Tesis por compendio / Alimentar a la futura población en crecimiento en un contexto de cambio climático exige nuevos enfoques y herramientas de mejora genética para desarrollar nuevas variedades de cultivos que sean resilientes y eficientes en el uso de los recursos. Entre las hortalizas, la berenjena (Solanum melongena) es reconocida como un cultivo importante y como tal está incluida en el Anexo 1 del Tratado Internacional sobre los Recursos Fitogenéticos para la Alimentación y la Agricultura, que incluye 34 cultivos considerados como los más relevantes para la humanidad. Antes del inicio de esta tesis, se disponía de pocas herramientas genéticas y genómicas para la mejora genética de la berenjena, las cuales se revisan en un capítulo introductorio. Asimismo, hemos reconocido la importancia de los parientes silvestres de la berenjena, que apenas se han utilizado en la mejora genética de la misma. A este respecto, para hacer un uso más eficiente de los parientes silvestres en la mejora genética, propusimos un enfoque ambicioso, llamado "introgressiomics", que consiste en un desarrollo sistemático y masivo de materiales que lleven introgresiones de parientes silvestres (CWR), los cuales generalmente son una fuente inexplorada e desaprovechada de variación genética. Los trabajos realizados en esta tesis están relacionados con la aplicación de este enfoque a la berenjena. En este marco, los objetivos generales de la tesis son el desarrollo de la información y herramientas genéticas y genómicas en el acervo genético de la berenjena, utilizando un enfoque multidisciplinario y multifacético para la mejora genética en el desarrollo de nuevas variedades mejoradas y resistentes usando especies relacionadas como fuente de variación. Concretamente, en el primer capítulo de esta tesis, secuenciamos el transcriptoma de dos especies relacionadas con la berenjena, la silvestre Solanum incanum y la especie cultivada africana S. aethiopicum, que tienen un gran interés en la mejora genética de la berenjena. Los transcriptomas se ensamblaron en 83,905 y 87,084 unigenes para S. incanum y S. aethiopicum respectivamente, los cuales fueron extensivamente anotados estructuralmente y funcionalmente. La busqueda de variantes alélicas identificó decenas de miles de polimorfismos intraespecíficos e interespecíficos, así como alrededor de un millar de SSRs en cada especie. En el segundo capítulo, un subconjunto de esos marcadores (11 SSRs y 35 SNPs) se analizaron para confirmar su utilidad para la huella genética, la evaluación de la diversidad y el establecimiento de relaciones entre las berenjenas cultivadas (común, escarlata y gboma). Observamos que los SSRs y los SNPs proporcionaron resultados diferentes en el establecimiento de las relaciones, lo que sugiere que cada tipo de marcador muestreó diferentes niveles de variación genética. Sin embargo, aunque ambos marcadores proporcionaron un nivel similar de información, los SNPs parecen proporcionar una mejor resolución que los SSRs para materiales filogenéticamente más distantes. En el tercer capítulo, para ampliar la estimación de la diversidad genética y las relaciones genéticas entre y dentro de las especies silvestres y cultivadas pertenecientes al complejo berenjena, realizamos un genotipado masivo, mediante un enfoque de genotipado por secuenciación, de 76 accesiones pertenecientes a 17 especies del acervo genético primario, secundario y terciario de la berenjena común. De los 75,399 sitios polimórficos identificados, 12,859 se asociaron a regiones CDS y se usaron para establecer una evaluación exhaustiva y detallada de la diversidad alélica natural y las relaciones genéticas en el acervo genético de la berenjena utilizando tres enfoques diferentes (estructura jerárquica de la población, dendrograma basado en UPGMA y análisis de PCoA). En el cuatro capítulo, desarrollamos un mapa genético interespecífico entre S. incanum y S. melongena, vinculado a otros / Feeding the future burgeoning population in a climate change scenario demands new breeding approaches and tools to develop new resource-efficient and resilient crop varieties. Among vegetable crops, eggplant (Solanum melongena) is recognized as an important food crop and as such is included in the Annex 1 of the International Treaty on Plant Genetic Resources for Food and Agriculture, which includes 34 crops considered as most relevant for mankind. Before the start of this thesis, few