Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering similar to 90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on their emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analysis workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Here we validate lincRNA catalogs generated with Evolinc-I against previously annotated Arabidopsis and human lincRNA data. Evolinc-I recapitulated earlier findings and uncovered an additional 70 Arabidopsis and 43 human lincRNAs. We demonstrate the usefulness of Evolinc-II by examining the evolutionary histories of a public dataset of 5,361 Arabidopsis lincRNAs. We used Evolinc-II to winnow this dataset to 40 lincRNAs conserved across species in Brassicaceae. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). These latter analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerse's Discovery Environment and is free for use by researchers.

No description available.

Mycoplasma hyopneumoniae, Mycoplasma flocculare e Mycoplasma hyorhinis são capazes de aderir e colonizar o trato respiratório de suínos. Enquanto a presença de M. flocculare é considerada assintomática, M. hyopneumoniae e M. hyorhynis são relacionados ao desenvolvimento de patologias. M. hyopneumoniae é o agente etiológico da pneumonia enzoótica suína e M. hyorhynis além dos pulmões pode atingir outros sítios e hospedeiros, estando relacionado a artrites, poliserosites e desenvolvimento de vários tipos de câncer em humanos. Apesar dos avanços tecnológicos na área de genômica, raros são os dados quanto ao papel de M. flocculare no trato respiratório suíno. Além do mais, informações relativas à transcrição gênica nessas espécies são escassas, apesar da importância desses microrganismos. Neste estudo são apresentados os dados da sequência do genoma de uma linhagem de M. flocculare, bem como do genoma de um novo isolado de M. hyopneumoniae. Com estas novas sequências foram realizadas análises de genômica comparativa visando a identificação de características que pudessem explicar os diferentes comportamentos quanto à patogenicidade dessas espécies. Além disso, a análise global dos transcritomas de cada uma das espécies foi realizada e o perfil transcricional entre M. hyopneumoniae, M. flocculare e M. hyorhynis foi analisado comparativamente objetivando identificar características peculiares para cada um dos mapas transcricionais, além de compreender a coordenação do modo de transcrição gênica em Mycoplasma. De um modo geral, as três espécies de Mycoplasma que habitam o trato respiratório suíno possuem grandes semelhanças na composição gênica, assim como na abundância de transcritos. A análise do repertório transcricional, mostra que os genomas são transcritos quase que em sua totalidade, incluindo as regiões intergênicas, nas três espécies. M. hyopneumoniae e M. flocculare apresentam conteúdo gênico e perfil transcricional muito semelhantes. Uma importante diferença encontrada entre estas duas espécies refere-se à presença exclusiva de genes e transcritos de adesinas específicas. M. hyorhynis possui genes e transcritos exclusivos, os quais sabidamente estão relacionados à sua capacidade mutacional, de invasividade e infecção de diferentes sítios. Por fim, a análise comparativa dos genomas, e a obtenção dos mapas transcricionais para M. hyopneumoniae, M. flocculare e M. hyorhynis, foram abordagens que resultaram em um grande número de informações, as quais são importantes para embasamento de futuros estudos de caracterização dos mecanismos moleculares, como os eventos de regulação da transcrição gênica, no gênero Mycoplasma. / Mycoplasma hyopneumoniae, Mycoplasma hyorhinis and Mycoplasma flocculare are able to adhere and to colonize the swine respiratory tract. While M. flocculare presence is virtually assymptomatic, M. hyopneumoniae and M. hyorhynis infections may cause respiratory disease. M. hyopneumoniae is the causative agent of swine enzootic pneumonia and M. hyorhynis may affect the lungs and other sites in a diversity of hosts and has been related to arthritis, poliserosites and to the development of several types of human cancer. Despite genomics technological advances, there are very few data about the possible role of M. flocculare in the swine respiratory tract. Moreover, little information about gene transcription is available in these species, despite the importance of these microorganisms. In this work the genome sequences of M. flocculare and a new isolate of M. hyopneumoniae are presented. A comparative genomic analyzes was performed to identify possible characteristics that may help to explain the different behaviors of these species in the swine respiratory tracts. Furthermore, a transcriptome map of each species was performed and a comparative transcriptional profile analysis between M. hyopneumoniae, M. flocculare and M. hyorhynis was undertaken to identify the exclusive features for each of the transcriptional maps, in addition to understanding the coordination mode of gene transcription in Mycoplasma. In general, the three Mycoplasma species that inhabit the swine respiratory tract have a similar gene composition as well as the abundance of transcripts. The transcriptome maps showed that most of the predicted genes are transcribed from these Mycoplasma genomes, as well as some intergenic regions. M. hyopneumoniae and M. flocculare present very similar gene content and transcriptional profile. However, an important difference between these two species is related to the exclusive presence of genes and transcripts of some specific adhesins. M. hyorhynis presents exclusive genes and transcripts that have been related to its invasiveness, mutation rate and infection of different sites. Finally, the comparative analysis of the genomes and transcriptional maps between M. hyopneumoniae, M. flocculare and M. hyorhynis have resulted in a large amount of information, which are important for future studies of the molecular characterization, as transcriptional regulation in the Mycoplasma spp.

