Dissertations / Theses on the topic 'Periderma'

The periderm is a complex structure that protects plants’ secondary organs and wounded tissues. This function is given by the phellem, a multilayered tissue formed by cells with suberized cell walls located on the outer part of the periderm. Suberin is a basic polymer for protection thanks to its lipid nature. Exceptionally, the cork oak has a great capacity to produce layers of phellem. Recently, transcriptomics studies, as well as reverse genetic approaches, have contributed to the knowledge of the formation and regulation of the periderm and the synthesis and transport of the suberin components. However, the molecular bases that control these processes are still quite unknown. For this reason, new regulatory and transport candidate genes have been characterized. In addition, a faster and less expensive roots transformation system has been developed. Finally, a global transcriptome analysis of the outer bark of cork oak during its growth has been performed
El periderma és una estructura complexa que protegeix els òrgans secundaris i els teixits cicatricials. Aquesta funció la dóna el fel·lema,teixit pluriestratificat format per cèl·lules amb parets suberificades situat a la part externa del periderma. La suberina és un polímer bàsic per la protecció gràcies a la seva naturalesa lipídica. De forma excepcional l’alzina surera té una gran capacitat per produir capes de fel·lema. En els últims anys, estudis transcriptòmics, així com de genètica inversa, han contribuït al coneixement de la formació i regulació del periderma i la síntesi i transport de la suberina. No obstant, les bases moleculars que controlen aquests processos són encara força desconegudes. Per aquest motiu s'han caracteritzat nous gens candidats reguladors i de transport. A més, s'ha posat a punt un sistema de transformació d'arrels més ràpid i menys costós. Per últim, s'ha realitzat un anàlisi global del transcriptoma de l'excorça externa de l'alzina surera durant el seu creixement

We have developed new molecular tools to characterize the FHT and StRIK genes in the tuber periderm. Regarding FHT gene, our results demonstrated that is induced very specifically in suberizing tissues what makes FHT a good marker of the suberization process. Regarding StRIK gene, it has been shown to be a good candidate for the periderm regulation since its silencing causes changes in genes expression related to the transposition of DNA, RNA processing and stress. Finally, by RNA-seq we have identified a wide range of new candidate genes for the formation of the cork oak periderm. Among these genes several are related to the formation of the cell wall, cell primary metabolism and suberin accumulation. Other relevant genes are those involved in the regulation of meristem such as auxin transporters and the ethylene metabolism and signaling. The expression patterns of some genes have been studied during the cork growing season.
Hem desenvolupat noves eines moleculars per a la caracterització dels gens FHT i StRIK en el peridermis del tubercle. Els nostres resultats mostren que FHT s’indueix de forma molt específica en teixits suberificats el que el fa un bon marcador del procés de suberificació. En relació al gen StRIK, hem vist que es un bon candidat a la regulació de la peridermis ja que el seu silenciament provoca canvis d’expressió en gens relacionats amb la transposició de l’ADN, el processament de l’RNA i l’estrès. Mitjançant RNA-seq hem identificat nous gens candidats per la formació de la peridermis en l’alzina surera, entre ells destaquen gens relacionats amb la formació de la paret cel·lular, el metabolisme primari i l’acumulació de suberina. També destaquen gens relacionats amb la regulació del meristema com ara els transportadors d’auxines i el metabolisme i senyalització per etilè. L’expressió d’alguns gens s’ha analitzat durant la formació del suro.