genetic and genomic tools and resources for eggplant breeding, which are reviewed in an introductory chapter, were available. We have recognized the importance of wild eggplant relatives, which have been barely used in eggplant breeding. In this respect, in order to make a more efficient use of wild relatives in plant breeding, we proposed an ambitious approach, called "introgressiomics", consisting of a systematic and massive development of materials carrying introgressions from crop wild relatives (CWRs), which usually are an unexplored and unexploited source of genetic variation for breeding traits. The works done in this thesis are related to the application of the introgressiomics approach to eggplant. In this framework, the general objectives of the thesis are the development of genetic and genomic information and tools in eggplant genepool, using a multidisciplinary and multi-pronged approach to assist eggplant breeding in the development of new improved and resilient varieties using eggplant relatives as a source of variation. Specifically, in the first chapter of this thesis, we sequenced the transcriptome of two eggplant related species, the wild Solanum incanum and the cultivated S. aethiopicum, that have a great interest in eggplant breeding. The transcriptomes were assembled in 83,905 and 87,084 unigenes for S. incanum and S. aethiopicum respectively, which were extensively structurally and functionally annotated. The variant call analysis identified tens of thousands intraspecific and interspecific polymorphisms, as well as around a thousand of SSRs in each species. In the second chapter, a subset of those markers (11 SSRs and 35 SNPs) was tested for confirming their usefulness for genetic fingerprinting, diversity evaluation and the establishment of relationships in cultivated eggplant (common, scarlet and gboma) genepools. We observed that SSRs and SNPs provided different results in the establishment of the relationships, suggesting that each marker type sampled different levels of genetic variation. However, although both markers provided a similar level of information, SNPs seem to provide a better resolution than SSRs for materials phylogenetically more distant. In the third chapter, in order to broaden the estimation of the genetic diversity and genetic relationships among and within wild and cultivated species belonging to eggplant complexes, we performed a massive genotyping, by a genotype-by-sequencing approach, of 76 accessions belonging to 17 species from the primary, secondary and tertiary genepool of common eggplant. Out of 75,399 polymorphic sites identified, 12,859 were associated to CDS regions and used to establish an exhaustive and detailed evaluation of the natural allelic diversity and genetic relationships in eggplant genepool using three different approaches (hierarchical population structure, UPGMA-based dendrogram, and PCoA analysis). In the four chapter, we developed an interspecific genetic map between S. incanum and S. melongena, linked to four previous eggplant maps and to one tomato map. A total of 243 molecular markers were successfully mapped consisting of 42 COSII, 99 SSRs, 88 AFLPs, 9 CAPS, 4 SNPs and one morphological polymorphic markers encompassed 1085 cM distributed in 12 linkage groups. Based on the syntheny with tomato, the candidate genes involved in the core chlorogenic acid synthesis pathway in eggplant (PAL, C4H, 4CL, HCT, C3¿H, HQT), five polyphenol oxidase genes (PPO1, PPO2, PPO3, PP / Alimentar la futura població en creixement en un context de canvi climàtic exigeix nous enfocaments i eines de millora genètica per desenvolupar noves varietats de cultius que siguin resilients i eficients en l'ús dels recursos. Entre les hortalisses, l'albergínia (Solanum melongena) és reconeguda com un cultiu important i com a tal està inclosa en l'Annex 1 del Tractat Internacional sobre els Recursos Fitogenètics per a l'Alimentació i l'Agricultura, que inclou 34 cultius considerats com els més rellevants per a la humanitat. Abans de l'inici d'aquesta tesi, es disposava de poques eines genètiques i genòmiques per a la millora genètica de l'albergínia, les quals es revisen en un capítol introductori. Així mateix, hem reconegut la importància dels parents silvestres de l'albergínia, que tot just s'han utilitzat en la millora genètica de la mateixa. Referent a això, per fer un ús més eficient dels parents silvestres a la millora