Mycoplasma hyopneumoniae, Mycoplasma flocculare e Mycoplasma hyorhinis são capazes de aderir e colonizar o trato respiratório de suínos. Enquanto a presença de M. flocculare é considerada assintomática, M. hyopneumoniae e M. hyorhynis são relacionados ao desenvolvimento de patologias. M. hyopneumoniae é o agente etiológico da pneumonia enzoótica suína e M. hyorhynis além dos pulmões pode atingir outros sítios e hospedeiros, estando relacionado a artrites, poliserosites e desenvolvimento de vários tipos de câncer em humanos. Apesar dos avanços tecnológicos na área de genômica, raros são os dados quanto ao papel de M. flocculare no trato respiratório suíno. Além do mais, informações relativas à transcrição gênica nessas espécies são escassas, apesar da importância desses microrganismos. Neste estudo são apresentados os dados da sequência do genoma de uma linhagem de M. flocculare, bem como do genoma de um novo isolado de M. hyopneumoniae. Com estas novas sequências foram realizadas análises de genômica comparativa visando a identificação de características que pudessem explicar os diferentes comportamentos quanto à patogenicidade dessas espécies. Além disso, a análise global dos transcritomas de cada uma das espécies foi realizada e o perfil transcricional entre M. hyopneumoniae, M. flocculare e M. hyorhynis foi analisado comparativamente objetivando identificar características peculiares para cada um dos mapas transcricionais, além de compreender a coordenação do modo de transcrição gênica em Mycoplasma. De um modo geral, as três espécies de Mycoplasma que habitam o trato respiratório suíno possuem grandes semelhanças na composição gênica, assim como na abundância de transcritos. A análise do repertório transcricional, mostra que os genomas são transcritos quase que em sua totalidade, incluindo as regiões intergênicas, nas três espécies. M. hyopneumoniae e M. flocculare apresentam conteúdo gênico e perfil transcricional muito semelhantes. Uma importante diferença encontrada entre estas duas espécies refere-se à presença exclusiva de genes e transcritos de adesinas específicas. M. hyorhynis possui genes e transcritos exclusivos, os quais sabidamente estão relacionados à sua capacidade mutacional, de invasividade e infecção de diferentes sítios. Por fim, a análise comparativa dos genomas, e a obtenção dos mapas transcricionais para M. hyopneumoniae, M. flocculare e M. hyorhynis, foram abordagens que resultaram em um grande número de informações, as quais são importantes para embasamento de futuros estudos de caracterização dos mecanismos moleculares, como os eventos de regulação da transcrição gênica, no gênero Mycoplasma. / Mycoplasma hyopneumoniae, Mycoplasma hyorhinis and Mycoplasma flocculare are able to adhere and to colonize the swine respiratory tract. While M. flocculare presence is virtually assymptomatic, M. hyopneumoniae and M. hyorhynis infections may cause respiratory disease. M. hyopneumoniae is the causative agent of swine enzootic pneumonia and M. hyorhynis may affect the lungs and other sites in a diversity of hosts and has been related to arthritis, poliserosites and to the development of several types of human cancer. Despite genomics technological advances, there are very few data about the possible role of M. flocculare in the swine respiratory tract. Moreover, little information about gene transcription is available in these species, despite the importance of these microorganisms. In this work the genome sequences of M. flocculare and a new isolate of M. hyopneumoniae are presented. A comparative genomic analyzes was performed to identify possible characteristics that may help to explain the different behaviors of these species in the swine respiratory tracts. Furthermore, a transcriptome map of each species was performed and a comparative transcriptional profile analysis between M. hyopneumoniae, M. flocculare and M. hyorhynis was undertaken to identify the exclusive features for each of the transcriptional maps, in addition to understanding the coordination mode of gene transcription in Mycoplasma. In general, the three Mycoplasma species that inhabit the swine respiratory tract have a similar gene composition as well as the abundance of transcripts. The transcriptome maps showed that most of the predicted genes are transcribed from these Mycoplasma genomes, as well as some intergenic regions. M. hyopneumoniae and M. flocculare present very similar gene content and transcriptional profile. However, an important difference between these two species is related to the exclusive presence of genes and transcripts of some specific adhesins. M. hyorhynis presents exclusive genes and transcripts that have been related to its invasiveness, mutation rate and infection of different sites. Finally, the comparative analysis of the genomes and transcriptional maps between M. hyopneumoniae, M. flocculare and M. hyorhynis have resulted in a large amount of information, which are important for future studies of the molecular characterization, as transcriptional regulation in the Mycoplasma spp.