The results obtained in this thesis indicate that StNAC103 promoter activity is induced in tissues undergoing suberin synthesis. Moreover StNAC103 transcript accumulation is concomitant to that of CYP86A33 and takes place after that of FHT. Nonetheless, an increase of the suberin and wax accumulation in the silenced periderms for StNAC103 suggests its role as a repressor in suberin and wax accumulation. Altogether these studies support the hypothesis that there exists a very fine regulation of the suberin and wax synthesis in the periderm, in which StNAC103 plays an important role.
Els resultats obtinguts en aquesta tesi indiquen que l’activitat del promotor d’StNAC103 s’indueix en teixits on és activa la síntesi de suberina i l’acumulació del transcrit corresponent es dóna concomitantment a la de l'ω-hidroxilasa d’acids grassos CYP86A33 i s’inicia posteriorment a la de la feruloïl transferasa d’ω-hidroxiacids i alcohols FHT. Tanmateix, l’augment en l’acumulació de suberina i ceres en els peridermes silenciats per StNAC103 suggereix un paper repressor d’aquest factor de transcripció. Tot plegat fa pensar que hi ha d’haver una regulació molt fina de la síntesi de suberina i ceres en el periderma i que StNAC103 hi té un paper destacat.

Orientador: Carmen Regina Marcati
Resumo: Avaliar a estrutura anatômica de plantas que crescem em diferentes ambientes é uma maneira de compreender como as plantas se adaptam às variações destes ambientes. Algumas destas adaptações influenciam no transporte de água e de fotoassimilados, na proteção dos tecidos internos, na força mecânica e na capacidade de armazenamento dos tecidos, que são funções associadas ao caule das plantas. Assim, neste trabalho, avaliamos a estrutura caulinar de duas espécies, Moquiniastrum polymorphum e Zanthoxylum rhoifolium que ocorrem simultaneamente em diferentes tipos vegetacionais: o cerrado sensu stricto, o cerradão, a floresta estacional semidecídua e a floresta ombrófila densa. Os três primeiros tipos vegetacionais têm um período de seca durante o ano, enquanto que na floresta ombrófila densa o regime pluviométrico é relativamente constante ao longo do ano. Os solos de cada local apresentam diferentes propriedades físicas e químicas e no cerrado sensu stricto o fogo é um fator ambiental que pode ocorrer naturalmente. Estes fatores podem influenciar a estrutura anatômica dos tecidos vegetais. Para a descrição anatômica coletamos amostras do caule (a 1,30 m do solo) contendo xilema secundário e casca, pelo método não destrutivo, de cinco indivíduos de cada tipo vegetacional, que foram processadas conforme técnicas usuais em anatomia da madeira. Para verificar as diferenças entre os tipos vegetacionais, nós comparamos as características anatômicas por meio de uma análise de variância. ... (Resumo completo, clicar acesso eletrônico abaixo)
Doutor

Potato (Solanum tuberosum L.) is the world's fourth largest food crop and large financial losses are incurred each year from wound and bruise related injuries. However, little is known about the coordinate induction of genes that may be associated with, or mark major wound-healing and periderm maturation events. Also, one of the key defense mechanisms for potato tubers is the robust barrier provided by the phellem (skin) of the native periderm. Many biological processes are involved in the formation of this stout tissue. However, little is known about induction of genes that may be associated with this process. The objectives of this research were to molecularly assess the processes of wound periderm development and maturation, and native periderm maturation in potato tubers. In this study, these processes were determined in coordination with expression profiles of selected genes. The cell cycle, cell wall protein, and pectin methyl esterase genes were determined from two diverse potato genotypes and two harvests NDTX4271-5R (ND) and Russet Burbank (RB) tubers; 2008 and 2009 harvests. Cell cycle genes encoding epidermal growth factor binding protein (StEBP), cyclin-dependent kinase B (StCDKB), and cyclin-dependent kinase regulatory subunit (StCKS1At) expression profiles were coordinated with related phellogen formation and the induction and cessation of phellem cell formation. Genes encoding the structural cell wall proteins extensin (StExt1) and extensin-like (StExtlk) expression profiles suggested involvement with closing layer formation and subsequent phellem cell layer formations. The coordinate induction and expression profile of StTLRP, a gene encoding a cell wall strengthening "tyrosine- and lysine-rich protein," suggested a role in the formation of the closing layer followed by phellem cell generation and lastly cell wall thickening in nonmeristematic phellogen cells. StPME and StPrePME expression increased during periderm development, implicating involvement in modifications for closing layer and phellem cell formation. Collectively, these results indicate that the genes monitored were involved in and their expression profiles markedly coordinated with periderm formation and the on-set of periderm maturation; results were more influenced by harvest than genotype. Importantly, StTLRP was the only gene examined that may be involved in phellogen cell wall strengthening or thickening after cessation of cell division.

