We developed a new program called GeneTack for ab initio frameshift detection in intronless protein-coding nucleotide sequences. The GeneTack program uses a hidden Markov model (HMM) of a genomic sequence with possibly frameshifted protein-coding regions. The Viterbi algorithm nds the maximum likelihood path that discriminates between true adjacent genes and a single gene with a frameshift. We tested GeneTack as well as two other earlier developed programs FrameD and FSFind on 17 prokaryotic genomes with frameshifts introduced randomly into known genes. We observed that the average frameshift prediction accuracy of GeneTack, in terms of (Sn+Sp)/2 values, was higher by a signicant margin than the accuracy of the other two programs. GeneTack was used to screen 1,106 complete prokaryotic genomes and 206,991 genes with frameshifts (fs-genes) were identifed. Our goal was to determine if a frameshift transition was due to (i) a sequencing error, (ii) an indel mutation or (iii) a recoding event. We grouped 102,731 genes with frameshifts (fs-genes) into 19,430 clusters based on sequence similarity between their protein products (fs-proteins), conservation of predicted frameshift position, and its direction. While fs-genes in 2,810 clusters were classied as conserved pseudogenes and fs-genes in 1,200 clusters were classied as hypothetical pseudogenes, 5,632 fs-genes from 239 clusters pos- sessing conserved motifs near frameshifts were predicted to be recoding candidates. Experiments were performed for sequences derived from 20 out of the 239 clusters; programmed ribosomal frameshifting with eciency higher than 10% was observed for four clusters. GeneTack was also applied to 1,165,799 mRNAs from 100 eukaryotic species and 45,295 frameshifts were identied. A clustering approach similar to the one used for prokaryotic fs-genes allowed us to group 12,103 fs-genes into 4,087 clusters. Known programmed frameshift genes were among the obtained clusters. Several clusters may correspond to new examples of dual coding genes. We developed a web interface to browse a database containing all the fs-genes predicted by GeneTack in prokaryotic genomes and eukaryotic mRNA sequences. The fs-genes can be retrieved by similarity search to a given query sequence, by fs- gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, programmed frameshifts etc. All the tools and the database of fs-genes are available at the GeneTack web site http://topaz.gatech.edu/GeneTack/

Transposable elements (TEs) are mobile DNA sequences that can move from one location to another in the genome. These elements encode regulatory features including transcriptional promotion and termination signals facilitating the production of new transcripts (or elements). The elements thus produced are inserted back into the genome. Due to their insertional capacity and encoded regulatory features, TEs have, in recent years, been recognized as significant contributors to regulatory variation both within and between species. In comparing the human and chimpanzee genomes it has been hypothesized that the genetic basis of the phenotypic differences that distinguish them may be the result of regulatory differences existing between the two species. Since TEs inserted in proximity to genes can significantly alter gene expression patterns, this research aims at exploring the influence of TE sequences and retrotransposons in particular in the evolution of gene regulation between humans and chimpanzees. A first systematic search of one particular class of retrotransposons - endogenous retroviruses (ERVs) was carried out in the chimpanzee genome. Forty two families of ERVs were identified in the chimpanzee genome including the discovery of 9 previously unknown families in humans. The vast majority of these families were found to have orthologs in the human genome except for two (CERV 1/PTERV1 and CERV 2) families. The two CERV families without orthologs in the human genome display a patchy distribution among primates. Nine families of chimpanzee ERVs have been transpositionally active since the human-chimpanzee divergence, while only two families have been active in the human lineage. The genomic differences [INDEL variation (80-12,000 bp in length)] between humans and chimpanzees are laid out. The INDEL variation located in or near genes is categorized in detail and is correlated with differences in gene expression patterns in a variety of organs and tissues. Results indicate that the majority of the INDEL variation between the two species is associated with retrotransposon sequences and that this variation is significantly correlated with differences in gene expression most notably in brain and testes. These findings are consistent with the hypothesis that retrotransposon mediated regulatory variation may have been a significant factor in human/chimpanzee evolution.