genètica, vam proposar un enfocament ambiciós, anomenat "introgressiomics", que consisteix en un desenvolupament sistemàtic i massiu de materials que portin introgresions de parents silvestres (CWR), els quals generalment són una font inexplorada i desaprofitada de variació genètica. Els treballs realitzats en aquesta tesi estan relacionats amb l'aplicació d'aquest enfocament a l'albergínia. En aquest marc, els objectius generals de la tesi són el desenvolupament de la informació i eines genètiques i genòmiques en el patrimoni genètic de l'albergínia, utilitzant un enfocament multidisciplinari i multifacètic per a la millora genètica en el desenvolupament de noves varietats millorades i resistents emprent spècies relacionades com a font de variació. Concretament, en el primer capítol d'aquesta tesi, seqüenciem el transcriptoma de dues espècies relacionades amb l'albergínia, la silvestre Solanum incanum i l'espècie cultivada africana S. aethiopicum, que tenen un gran interès en la millora genètica de l'albergínia. Els transcriptomes s'ensamblaren en 83,905 i 87,084 unigenes per S. incanum i S. aethiopicum respectivament, els quals van ser extensivament anotats estructuralment i funcionalment. La recerca de variants al·lèliques va identificar desenes de milers de polimorfismes intraespecífics i interespecífics, així com al voltant d'un miler de SSRs en cada espècie. En el segon capítol, un subconjunt d'aquests marcadors (11 SSRs i 35 SNPs) es van analitzar per confirmar la seva utilitat per l'empremta genètica, l'avaluació de la diversitat i l'establiment de relacions entre les albergínies conreades (comú, escarlata i gboma). Observem que els SSRs i els SNPs van proporcionar resultats diferents en l'establiment de les relacions, el que suggereix que cada tipus de marcador va mostrejar diferents nivells de variació genètica. No obstant això, encara que tots dos marcadors van proporcionar un nivell similar d'informació, els SNPs semblen proporcionar una millor resolució que els SSRs per materials filogenèticament més distants. En el tercer capítol, per a ampliar l'estimació de la diversitat genètica i les relacions genètiques entre i dins de les espècies silvestres i conreades pertanyents al complex albergínia, vam realitzar un genotipat massiu, mitjançant un enfocament de genotipat per seqüenciació, de 76 accessions pertanyents a 17 espècies del patrimoni genètic primari, secundari i terciari de l'albergínia comuna. Dels 75,399 llocs polimòrfics identificats, 12,859 es van associar a regions CDS i es van usar per a establir una avaluació exhaustiva i detallada de la diversitat al·lèlica natural i les relacions genètiques en el patrimoni genètic de l'albergínia utilitzant tres enfocaments diferents (estructura jeràrquica de la població, dendrograma basat en UPGMA i anàlisi de PCoA). En el quart capítol, desenvolupem un mapa genètic interespecífic entre S. incanum i S. melongena, vinculat a altres quatre mapes anterior / Gramazio, P. (2018). GENETICS AND GENOMICS OF CULTIVATED EGGPLANTS AND WILD RELATIVES [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/104605 / Compendio

Forest trees are an important pool of biodiversity at the gene, individual and an ecosystem level. This variation is a result of complex environmental interactions, as well as neutral and selective forces acting on populations. Patterns of standing genetic variation are the result of adaption to past and contemporary climate change, but also historical demographic events, and disentangling the role of these forces is a central problem in population genomics. The overall goal of this study is to characterize the relative effects of demography and selection in the genome of Populus trichocarpa, a riparian deciduous tree species of North America. Specifically, I used a variety of methods to summarize patterns of genetic diversity and population structure in P. trichocarpa, and to reconstruct its demographic history. I subsequently incorporated these demographic insights to guide the application of several methods to identify genome-wide targets of natural selection within and among rangewide populations adapted to heterogeneous selection regimes. Results of this study provide insights into the history of divergence and differentiation in P. trichocarpa populations and help us identify the functional genetic variants contributing to phenotypic divergence and fitness of the individuals in it. / Ph. D. / The