La caracterització funcional de dos gens en la peridermis, la ω hidroxilasa d'àcids grassos CYP86A33 -candidata per la funcionalització del carboni ω-terminal dels monòmers alifàtics de la suberina- i la ketoacyl-CoA sintasa StKCS6 -candidata per elongar àcids grassos o derivats llargs de suberina i ceres- es realitza per silenciament per RNA d'interferència en patata.
La deficiència de CYP86A33 comporta una gran reducció dels monòmers principals de la suberina, l'àcid gras ω-hidroxilat i l'α,ω-diàcid C18:1, juntament amb una reducció total de la quantitat de suberina del 60%. Aquesta deficiència altera l'estructura lamel·lar típica de la suberina, així com també la funció barrera de la peridermis.
La deficiència en StKCS6 comporta que els monòmers de la suberina de 28 carbonis o més llargs es redueixin i que els de 26 carbonis o més curts s'incrementin. Aquesta deficiència suggereix que la llargada dels compostos alifàtics pot contribuir a les propietats impermeabilitzants de la peridermis.
The functional characterization of two genes in the periderm, the ω-hydroxylase CYP86A33 -candidate for the functionalization of the ω-terminal carbon of suberin aliphatic compounds- and the putative ketoacyl-CoA synthase StKCS6 -candidate for the elongation of VLCFA and derivatives of suberin and waxes of periderm- is performed by RNA interference-mediated silencing in potato
The CYP86A33 deficiency leads to a great reduction of the main suberin monomers, the C18:1 ω-hydroxyacid and α,ω-diacid, together with an overall decrease of the suberin total amount by 60%. The deficiency in these ω-oxidized fatty acids alters the typical suberin lamellar structure as well as the periderm water barrier function.
StKCS6 deficiency leads to a decrease of suberin and wax compounds with chain-length C28 and higher and an increase of those with chain-length C26 and lower. This deficiency suggests that the aliphatics chain-length can contribute to the sealing properties of periderm.

Orientador: Carmen Regina Marcati
Resumo: A casca é um sistema biológico complexo que desempenha diversas funções na planta, incluindo condução de fotoassimilados, suporte mecânico, armazenamento de substâncias e proteção contra herbívoros, patógenos e intempéries como o fogo. A casca é composta, principalmente, pelo floema secundário e pela periderme, e reveste tanto caules quanto raízes. O caule está exposto à atmosfera e tem funções de elevação e suporte da planta, enquanto a raiz está exposta ao solo e tem funções de fixar a planta ao solo, armazenar substâncias e absorver e conduzir água e nutrientes. Contudo, pouco se sabe se as diferentes funções de caules e raízes indicam diferentes funções na casca de cada órgão. Neste trabalho, comparamos a casca de caules e raízes de 15 espécies representativas do cerrado paulista e testamos se a casca do caule apresentaria funções de suporte e proteção, enquanto a casca da raiz apresentaria função de armazenamento de substâncias. Também testamos se encontraríamos maior eficiência na condução de fotoassimilados na casca da raiz. Para tanto, selecionamos 15 espécies de árvores e arbustos do cerrado sensu stricto e amostramos a casca do caule e da raiz. Analisamos a estrutura (espessura e anatomia), a densidade e a química (água, açúcares solúveis, amido, nitrogênio, fósforo e carbono) e relacionamos com as funções da casca em cada órgão. Na casca do caule, encontramos maior espessura da periderme, devido ao felema mais largo com células maiores e mais espessas, e menor dens... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Bark is a complex biological system that performs multiple functions in plant, including photoassimilates conduction, mechanical support, storage and protection against herbivores, pathogens and fire. Bark comprises mainly the secondary phloem and the periderm, and covers both trunks and roots. The trunk is exposed to the atmosphere and has the main functions of plant elevation and plant support, whereas the root is exposed to the ground and has the main functions of fix the plant to the ground, store substances, provide water and nutrients to the plant. However, remain unclear whether the different functions of trunk s and roots indicate different functions in the bark of each organ. In this work, we compared the bark of trunk and roots of species in the cerrado of São Paulo, tested whether the trunk bark presents both support and protection functions, whereas the root bark presents storage function. We also tested whether we would find higher efficiency of photoassimilates conduction in the root bark. For this purpose, we selected 15 representative species of trees and shrubs in the cerrado sensu stricto and sample both trunk and root barks. We analyzed the structure (thickness and anatomy), density and chemistry (water, soluble sugars, starch, nitrogen, phosphorus and carbon) and associated to the bark functions in each organ. In the trunk bark, we found thicker periderm, due to thicker phellem with larger cell and thicker wall cells, and lower periderm density, suggesting... (Complete abstract click electronic access below)
Doutor