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2017-03-20T21:49:24Z No. of bitstreams: 1 DiegoMarquesDaCostaSantos_DISSERT.pdf: 2551094 bytes, checksum: 6ba7eac7b523f238609d30d5347a6556 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2017-03-23T18:43:14Z (GMT) No. of bitstreams: 1 DiegoMarquesDaCostaSantos_DISSERT.pdf: 2551094 bytes, checksum: 6ba7eac7b523f238609d30d5347a6556 (MD5) / Made available in DSpace on 2017-03-23T18:43:15Z (GMT). No. of bitstreams: 1 DiegoMarquesDaCostaSantos_DISSERT.pdf: 2551094 bytes, checksum: 6ba7eac7b523f238609d30d5347a6556 (MD5) Previous issue date: 2016-08-30 / O c?ncer colorretal (CCR) ? um tipo de c?ncer que acomete a regi?o do intestino grosso e reto; sendo o terceiro c?ncer mais comum em homens e o segundo em mulheres no mundo. A maior parte da susceptibilidade ao CCR ? proveniente de variantes gen?ticas m?ltiplas, cada uma com um efeito individual que, quando combinada, causa a diversidade de risco para o desenvolvimento desse c?ncer. Dentre os tipos de muta??es encontrados no genoma humano, as inser??es e dele??es (INDEL) s?o a segunda classe mais comum; e o entendimento deste tipo de muta??o possui um potencial de impactar na express?o, na estrutura e at? mesmo fun??o da prote?na. Entretanto, sabe-se relativamente pouco sobre o impacto das INDEL no risco de CCR, especialmente na popula??o miscigenada do Brasil. Dessa forma o objetivo deste trabalho ? realizar um estudo do tipo caso-controle para determinar a associa??o de 16 INDEL com a susceptibilidade ao CCR na popula??o do Rio Grande do Norte. Al?m disso, foi tamb?m avaliado a distribui??o relativa da ancestralidade entre o grupo caso e controle. Os polimorfismos e os marcadores utilizado para a distribui??o da ancestralidade foram genotipados utilizando ABI PRISM 3130 e o GeneMapper ID v3.2. A an?lise estat?stica foi realizada utilizando o R v 3.1. Em rela??o ? ancestralidade gen?mica, foi observada diferen?a significativa na distribui??o da contribui??o Africana entre os grupos. Em rela??o ? an?lise de associa??o entre o polimorfismo e o risco de desenvolver CCR, foi observado que o alelo D do polimorfismo estudado no gene IL4, e o alelo I do polimorfismo do TYMS foram associados com o aumento do risco de desenvolver CCR. No presente trabalho, tamb?m foi avaliado o risco que a combina??o genot?pica do TYMS (rs151264360) e do IL4 (rs79071878) aumenta consideravelmente o risco de ter CCR; e foi observado que se faz necess?rio a presen?a de pelo menos 3 alelos de risco para conferir risco de ter CCR. / Colorectal cancer (CRC) is a type of cancer that affects large intestine and rectum region, and this is the third most common cancer worldwide in men and the second in women. The genetic susceptibility to CRC comes from multiple genetic variants. Individually, these genetic variants have modest effect. However, theses variants, when combined, cause a wide range of risk. Among all mutations types found in the human genome, insertion-deletions (INDEL) are the second most common class, which has a potential impact on the expression, structure and protein function. However, there are a few studies about INDEL impact on CRC risk. Thus the aim of this study is to evaluate the association of 16 INDEL with CRC susceptibility in Rio Grande do Norte population. Furthermore, it was also evaluated the relative ancestry distribution between case and control groups. Polymorphism and marker used for ancestry distribution were genotyped using ABI PRISM 3130 and GeneMapper ID v 3.2. Statistical analysis was performed using the R v 3.1. Regarding the genetic ancestry, there was significant difference in the distribution of the African contribution between groups. Regarding the polymorphism association in CRC risk, it was observed that the D allele of IL4 and I allele of TYMS polymorphisms were associated with increased CRC risk. In this study, it was also evaluated the combined effect of IL4 and TYMS polymorphism in CRC risk, and it was observed that at least 3 allelic risks were necessary to confer CRC risk.