extant genetic variation in the forest tree populations is a product of evolutionary history and complex environmental interactions. This genetic variation can therefore be leveraged to identify both the adaptive genetic variation and understand the demographic events that might have caused these patterns. We, in this study, present and analyze the range-wide population genomic dataset of western poplar (Populus trichocarpa) and show that the current distribution of western poplar originated from the southern western poplar populations around hundred thousand years ago. Our study also identified large number of loci associated with environmental local adaptation. We identified number of genes involved in temperature sensing, light signaling pathways, and plant immunity, suggesting role of biotic and abiotic factors as major drivers of adaptation. We also detected significant overlap between highly divergent loci and adaptive genetic variation, indication the role of adaptation in species diversification. Overall, the results of this study advance our understanding of the demographic history and the major drivers of local adaptation in western poplar populations. It also gives us an observational and experimental evidence of role of environment and demographic history in shaping the genetic make-up of organism.

No / N-terminal lipidation is a major mechanism by which bacteria can tether proteins to membranes and one which is of particular importance to Gram-positive bacteria due to the absence of a retentive outer membrane. Lipidation is directed by the presence of a cysteine-containing `lipobox' within the lipoprotein signal peptide sequence and this feature has greatly facilitated the identification of putative lipoproteins by gene sequence analysis. The properties of lipoprotein signal peptides have been described previously by the Prosite pattern PS00013. Here, a dataset of 33 experimentally verified Gram-positive bacterial lipoproteins (excluding those from Mollicutes) has been identified by an extensive literature review. The signal peptide features of these lipoproteins have been analysed to create a refined pattern, G+LPP, which is more specific for the identification of Gram-positive bacterial lipoproteins. The ability of this pattern to identify probable lipoprotein sequences is demonstrated by a search of the genome of Streptococcus pyogenes, in comparison with sequences identified using PS00013. Greater discrimination against likely false-positives was evident from the use of G+LPP compared with PS00013. These data confirm the likely abundance of lipoproteins in Gram-positive bacterial genomes, with at least 25 probable lipoproteins identified in S. pyogenes

No / Streptococcus agalactiae is a significant pathogen causing invasive disease in neonates and thus an understanding of the molecular basis of the pathogenicity of this organism is of importance. N-terminal lipidation is a major mechanism by which bacteria can tether proteins to membranes. Lipidation is directed by the presence of a cysteine-containing 'lipobox' within specific signal peptides and this feature has greatly facilitated the bioinformatic identification of putative lipoproteins. We have designed previously a taxon-specific pattern (G+LPP) for the identification of Gram-positive bacterial lipoproteins, based on the signal peptides of experimentally verified lipoproteins (Sutcliffe I.C. and Harrington D.J. Microbiology 148: 2065-2077). Patterns searches with this pattern and other bioinformatic methods have been used to identify putative lipoproteins in the recently published genomes of S. agalactiae strains 2603/V and NEM316. A core of 39 common putative lipoproteins was identified, along with 5 putative lipoproteins unique to strain 2603/V and 2 putative lipoproteins unique to strain NEM316. Thus putative lipoproteins represent ca. 2% of the S. agalactiae proteome. As in other Gram-positive bacteria, the largest functional category of S. agalactiae lipoproteins is that predicted to comprise of substrate binding proteins of ABC transport systems. Other roles include lipoproteins that appear to participate in adhesion (including the previously characterised Lmb protein), protein export and folding, enzymes and several species-specific proteins of unknown function. These data suggest lipoproteins may have significant roles that influence the virulence of this important pathogen.