Non-syndromic orofacial clefting (nsOFC) is among the most common congenital birth defects occurring up to 1 in 800 live births, with genetic and environmental causes. Genome wide association studies (GWAS) have identified several genetic loci that confer risk for nsOFC. However, more than half the heritable risk for nsOFC remains unknown and is considered ‘missing’. Moreover, continued sequencing of nsOFC patient DNA by whole exome sequencing and whole exome sequencing identify hundreds of single nucleotide polymorphism (SNPs). The identification of causal SNPs, however, continues to be a challenge in the OFC community. This is fueled partly by a lack of understanding of: (i) molecular mechanism and, (i) the gene regulatory network (GRN) governing differentiation of the relevant tissue, the embryonic superficial epithelia, also known as the periderm. Research has demonstrated that aberrant differentiation of the periderm, particularly the oral periderm results in pathological adhesions of surfaces within the developing oral cavity resulting in OFC. Further these adhesions can extend to the limbs which is a hallmarks feature in some forms of syndromic OFC (sOFC). In zebrafish, our model system of choice, knock-out of interferon regulatory factor 6 (irf6) ablated periderm marker expression and subsequently induces early embryonic lethality. The ortholog of IRF6 is a major genetic locus of Van der Woude syndrome (VWS) the most common form of sOFC and variants of IRF6 elevate risk for nsOFC. Therefore, we hypothesize that GRN of zebrafish periderm differentiation under the control of irf6 is a tool that can be used to identify novel OFC loci. Supporting this view, we have recently demonstrated that knock-down of an irf6 dependent gene encoding transcription factor Grainy-head like 3 (Grhl3) results in aberrant zebrafish periderm differentiation and GRHL3 was recently discovered as a novel VWS genetic locus. Hence it is likely that orthologs of genes encoding additional members of the periderm GRN harbor mutations in OFC patients. To identify cis–regulatory and transcriptional components in the periderm GRN, we performed: (i) a screen for periderm enhancers through in vivo green fluorescent protein (GFP) reporter assays, and, (ii) irf6 RNA-seq, followed by irf6 ChIP-seq to identify direct targets. From our screen for cis-regulatory elements we have identified a candidate human ZNF750 enhancer that directs GFP reporter expression in the zebrafish periderm. From our screen for irf6 direct targets we have identified several transcription factors including klf17, tfap2a and grhl3, all of which have variants in the human orthologs found in OFC patients. We further resolve the structure of the periderm differentiation GRN in zebrafish by assessing loss of function profiles for klf17, tfap2a and grhl3. Additionally, among the irf6 direct targets is a gene encoding another transcription factor, Zinc finger protein 750 (Znf750). We provide evidence to show that znf750 is expressed weakly in the zebrafish periderm. Further, we sequenced DNA in 500 nsOFC patient samples and identify a novel missense Ser160Pro ZNF750 variant which phenocopies the early embryonic lethality observed in irf6 mutants. Therefore, investigation of the zebrafish periderm GRN structure has facilitated the identification of OFC-associated risk loci.