Nowadays intensive research is conducted for application of genetic polymorphisms for degraded samples analysis, identification and kinship determination. Another area of research in forensic genetics is biogeographical and phenotypic traits (eye, hair and skin color) determination. First part of presented work dealt with population study on the Czech popu- lation using Investigator DIPplex (QIAGEN, Germany) marker set containing 30 autosomal insertion-deletion polymorphisms. Power of Discrimination (PD), which is the probability of random selection of two persons with different genotypes, was 99.9999999999% for the whole marker set. This part of study concluded that ana- lyzed marker set is suitable as an additional marker panel for identification and kinship determination in the Czech Republic. Second part of the presented study was devoted to population research of Cen- tral Croatia using Mentype Argus X-8 kit (QIAGEN, Germany) containing 8 short tandem repeat polymorhisms located on X choromosomes (X-STR) divided into 4 linkage groups. PD for the whole kit reached 99.9999% and 99.99999999% for males and females, respectively. This kit could be used in Central Croatian population for kinship analysis and for identification as an additional marker panel. The next part of the presented study was the...

<p>Though pathogenic strains represent a small portion of the total variety of existing <em>Escherichia coli </em>strains, they contribute extensively to human morbidity and mortality. Disease outbreaks caused by enterohaemorrhagic <em>E. coli</em> of the serotype O157:H7 and the “Big Six” serotypes (i.e., O26, O45, O103, O111, O121 and O145) have driven the development of assays for pathogen detection. From culture-based assays requiring several days for confirmation of target organisms, to quantitative PCR (qPCR) tests that provide pathogen identification in several hours’ time, the sensitivity, specificity and speed of bacterial diagnostics have seen improvements that increased the efficacy of assays used to detect pathogens at clinically relevant levels. One relatively unexplored field of diagnostics is the use of conserved signature insertion/deletions (CSIs) as stable genetic markers for pathogen detection. This thesis presents two qPCR assays that target an <em>E. coli</em> O157:H7-specific insertion in a CSI. In a more preliminary study, an EvaGreen-based qPCR assay was developed that had a detection limit of 16 <em>E. coli</em> O157:H7 genome equivalents. An improved format of the O157:H7-specific CSI assay, using TaqMan probes, was later established. TaqMan probes are sequence-specific, while DNA-intercalating EvaGreen dye is sequence-independent. Though the TaqMan probe-based assay had a higher detection limit of 100 genome equivalents, the assay maintained detection sensitivity in presence of genetically similar (<em>E. coli</em> K-12) and dissimilar (fish sperm) DNA in excess amounts (1000-fold and 800-fold excess of target DNA, respectively), demonstrating its potential for pathogen detection in environmental samples where the presence of background flora may influence detection. These assays thus represent an exploration into the use of CSIs as diagnostic tools. This thesis also provides a guide for future developments of pathogen detection using CSIs, such as those that may be present in toxigenic species of Cyanobacteria and human pathogens, including <em>Vibrio</em> and <em>Campylobacter</em>.</p> / Master of Science (MSc)

Submitted by JULIANA MARTINEZ null (jumrtz@hotmail.com) on 2018-01-30T20:15:12Z No. of bitstreams: 1 Tese de Doutorado - Juliana Martinez_versaofinal.pdf: 5281561 bytes, checksum: 3904c01cc47c8b76f9c22a3a88eeb574 (MD5) / Approved for entry into archive by Maria Irani Coito null (irani@fcfar.unesp.br) on 2018-02-02T16:30:55Z (GMT) No. of bitstreams: 1 martinez_j_dr_arafcf_int.pdf: 5281561 bytes, checksum: 3904c01cc47c8b76f9c22a3a88eeb574 (MD5) / Made available in DSpace on 2018-02-02T16:30:55Z (GMT). No. of bitstreams: 1 martinez_j_dr_arafcf_int.pdf: 5281561 bytes, checksum: 3904c01cc47c8b76f9c22a3a88eeb574 (MD5) Previous issue date: 2017-11-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Na rotina da genética forense, o uso exclusivo dos marcadores STRs (Short Tandem Repeats) em situações que a amostra biológica apresenta-se degradada pode gerar um resultado final estatístico inconclusivo, tornando fundamental a análise de marcadores adicionais para a resolução do caso. Utilizado como método complementar, os polimorfismos InDels (inserção/deleção) têm mostrado grande potencial para superar as limitações dos marcadores tradicionais. A análise de regiões do cromossomo X também vem ganhando significativa importância nesses estudos, especialmente nos casos em que a análise dos autossômicos não é suficiente. Nessa perspectiva, este trabalho teve por objetivo geral caracterizar a população do estado de São Paulo para 32 polimorfismos