Tandemly arrayed genes (TAG) play an important functional and physiological role in the genome. Most previous studies have focused on individual TAG families in a few species, yet a broad characterization of TAGs is not available. We identified all the TAGs in the genomes of human, chimp, mouse, and rat and performed a comprehensive analysis of TAG distribution, TAG sizes, TAG gene orientations and intergenic distances, and TAG gene functions. TAGs account for about 14-17% of all the genomic genes and nearly one third of all the duplicated genes in the four genomes, highlighting the predominant role that tandem duplication plays in gene duplication. For all species, TAG distribution is highly heterogeneous along chromosomes and some chromosomes are enriched with TAG forests while others are enriched with TAG deserts. The majority of TAGs are of size two for all genomes, similar to the previous findings in C. elegans, A. thaliana, and O. sativa, suggesting that it is a rather general phenomenon in eukaryotes. The comparison with the genome patterns shows that TAG members have a significantly higher proportion of parallel gene orientation in all species, corroborating Graham's claim that parallel orientation is the preferred form of orientation in TAGs. Moreover, TAG members with parallel orientation tend to be closer to each other than all neighboring genes with parallel orientation in the genome. The analysis of GO function indicate that genes with receptor or binding activities are significantly over-represented by TAGs. Simulation reveals that random gene rearrangements have little effect on the statistics of TAGs for all genomes. It is noteworthy to mention that gene family sizes are significantly correlated with the extent of tandem duplication, suggesting that tandem duplication is a preferred form of duplication, especially in large families. There has not been any systematic study of TAG genes' expression patterns in the genome. Taking advantage of recent large-scale microarray data, we were able to study expression divergence of some of the TAGs of size two in human and mouse for which the expression data is available and examine the effect of sequence divergence, gene orientation, and physical proximity on the divergence of gene expression patterns. Our results show that there is a weak negative correlation between sequence divergence and expression similarity between the two members of a TAG, and also a weak negative correlation between physical proximity of two genes and their expression similarity. No significant relationship was detected between gene orientation and expression similarity. Moreover, we compared the expression breadth of upstream and downstream duplicate copies and found that downstream duplicate does not show significantly narrower expression breadth. We also compared TAG gene pairs with their neighboring non-TAG pairs for both physical proximity and expression similarity. Our results show that TAG gene pairs do not show any distinct differences in the two aspects from their neighboring gene pairs, suggesting that sufficient divergence has occurred to these duplicated genes during evolution and their original similarity conferred by duplication has decayed to a level that is comparable to their surrounding regions. / Master of Science

Yes / Buruli ulcer (BU) is an insidious neglected tropical disease. Cases are reported around the world but the rural regions of West and Central Africa are most affected. How BU is transmitted and spreads has remained a mystery, even though the causative agent, Mycobacterium ulcerans, has been known for more than 70 years. Here, using the tools of population genomics, we reconstruct the evolutionaryhistoryofM. ulceransbycomparing165isolatesspanning48yearsandrepresenting11endemiccountriesacrossAfrica. The genetic diversity of African M. ulcerans was found to be restricted due to the bacterium’s slow substitution rate coupled with its relatively recent origin. We identified two specific M. ulcerans lineages within the African continent, and inferred that M. ulcerans lineage Mu_A1 existed in Africa for several hundreds of years, unlike lineage Mu_A2, which was introduced much more recently, approximately during the 19th century. Additionally, we observed that specific M. ulcerans epidemic Mu_A1 clones were introduced during the same time period in the three hydrological basins that were well covered in our panel. The estimated time span of the introduction events coincides with the Neo-imperialism period, during which time the European colonial powers divided the African continent among themselves. Using this temporal association, and in the absence of a known BU reservoir or—vector on the continent, we postulate that the so-called "Scramble for Africa" played a significant role in the spread of the disease across the continent. / K.V. was supported by a PhD-grant of the Flemish Interuniversity Council—University Development Cooperation (Belgium). B.d.J. and C.M. were supported by the European Research Council-INTERRUPTB starting grant (no. 311725). T.P.S. was supported by a fellowship from the National Health and Medical Research Council of Australia (1105525). Funding for this work was provided by the Department of Economy, Science and Innovation of the Flemish Government, the Stop Buruli Consortium supported by the UBS Optimus Foundation, and the Fund for Scientific Research Flanders (Belgium) (FWO grant no. G.0321.07N). The computational resources used in this work were provided by the HPC core facility CalcUA and VSC (Flemish Supercomputer Center), funded by the University of Antwerp, the Hercules Foundation and the Flemish Government—department EWI. Aspects of the research in Cameroon and Benin were funded by the Raoul Follereau Fondation France.