Mestrado em Engenharia Florestal e dos Recursos Naturais - Instituto Superior de Agronomia
This work had three main goals: (1) to study the process of the phellogen and first periderm formation in young plants of cork-oak (Quercus suber); (2) to study the process of cork-tissue formation in adult cork-oak trees under cork exploitation, including the suberification process of cork cell walls and, (3) to study the structure of suberized cell walls in the periderm of potatoes, including a wild-type and three mutatans, where genes involved in suberin synthesis were supressed. To this end were used optical microscopy techniques, including bright field, epi-fluorescence and polarized light, together with scanning electron microscopy (SEM). The main results were: · the phellogen is formed in cork-oak before a month’s life of the young plants; · in the cork forming tissue three zones can be seen – the outer one, where cells are still dividing; – a middle one, were cork cell walls are thickening, and the inner one, contiguous to the mature cells, were cells still kept abundant cytoplasm material, although their cell walls already show their definitive thickness and, · the silencing of the genes involved in the ester-linking between the aliphatic and aromatic domains of suberin have the higher effect in the disrupting of suberized cell walls in potato periderm.

La peridermis és una estructura complexa que protegeix els òrgans vegetals madurs (secundaris) i les zones que han sofert ferides de la pèrdua d'aigua i dels patògens. Aquesta funció barrera és deguda al fel·lema o súber, un teixit format per cèl·lules suberificades. Tant el fel·lema com la suberina són crucials per la vida de les plantes terrestres, però pràcticament no es coneix res dels processos moleculars que regulen la seva formació, probablement degut a la manca de models adequats. En aquesta tesi s'han identificat i caracteritzat gens induïts al fel·lema mitjançant la combinació de dues plantes models. L'escorça d'alzina surera (Quercus suber) s'ha utilitzat per aïllar gens candidats de la formació del fel·lema i per investigar el comportament d'alguns d'aquests gens durant l'estació de creixement, mentre que la pela de la patata (Solanum tuberosum) s'ha utilitzat en estudis de genètica reversa per demostrar la funció d'alguns gens reguladors al fel·lema.
The periderm is a complex structure that protects plant mature (secondary) organs and wounded tissues from water loss, injuries and pathogens. This barrier capacity is accomplished by the cork layer of the periderm, a tissue made of dead cells with suberin deposited into cell walls. Although cork and suberin are critical for the survival of land plants, very few is known about the molecular processes involved in their biosynthesis and differentiation, probably due to the lack of appropriate plant models. Here we developed a strategy to identify and characterize cork candidate genes using a combination of two model plants for periderm studies. The bark of cork oak (Quercus suber) was used to identify candidate genes and to analyze the seasonal behaviour of some of these genes. The potato (Solanum tuberosum) tuber was used to demonstrate the role of some selected candidates in the regulation of cork by reverse genetic analyses.

Short shelf life has caused a decline in the sale of B.C.-grown carrots from 8.1 million kgs in 1987 to 6.1 million kgs in 1990. This is due to greater postharvest water loss of B.C.-grown carrots compared to those from California and Washington. The aim of this study was to improve our understanding of the factors affecting carrot water loss by (1) establishing a procedure to measure surface area of carrot roots, (2) determining the effect of K fertilization on carrot growth, yield and water loss, and (3) detemiining the effects of periderm damage and interaction between periderm damage and K fertilization on water loss of carrots. Baugerod (1993), slicing and surface replica methods for determining surface area of carrot roots were compared using eight carrot varieties on two harvests, and on size grades small, medium, and large of carrots. Surface area values using the three methods were statistically different but the variation was less than 6%. Baugerod method is applicable to carrots of different sizes and can therefore be used to determine surface area of carrots. Carrots were fertilized with five levels of KCI and one level of K2S04 on muck soil, and stored at 13°C and two levels of relative humidity (RH) to assess the effect of rate and source of K on carrot growth, yield, and water loss. Five levels of carrot periderm damage were used to study the effect of periderm damage on water loss. The rate and source of K had no significant effects on growth and water loss. No significant effects of interaction between rate of application of KCI and periderm damage on water loss were observed. Increase in rate of KCI significantly reduced marketable yields probably due to a reduction in carrot stand. KCI significantly reduced marketable yield of carrots compared with K 2S04 applied at same rate. Periderm damage and low RH significantly accelerated water loss and thereby reduced the shelf life of carrots in storage. It was concluded that there was adequate K in muck soil in Cloverdale area (B.C.) to meet carrot requirement, and that K fertilization is unnecessary. The short shelf life of B.C.-grown carrots is likely due to periderm damage and/or storing of carrots at low RH. It could be extended by minimising periderm damage and/or storing carrots at high RH to reduce water loss, hence improving their acceptability.