de inserção/deleção no cromossomo X (32 X-InDels) e avaliar a utilidade desse multiplex na resolução de casos forenses. Para tanto, buscou-se identificar a diversidade genética desses polimorfismos nessa população, a segregação dos alelos entre os genitores (pai e mãe) para as suas respectivas filhas e a eficiência desse painel na amplificação de DNA extraído de amostras ósseas. Para identificar a diversidade genética, foram analisados os perfis genotípicos de 500 indivíduos não aparentados nascidos no estado de São Paulo. Todos os marcadores mostraram-se polimórficos para a população, sendo MID3701 o que apresentou maior diversidade e somente MID2637 se mostrou pouco informativo. O marcador MID1361 apresentou-se em desequilíbrio de Hardy-Weinberg e uma variante alélica foi identificada em seu alelo curto. O painel demonstrou alta eficiência forense, confirmado pelo poder acumulado de discriminação (0,999999999993 em mulheres e 0,99999993 em homens) e pelo valor acumulado da chance média de exclusão (0,999996 em trios e 0,9995 em duos). No comparativo com outras populações, valores significativos da distancia genética foram obtidos, verificando-se que São Paulo está mais próximo à três departamentos colombianos e às populações européias. A proporção de ancestralidade identificada foi 41,8% para europeus, 31,6% para africanos e 26,6% para nativo-americanos. Na análise de segregação realizada em 101 trios, o padrão de transmissão esperado entre pai-mãe/filha foi o observado, o que confirma a baixa taxa de mutação desses marcadores. Por fim, os 32 X-InDels apresentaram as características necessárias para a análise de amostras biológicas em baixa concentração e/ou degradadas, mas algumas dificuldades na amplificação podem ser encontradas a depender das condições ambientais a que as amostras foram expostas. Conclui-se que o conhecimento acerca dos marcadores de inserção/deleção no cromossomo X pode ser ampliado, uma vez que na literatura ainda há pouco material disponível sobre o assunto; entretanto os dados deste trabalho já demonstram seu potencial como método alternativo para a análise de amostras forenses, pois foram identificados elevados valores de poder de discriminação e exclusão, baixa taxa de mutação e um elevado potencial de amplificação de amostras biológicas degradadas. / In forensic genetics routine, the exclusive use of STRs (Short Tandem Repeats) markers when the biological sample is degraded can generate an inconclusive final statistical result, making essential the analysis of additional markers for case resolution. Used as a complementary method, InDels (insertion/deletion) polymorphisms have shown great potential to overcome the limitations of traditional markers. Polymorphisms in the X chromosome is also gaining significant importance in these studies, especially in those cases in which the analysis of the autosomal markers is not enough. In this perspective, this study aimed to characterize the São Paulo state population for 32 X chromosome insertion/deletion polymorphisms (32 X-InDels) and to evaluate the utility of this multiplex in the resolution of forensic cases. Therefore, it was analyzed the genetic diversity of this population, the alleles segregation between the parents and their respective daughters, and the amplification efficiency of this panel in DNA extracted from human bones. To identify genetic diversity, the genotypic profiles of 500 unrelated individuals born in São Paulo state was analysed. All markers were polymorphic for the population, with MID3701 being the most diverse, and MID2637 the less informative. The MID1361 marker was in Hardy-Weinberg disequilibrium and an allelic variant was identified in its short allele. The panel showed high forensic efficiency, confirmed by the accumulated power of discrimination (0.9999999999993 in females and 0.99999993 in males) and by the accumulated mean exclusion chance (0.999996 in trios and 0.99995 in duos). Comparing with other populations, significant values of genetic distance were obtained and São Paulo is closer to three Colombian departments and to European populations. The ethnic contributions identified 41.8% of Europeans, 31.6% of Africans and 26.6% of Native Americans admixture. In segregation analysis performed in 101 trios, the expected transmission pattern between parent/daughter was observed, which confirms the low mutation rate of these markers. Finally, the 32 X-InDels presented the necessary characteristics for the analysis of degraded biological samples, but some amplification difficulties can be found depending on the environmental conditions in which the samples were exposed. It can be concluded that knowledge about the X chromosome insertion/deletion markers can be expanded, because there is still little information available in the literature; meanwhile data from this work demonstrate its potential as an alternative method for the analysis of forensic samples.