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13604号 / 論医博第2314号 / 京都大学大学院医学研究科医学専攻 / (主査)教授 村川 泰裕, 教授 松田 文彦, 教授 武藤 学 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM

京都大学 / 新制・課程博士 / 博士(ゲノム医学) / 甲第25211号 / 医博JD第3号 / 京都大学大学院医学研究科ゲノム医学国際連携専攻 / (主査)教授 村川 泰裕, 教授 平井 豊博, 教授 William Foulkes (ﾏｷﾞﾙ大学), 准教授 George Thanassoulis (ﾏｷﾞﾙ大学), 教授 Krzysztof Kiryluk (ｺﾛﾝﾋﾞｱ大学) / 学位規則第4条第1項該当 / Doctor of Philosophy in Human Genetics / Kyoto University / DFAM

[ES] Durante las últimas décadas, se han realizado importantes avances en el estudio de las causas genéticas de enfermedades raras y comunes, donde un gran número de variantes han sido identificadas y asociadas a múltiples enfermedades. Con las tecnologías de secuenciación de nueva generación, hoy en día somos capaces de investigar, con un alto rendimiento, la contribución de variantes de alta y baja frecuencia a distintos tipos de enfermedades, permitiéndonos así estudiar su importancia en el desarrollo de las mismas. En ésta tesis se ha utilizado la secuenciación del exoma como tecnología para el estudio de variantes raras en una enfermedad compleja, la alergia gastrointestinal inducida por múltiples alimentos. Para ello, se realizó la secuenciación del exoma completo de una cohorte de 31 individuos (ocho afectados y 23 no afectados) provenientes de siete familias diferentes. Se desarrolló un flujo de trabajo para procesar los datos generados a partir de diferentes librerías e instrumentos de secuenciación, así como un control de calidad exhaustivo con el fin de maximizar el número de variantes de alta calidad. Diferentes tipos de mutaciones fueron investigadas, incluyendo polimorfismos de nucleótido único, inserciones/deleciones, variantes del número de copia y haplotipos HLA, y se realizaron diferentes métodos de filtrado para su interpretación. Finalmente, se encontraron una serie de mutaciones que podrían estar asociadas con la enfermedad y se describe su posible papel en la patogénesis de las alergias gastrointestinales. Los resultados de esta tesis suponen importantes avances en el estudio de la compleja arquitectura genética de las alergias gastrointestinales y abren las puertas a futuras líneas de investigación, que serán necesarias para entender completamente las bases genéticas de esta enfermedad. / [CA] Durant les últimes dècades, s'han realitzat importants avanços en l'estudi de les causes genètiques de malalties rares i comunes, on un gran nombre de variants han sigut identificades i associades a múltiples malalties. Amb les tecnologies de seqüenciació de nova generació, avui en dia som capaços d'investigar, amb un alt rendiment, la contribució de variants d'alta i baixa freqüència a diferents tipus de malalties, permetent-nos així estudiar la seva importància en el desenvolupament de les mateixes. En aquesta tesis s'ha utilitzat la seqüenciació del exoma com a tecnologia per a l'estudi de variants rares en una malaltia complexa, l'al·lèrgia gastrointestinal induïda per múltiples aliments. Per això, es va realitzar la seqüenciació del exoma complet d'una cohort de 31 individus (vuit afectats i 23 no afectats) provinents de set famílies diferents. Es va desenvolupar un flux de treball per a processar les dades generades a partir de diferents llibreries e instruments de seqüenciació, així com un control de qualitat exhaustiu amb la fi de maximitzar el nombre de variants d'alta qualitat. Diferents tipus de mutacions foren investigades, incloïent polimorfismes de nucleòtid únic, insercions/delecions, variants del nombre de còpia i haplotips HLA, i es realitzaren diferent mètodes de filtrat per a la seva interpretació. Finalment, es trobaren una sèrie de mutacions que podrien estar associades amb la malaltia i es descriu el seu possible paper en la