Activation-tagging is a functional genomics technique where strong enhancers are inserted randomly into target genomes to over-activate endogenous genes. Phenotypes of interest can be selected for investigation of genetic factors contributing to the mutant phenotype. From initial screens of a population of activation-tagged potato, a mutant with chocolate-coloured tuber skin has been identified. In this thesis, a novel sequence capture method for identifying T-DNA loci in activation tagged potato was used to characterize chocolate’s single T-DNA insertion locus. Transcriptome analysis of tuber periderm tissue was used to identify major processes occurring in the chocolate mutant. Our data suggest activation of a chitin-binding receptor-like kinase located 65 kb from T-DNA insert may cause activation of immune signaling pathways in chocolate. The present work explores a putative model of transcriptional and cellular responses involved in gain-of-function immune receptor activation. Selectively, these findings illustrate the periderm tissue as an important area of defense charged against biotic and abiotic stresses. Periderm development and anatomy are highly important for tuber storage. Further characterization of potato tuber periderm may contribute knowledge to model periderm systems and have implications for molecular breeding strategies to improve tuber storage quality.
Thesis (Master, Biology) -- Queen's University, 2012-09-27 11:45:16.478

Tese de mestrado, Bioinformática e Biologia Computacional (Bioinformática) Universidade de Lisboa, Faculdade de Ciências, 2017
As florestas de sobreiro (Quercus suber L.) são recursos únicos e emblemáticos em Portugal, com elevado impacto económico, ecológico e social. A disponibilidade recente da sequência do genoma de sobreiro forneceu um importante contributo para revitalizar a pesquisa em temas como desenvolvimento de cortiça e melhoramento da planta, assim como promover a competitividade da indústria da cortiça. No entanto, é ainda necessário adicionar mais detalhe à anotação estrutural do genoma, nomeadamente ao nível dos transcritos, incluindo previsão de eventos de splicing alternativo. O splicing alternativo (AS) é um processo usado durante a expressão génica que origina diferentes variantes de transcritos (isoformas) e produtos proteicos a partir um único gene. No presente estudo, procedemos à análise de dezasseis bibliotecas de RNA-seq, preparadas a partir de quatro tecidos de sobreiro (folhas, felema, entrecasco e xilema), de modo a prever novas formas de AS para genes já previstos e melhorar a anotação estrutural do genoma. Um protocolo bioinformático foi definido para testar o desempenho do software HISAT2 e STAR para mapeamento de reads de RNAseq no genoma de referência, e do software Cufflinks e StringTie para (re)construção de transcritos. O alinhamento de reads no genoma efetuado com STAR resultou em taxas de mapeamento (de 84,22% a 86,86%) superiores aos resultados atingidos com HISAT2 (73,88% a 76,55%). Assim, os resultados de mapeamento com STAR foram utilizados para a (re)construção de transcritos. O uso do StringTie para este processo foi globalmente mais conservador do que com Cufflinks, gerando menos transcritos novos, mas com melhor cobertura de reads por pares de base. Para melhorar a precisão da anotação e reduzir falsos positivos, foi realizado um passo adicional de otimização com StringTie. Desta otimização resultou uma anotação que prevê a ocorrência de 7 958 novos transcritos (8% dos transcritos totais), dos quais 5 453 são novas isoformas para genes previstos na anotação de referência. Esta nova anotação foi utilizada como referência para estimar a abundância dos transcritos em cada um dos tecidos estudados e efetuar a análise de expressão diferencial. Cerca de 16% de todos os genes expressos nos quatro tecidos e que contêm intrões apresentaram splicing alternativo, e os principais eventos de splicing foram alternative acceptor site e intron retention. Grupos de transcritos com expressão diferencial entre os quatro tecidos foram identificados e a análise de enriquecimento funcional confirmou os principais