The first draft sequence of the human genome was published over a decade ago, yet interpreting the functional importance of nucleotides in genomes is still an ongoing challenge. I took a comparative genomic approach to identify functional sequence using signatures of natural selection in DNA sequences. Mutations that are purged or propagated by selection mark sequences of significance for biological fitness. I developed and refined methods for estimating the quantity of sequence constrained with respect to insertions and deletions (indels) between two genome sequences, a quantity I termed α_selIndel. This sequence is evolving more slowly than surrounding neutral sequence due to the purging of deleterious indel variants, and thus this sequence is likely to be functional. I estimated α_selIndel between diverse mammalian and avian species pairs, and found a strong negative correlation between α_selIndel and the divergence between the species’ genome sequences. This implies that functional sequence turns over rapidly as it is lost and gained over time. I quantified the variable levels of sequence constraint, and rates of sequence turnover, for different types of human biochemically annotated element. Furthermore, I found that similar rates of functional turnover have occurred across mammalian and avian evolution. Finally, I identified positively selected amino acid residues that may be important for Darwin’s finch beak development, and found evidence of adaptively evolving reproductive proteins in the ancestral songbird lineage. Collectively these results demonstrate the wide-spread nature of lineage-specific functional sequence with implications for understanding species traits and the use of model organisms to inform human biology.

The Neutral Indel Model is able to predict accurately the distribution of indel events in alignments of neutrally evolving genomic sequence. Here, I apply this model to a diverse range of metazoan species pairs, to a number of ends. First, I apply the Neutral Indel Model to alignments of genome sequences for species within the mammalian clade in order to estimate the quantities of functional DNA shared between species pairs. I demonstrate that as the evolutionary divergence between species pairs increases, estimates of functional sequence drop off dramatically. This pattern is not replicated in extensive simulations of genome sequence alignments, suggesting that functional (and mostly non-coding) sequence is turning over at a rapid rate. I also estimate that between 200 and 300 Mb (6.5-10%) of the human genome is under evolutionary constraint, a considerably higher quantity of sequence than has been estimated by previous whole genome analyses. Second, extending my analyses to consider more diverse metazoan species, I provide estimates for functional bases within organisms’ genomes that appear to mirror our conceptions of organismal complexity. Thirdly, I develop the Neutral Indel Model as a method for assessing genome sequence quality, by quantifying indel errors within alignments of closely related (ds < 0.1) species pairs. Applying this method to six primate genome sequence assemblies, I demonstrate that the frequency of indel error events per base varies up to six-fold. Further to this, I show that second generation sequencing technologies can be used to create high quality genome sequence assemblies and to ameliorate errors in pre-existing assemblies. Finally, I analyse patterns of indel mutations in primate transposable elements and show that indels are not randomly distributed within these sequences due to regularly spaced homo-nucleotide motifs.