Mycoplasma hyopneumoniae, Mycoplasma flocculare e Mycoplasma hyorhinis são capazes de aderir e colonizar o trato respiratório de suínos. Enquanto a presença de M. flocculare é considerada assintomática, M. hyopneumoniae e M. hyorhynis são relacionados ao desenvolvimento de patologias. M. hyopneumoniae é o agente etiológico da pneumonia enzoótica suína e M. hyorhynis além dos pulmões pode atingir outros sítios e hospedeiros, estando relacionado a artrites, poliserosites e desenvolvimento de vários tipos de câncer em humanos. Apesar dos avanços tecnológicos na área de genômica, raros são os dados quanto ao papel de M. flocculare no trato respiratório suíno. Além do mais, informações relativas à transcrição gênica nessas espécies são escassas, apesar da importância desses microrganismos. Neste estudo são apresentados os dados da sequência do genoma de uma linhagem de M. flocculare, bem como do genoma de um novo isolado de M. hyopneumoniae. Com estas novas sequências foram realizadas análises de genômica comparativa visando a identificação de características que pudessem explicar os diferentes comportamentos quanto à patogenicidade dessas espécies. Além disso, a análise global dos transcritomas de cada uma das espécies foi realizada e o perfil transcricional entre M. hyopneumoniae, M. flocculare e M. hyorhynis foi analisado comparativamente objetivando identificar características peculiares para cada um dos mapas transcricionais, além de compreender a coordenação do modo de transcrição gênica em Mycoplasma. De um modo geral, as três espécies de Mycoplasma que habitam o trato respiratório suíno possuem grandes semelhanças na composição gênica, assim como na abundância de transcritos. A análise do repertório transcricional, mostra que os genomas são transcritos quase que em sua totalidade, incluindo as regiões intergênicas, nas três espécies. M. hyopneumoniae e M. flocculare apresentam conteúdo gênico e perfil transcricional muito semelhantes. Uma importante diferença encontrada entre estas duas espécies refere-se à presença exclusiva de genes e transcritos de adesinas específicas. M. hyorhynis possui genes e transcritos exclusivos, os quais sabidamente estão relacionados à sua capacidade mutacional, de invasividade e infecção de diferentes sítios. Por fim, a análise comparativa dos genomas, e a obtenção dos mapas transcricionais para M. hyopneumoniae, M. flocculare e M. hyorhynis, foram abordagens que resultaram em um grande número de informações, as quais são importantes para embasamento de futuros estudos de caracterização dos mecanismos moleculares, como os eventos de regulação da transcrição gênica, no gênero Mycoplasma. / Mycoplasma hyopneumoniae, Mycoplasma hyorhinis and Mycoplasma flocculare are able to adhere and to colonize the swine respiratory tract. While M. flocculare presence is virtually assymptomatic, M. hyopneumoniae and M. hyorhynis infections may cause respiratory disease. M. hyopneumoniae is the causative agent of swine enzootic pneumonia and M. hyorhynis may affect the lungs and other sites in a diversity of hosts and has been related to arthritis, poliserosites and to the development of several types of human cancer. Despite genomics technological advances, there are very few data about the possible role of M. flocculare in the swine respiratory tract. Moreover, little information about gene transcription is available in these species, despite the importance of these microorganisms. In this work the genome sequences of M. flocculare and a new isolate of M. hyopneumoniae are presented. A comparative genomic analyzes was performed to identify possible characteristics that may help to explain the different behaviors of these species in the swine respiratory tracts. Furthermore, a transcriptome map of each species was performed and a comparative transcriptional profile analysis between M. hyopneumoniae, M. flocculare and M. hyorhynis was undertaken to identify the exclusive features for each of the transcriptional maps, in addition to understanding the coordination mode of gene transcription in Mycoplasma. In general, the three Mycoplasma species that inhabit the swine respiratory tract have a similar gene composition as well as the abundance of transcripts. The transcriptome maps showed that most of the predicted genes are transcribed from these Mycoplasma genomes, as well as some intergenic regions. M. hyopneumoniae and M. flocculare present very similar gene content and transcriptional profile. However, an important difference between these two species is related to the exclusive presence of genes and transcripts of some specific adhesins. M. hyorhynis presents exclusive genes and transcripts that have been related to its invasiveness, mutation rate and infection of different sites. Finally, the comparative analysis of the genomes and transcriptional maps between M. hyopneumoniae, M. flocculare and M. hyorhynis have resulted in a large amount of information, which are important for future studies of the molecular characterization, as transcriptional regulation in the Mycoplasma spp.