processos biológicos esperados para cada tecido: os transcritos mais expressos nas folhas e no xilema estavam relacionados com a fotossíntese e com transporte, respetivamente; transcritos mais expressos na periderme (felema e entrecasco) mostraram um enriquecimento em categorias funcionais relacionadas com a síntese de suberina e outros componentes de parede celular presentes nas células de cortiça. Estes grupos específicos mostraram também um enriquecimento em transcritos envolvidos na resposta ao stresse (biótico ou abiótico). Nos tecidos que compõem a periderme, este enriquecimento foi observado principalmente no entrecasco, enquanto que no felema foi detetado um enriquecimento em transcritos envolvidos no metabolismo secundário. A presente tese permitiu a definição de um protocolo padrão que poderá ser usado para estudar o splicing alternativo no sobreiro e para uma análise mais aprofundada na nova versão do genoma, que estará disponível em breve.
Cork oak (Quercus suber L.) forests are unique and emblematic resources for Portugal, with high economical, ecological and social significance. The recent availability of the cork oak genome sequence provided an important contribution to reinvigorate research in fundamental topics such as cork development and plant improvement, and to promote the competitiveness of cork industry. Yet, further analysis is required to add detail to genome structure annotation, namely at the transcript level, also taking into account alternative splicing. Alternative splicing (AS) is a process used during gene expression to yield different transcript variants and protein products derived from a single gene. In the present study, we analyzed sixteen RNA-seq libraries prepared from four cork oak tissues (leaf, xylem, phellem and inner bark), in order to predict new AS forms for the already predicted genes and improve genome structural annotation. A bioinformatics pipeline was defined in order to test the performance of HISAT2 and STAR for read mapping against the reference genome, and Cufflinks and StringTie for transcript assembly. STAR yielded higher mapping efficiencies (84.22% to 86.86%) for the cork oak datasets, as compared to HISAT2 (73.88% to 76.55%), and the corresponding mapping data was selected for transcript assembly. The use of StringTie for this step was globally more conservative than Cufflinks, generating less novel transcripts, but with better support by read per base coverage. A further optimization step was performed using StringTie in order to improve annotation precision. The final transcript annotation was selected from this optimization step, predicting 7,958 novel transcripts (8% of total transcripts in the new annotation), 5,453 of which were novel isoforms for genes in reference annotation. This new annotation was used as reference to estimate transcript abundance in each tissue and differential expression analysis. Approximately 16% of all intron-containing genes expressed in the four tissues were alternatively spliced and the main event found in the four cork oak tissues was alternative acceptor site, followed by intron retention. Transcript clusters showing differential expression among the four tissues were identified and functional enrichment analysis confirmed the main biological processes expected for each tissue: transcripts highly expressed in leaves and xylem were mostly related to photosynthesis and transport, respectively; transcripts highly expressed in peridermis (phellem and inner bark) showed an enrichment in functional categories related to the synthesis of suberin and other component of cork cell walls. These tissue-specific clusters also showed an enrichment in transcripts involved in the response to stress (biotic or abiotic). Yet, in peridermis, this enrichment was mostly observed in inner bark samples, while phellem samples showed an enrichment in transcripts related to secondary metabolism. This thesis allowed the definition of a standard workflow that can be used to study alternative splicing in cork oak and used for further analysis on the new improved genome version that will be available soon.