Submitted by Hellen Luz (hellencrisluz@gmail.com) on 2017-08-10T18:18:49Z No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PolimorfismosGenicosTipo.pdf: 1974852 bytes, checksum: aa3b04d35c7266ffc0e87975cc193ae5 (MD5) / Approved for entry into archive by Irvana Coutinho (irvana@ufpa.br) on 2017-08-11T13:15:55Z (GMT) No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PolimorfismosGenicosTipo.pdf: 1974852 bytes, checksum: aa3b04d35c7266ffc0e87975cc193ae5 (MD5) / Made available in DSpace on 2017-08-11T13:15:55Z (GMT). No. of bitstreams: 2 license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Dissertacao_PolimorfismosGenicosTipo.pdf: 1974852 bytes, checksum: aa3b04d35c7266ffc0e87975cc193ae5 (MD5) Previous issue date: 2017-07-26 / CAPES - Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / A fisiopatologia da depressão ainda permanece não totalmente compreendida. E apesar das contribuições da hipótese monoaminérgica para a compreensão de parte dos aspectos neurobiológicos desse transtorno, surgiram estudos com o objetivo de investigar o papel da neuroinflamação, dos polimorfismos em genes que influenciam a atividade inflamatória e as funções dos receptores monoaminérgicos no desenvolvimento do transtorno depressivo maior (TDM). Contudo, são poucas as pesquisas que analisaram o papel de vias inflamatórias upstream (como o papel dos genes NFKB1 e PAR1, capazes de influenciar a transcrição gênica de citocinas pró-inflamatórias) e do polimorfismo do gene codificante do receptor alfa 2 adrenérgico (gene ADRA2B) em indivíduos com o diagnóstico de depressão. Portanto, o objetivo deste estudo foi analisar o papel dos polimorfismos do tipo INDEL dos genes NFKB1 (rs28362491), PAR1 (rs11267092) e ADRA2B (rs34667759) no desenvolvimento do transtorno depressivo maior. Doze pacientes com diagnóstico de TDM e 145 controles saudáveis tiveram amostras de sangue coletadas e os polimorfismos dos 3 genes foram genotipados por uma única reação multiplex. Os produtos do PCR multiplex foram separados por eletroforese capilar e os dados analisadas no software GeneMapper 3.7 (Applied Biosystems). Esta pesquisa encontrou uma associação estatisticamente significante entre a variável depressão e os portadores do genótipo Del/Del do gene ADRA2B (p = 0,002): esses indivíduos apresentaram uma chance 6,41 vezes maior de desenvolver depressão quando comparados aos portadores dos genótipos Del/Ins e Ins/Ins. Não houve significância estatística entre os polimorfismos INDEL dos genes NFKB1 e PAR1 e o fenótipo depressivo. Nossos resultados sugerem que o marcador INDEL do gene ADRA2B (rs34667759), especificamente o alelo deleção, seja um possível biomarcador genético de vulnerabilidade para o desenvolvimento do TDM. / The pathophysiology of depression still remains not fully understood. And despite the contributions of the monoaminergic hypothesis to the understanding of neurobiological aspects of this disorder, studies have been carried out to investigate the role of neuroinflammation, polymorphisms in genes that influence inflammatory activity and monoaminergic receptor functions in the development of major depressive disorder (MDD). However, few studies have analyzed the role of upstream inflammatory pathways (such as the role of NFKB1 and PAR1 genes, which are capable of influencing transcription of proinflammatory cytokines) and of the alpha 2 adrenergic receptor encoding gene's polymorphism (ADRA2B gene) in individuals diagnosed with depression. Therefore, the objective of this study was to analyze the role of the INDEL type polymorphisms of NFKB1 (rs28362491), PAR1 (rs11267092) e ADRA2B (rs34667759) genes in the development of major depressive disorder. Twelve patients diagnosed with MDD and 145 healthy controls had blood samples collected and the INDEL polymorphisms of these 3 genes were genotyped by a single multiplex reaction. The multiplex PCR products were separated by capillary electrophoresis and the data analyzed in GeneMapper 3.7 software (Applied Biosystems). This research found a statistically significant association between depression and Del/Del genotype of the ADRA2B gene (p = 0.002): these individuals presented a 6.41 times greater chance of developing depression when compared to Del/Ins and Ins/Ins genotypes. There was no statistical significance between the INDEL polymorphisms of NFKB1 and PAR1 genes and depressive phenotype. Our results suggest that the INDEL marker of the ADRA2B gene (rs34667759), specifically the deletion allele, is a possible genetic biomarker of vulnerability for the development of MDD.