patogènesis de les al·lèrgies gastrointestinals. Els resultats d'aquesta tesis suposen importants avanços en l'estudi de la complexa arquitectura genètica de les al·lèrgies gastrointestinals i obrin les portes a futures línies d'investigació, que seran necessàries per entendre completament les bases genètiques d'aquesta malaltia. / [EN] The study of genetics has been making significant progress towards understanding the causes of rare and common disease during the past decades. Across a wide range of disorders, there have been hundreds of associated loci identified and associated with multiple disorders. Now, with the advent of next-generation sequencing technologies, we are able to interrogate the contribution of high and low frequency variation to disease in a high throughput manner. This provides an opportunity to investigate the role of rare variation in complex disease risk, potentially offering insights into disease pathogenesis and biological mechanisms. In this thesis, it has been assessed the use of whole-exome sequencing technology to investigate the role of rare variation in a complex disease, gastrointestinal food allergy induced by multiple food proteins. For that, a cohort of 31 individuals (eight affected and 23 non-affected) from seven different families was whole exome sequenced. Data obtained from multiple sequencing systems and libraries were analysed, and a workflow was developed, focusing on a comprehensive quality control to maximise the number of real positive calls. Different types of genome variations were investigated, including single nucleotide variants, insertions/deletions, copy number variants and HLA haplotypes. By approaching different methods of variant filtering, a set of rare variants that could be associated with the disease was identified. The possible role of these candidate variants in the pathogenesis of gastrointestinal food allergies was also discussed. These results reveal important insights into the genetic architecture of gastrointestinal food allergies and lead to additional lines of investigation that will be required in order to fully understand the genetic basis of this disease. / Sanchis Juan, A. (2019). Exome Sequencing in Gastrointestinal Food Allergy Induced by Multiple Food Protein [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/134361

The formation and persistence of species are the subject of much debate among biologists. Many species of Drosophila are behaviourally isolated, meaning that heterospecific individuals are not attracted to one another and do not interbreed. Often, this behavioural isolation is at least in part due to differences in pheromonal preference. Drosophila pheromones are long-chain cuticular hydrocarbons (CHCs). Desaturases are enzymes that are important for the production of CHCs. This thesis investigates the evolution of the gene family across 12 species of Drosophila. Desaturase genes were located in all species. Some genes, those that have previously been shown to have important roles in pheromonal communication, have experienced duplication and loss in several species. Two previously undiscovered duplicates were identified. Generally the desaturase gene family is governed by purifying selection, although following duplication these constraints are relaxed and in some cases duplicated genes show compelling evidence of positive selection. One of the loci under positive selection, the novel duplicate desat1b of the obscura group, was found to have a sex-biased expression pattern and alternative splicing in its 5′ UTR. In RNAi knock-down experiments of desaturase gene function in D. melanogaster, several desaturases were shown to affect CHC profiles of males and females, including some that were previously unlinked to CHC production.