per´ıodo y tambien,´ por alquilar los lugares ‘mas´ baratos’ para nuestros fabulosos retreats. Salva, that when was in the group was always solving my computer problems, of course they were never my fault. Alex, for your enjoyable company during the first years of this period. The girls of the wet lab: Ester, Susana and Ewa, was always nice to share a moment with you. Veronica,´ ‘obrigado’ for your funny company, and for the olive picture that you found. Hrant, for the nice company in the dark side of the lab. Jesse, to always have the correct pronunciation of the English words. Fran because was almost always available to go out. Pedro, Rosa, and Uciel for the nice advices. Damian, who has very ‘interesting’ ideas, thanks for helping me with the olive at the beginning. I want to thanks also the people that stayed in the lab for a short period, but have left nice memories: Houda and Radina. Thanks to the nice people with whom I’ve shared many adventures inside and outside the CRG. Davide, who always was on time, ready for all, from dinners out to a walk in the mountains. Silvina, for your modernist advices. Mimma for all the countless dinners that we’ve shared. Alessandra for all the room escapes that we have won together. To my friends that in some moments of this period had shared time with me. Diana, gracias por tus concejos y por las bonitas escapadas juntas. Patty, por compartir tus locuras conmigo. Rosany y Meltem, por ser mis primeras gu´ıas en Barcelona. To the people that was present before and from whom I’ve learned a lot: Mercedes, Maximino and Mar´ıa. xi Charlotte and Josep, who made easier all the bureaucratic process along all these years. The security training office because, without knowing, allowed me to meet a person that becomes an important part of this history. My first friend at the CRG, Riccardo. Thank you for being the accomplice of my crazy ideas. All these years will be not the same without you. Thank you very much for your patience during this period, overall the last part of it. I know that probably you wanted to run away when I was writing the thesis, but still you were here, smiling and always giving me the strength to continue. Pancrazio e Carmen, con cui ho condiviso molti bei momenti. Grazie per aver reso i miei giorni piu´ belli con la vostra presenza. Per essere cos´ı ospitali e per avermi fatto sentire parte della vostra famiglia. The most important part of a history is the end. Quiero agradecer a mi familia. Mis t´ıos Jose´ y Vilma, quienes han estado presentes siempre que los he necesitado. Rita, que desde que tengo memoria ha estado cuidandonos.´ Mis hermanos, Jose´ Luis y Carlos, que siempre estan´ all´ı para escucharme. Mis padres Jose´ y Delia por su incondicional amor y apoyo. Jose´ que siempre me da fuerzas y animo´ para terminar las cosas que inicio. Delia, una persona que desde la distancia sabe guiarme y que sus consejos cambiaron esta historia. Finalmente a ti, que sin ti nada ser´ıa posible. Thank you all! Irene Consuelo Julca Chavez.´ Barcelona, September 2017. Abstract The olive tree (Olea europaea, Oleaceae) is an iconic plant of Mediter- ranean countries for cultural, historical and biological reasons. The olive species comprises six subspecies (europaea, maroccana, cerasiformis, laperrinei, guanchica, and cuspidata) that together form the so-called O. europaea com- plex. Likewise, the subsp. europaea is divided into two taxonomic varieties: var. europaea, that comprises all the cultivated forms, and var. sylvestris (also called oleaster), that includes the wild forms. The olive tree has been inten- sively cultivated since 6,000 years ago, coinciding with the emergence of early Mediterranean civilizations. Because of the interest of the drupes both as table olives and as raw material to produce olive oil, the olive tree is an es- sential crop across the Mediterranean basin. This doctoral thesis aims to pro- vide insights into the biology and the evolution of the cultivated olive and relatives. To this end, we sequenced, assembled, and annotated a reference genome obtained from a single individual (O. europaea L. var. europaea). Phy- logenomic analysis and assessment of allelic relative coverage suggest up to four polyploidization events in the evolutionary history of the olive. Two an- cient allopolyploidization events at the base of the family Oleaceae (Eocene- Late Cretaceous), and the tribe Oleeae (Oligocene-Miocene), followed by two polyploidizations in the ancestor of O. europaea (Miocene-Pliocene) since its divergence from Phillyrea angustifolia. In order to study the diversity and phylogenetic relationships in the O. europaea complex, we additionally se- quenced the genome of at least one individual per subspecies. Our results show that cultivated olive trees exhibit less nucleotide diversity when com- pared with wild relatives. Different sets of genes were found to be under positive selection in each cultivar included in this study (‘Arbequina’, ‘Be- ladi’, ‘Farga’, ‘Picual’, ‘Sorani’). In addition to hybridization involving poly- ploidization (allopolyploidization), phylogenomic analysis revealed exten- sive homoploid hybridization among lineages of the O. europaea complex, xiii xiv which results in a continuous gene flow from wild to domesticated olive trees. In particular, cv. ‘Farga’ has a different origin than the other culti- vars included in this study, and shows evidence for secondary domestica- tion events in the Iberian Peninsula. In summary, this study helps unravel the evolutionary history of O. europaea, and uncover a complex scenario of polyploidization and hybridization that resulted in recurrent gene duplica- tions.
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