Citrus es el género de la subfamilia Aurantioideae de mayor importancia económica. Su origen es la región sureste de Asia, en un área que incluye China, India y la península de Indochina y los archipiélagos de los alrededores. Aunque se han realizado múltiples estudios, la taxonomía del género Citrus aun no está bien definida, debido al alto nivel de diversidad morfológica encontrado en este grupo, la compatibilidad sexual entre sus especies y la apomixis de muchos genotipos. En la presente tesis doctoral se ha estudiado una amplia diversidad del género Citrus, especies relacionadas y otros taxones de la subfamilia Aurantioideae, para poder aclarar su organización y filogenia mediante el empleo de diferentes tipos de marcadores moleculares y métodos de genotipado. Más concretamente, el germoplasma de mandarino juega un papel muy importante en la mejora de variedades y patrones, pero su organización genética no está bien definida. Por lo tanto, se ha realizado un análisis en profundidad de su diversidad y organización genética. El desarrollo de marcadores moleculares de Inserción-Deleción (indel), por primera vez en cítricos, ha permitido demostrar su utilidad para estudios de diversidad y filogenia en el género Citrus. En combinación con los marcadores de tipo microsatélite (SSR), se ha cuantificado la contribución de los tres principales taxones de cítricos (C. reticulata, C. maxima and C. medica) a los genomas de las especies secundarias y cultivares modernos. También se ha definido su estructura genética a partir de los datos obtenidos en la secuenciación de 27 fragmentos de genes nucleares relacionados con la biosíntesis de compuestos que determinan la calidad de los cítricos y genes relacionados con la respuesta de la planta a estreses abióticos. El análisis de la filogenia nuclear ha permitido determinar la relación existente entre la especie C. reticulata y Fortunella, que se diferencian claramente del grupo formado por las otras dos principales especies de cítricos (C. maxima y C. medica). Este resultado está en concordancia con el origen geográfico de las especies estudiadas. A partir de este estudio, se han desarrollado marcadores moleculares de tipo SNP con un alto valor filogenético, que han sido transferidos a géneros relacionados de los cítricos. Estos marcadores han dado un resultado muy positivo en el género Citrus y serán de gran utilidad para el establecimiento de la huella genética del germoplasma en un nivel de diversidad más amplio. Se ha estudiado la organización genética dentro del germoplasma mandarino (198 genotipos de tipo mandarino pertenecientes a dos colecciones, INRA-CIRAD e IVIA), así como la introgresión de otros genomas mediante el uso de 50 y 24 marcadores de tipo SSR y indel, respectivamente, además de cuatro marcadores InDel mitocondrial (ADNmt). Se ha observado que muchos genotipos, que se creía que eran mandarinos puros, presentan introgresión de otros genomas ancestrales. Dentro del germoplasma de mandarino, se han identificado a nivel nuclear cinco grupos parentales, a partir de los cuales se originaron muchos genotipos, dando lugar a estructuras hibridas complejas. Se ha observado incluso, genotipos con un origen maternal no mandarino, determinado por los marcadores de ADNmt. La presente tesis doctoral ha aportado nueva información sobre las relaciones filogenéticas entre las especies del género Citrus, géneros cercanos, así como de las especies secundarias. Además, se han desarrollado nuevos marcadores moleculares que se complementan entre sí. Se ha establecido una nueva organización genética del germoplasma mandarino y se han caracterizado adecuadamente las dos colecciones de cítricos en estudio. Por lo tanto, todas estas contribuciones, ayudarán a los programas de mejora para la obtención de nuevas variedades de cítricos de alta calidad y permitirán optimizar la conservación y uso de los recursos genéticos existentes, así como su caracterización genética y fenotípica. / García Lor, A. (2013). Organización de la diversidad genética de los cítricos [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/31518 / TESIS