No description available.

Transcriptome analysis based on deep expressed sequence tag (EST) sequencing allows quantitative comparisons of gene expression across multiple species. Using pyrosequencing, we generated over 7 million ESTs from four stages of developing seeds of Ricinus communis, Brassica napus, Euonymus alatus and Tropaeolum majus, which differ in their storage tissue for oil, their ability to photosynthesize and in the structure and content of their triacylglycerols (TAG). The larger number of ESTs in these 16 datasets provided reliable estimates of the expression of acyltransferases and other enzymes expressed at low levels. Analysis of EST levels from these oilseeds revealed both conserved and distinct species-specific expression patterns for genes involved in the synthesis of glycerolipids and their precursors. Independent of the species and tissue type, ESTs for core fatty acid synthesis enzymes maintained a conserved stoichiometry and a strong correlation in temporal profiles throughout seed development. However, ESTs associated with non-plastid enzymes of oil biosynthesis displayed dissimilar temporal patterns indicative of different regulation. The EST levels for several genes potentially involved in accumulation of unusual TAG structures were distinct. Comparison of expression of members from multi-gene families allowed the identification of specific isoforms with conserved function in oil biosynthesis. In all four oilseeds, ESTs for Rubisco were present, suggesting its possible role in carbon metabolism, irrespective of light availability. Together, these data provide a resource for use in comparative and functional genomics of diverse oilseeds. Expression data for more than 350 genes encoding enzymes and proteins involved in lipid metabolism are available at the 'ARALIP' website ().

Gene duplications can facilitate genetic innovation, reduce pleiotropy and catalyze reproductive incompatibilities and speciation. Therefore, the molecular and transcriptional fate of duplicate genes plays an important role in the evolutionary trajectory of entire genomes and transcriptomes. Using the polyploid African clawed frog Xenopus, I have investigated mechanisms that promote the retained expression of duplicate genes (paralogs) after whole genome duplication. The studies herein estimated molecular evolution and characterized expression divergence of thousands of duplicate genes and a singleton ortholog from a diploid outgroup. In this thesis, I have discussed the multiple mechanisms for the retention of duplicate genes in a polyploid genome and examined the potential effects that gene characteristics before duplication have on the odds of duplicate gene persistence. I have also explored the use of microarrays for comparative transcriptomics between duplicate genes, and between diverged genomes. The main objectives of my thesis were to better understand the genetic mechanisms that promote the retained expression of gene duplicates. My research utilized the duplicated genome from the allopolyploid clawed frog Xenopus. Genome duplication in clawed frogs offers a compelling opportunity to study factors that influence the genetic fates of gene duplicates because many paralogs in these frogs are of the same age, permitting one to control for the influence of time when evaluating the impact of duplication. My work has major impacts on several biological fronts including evolutionary genomics and comparative transcriptomics, and also on technical aspects of using microarrays. I have provided among the most comprehensive studies of its kind, in terms of examining molecular and regulatory aspects of thousands of expressed duplicates of the same age, and exploring various alternative hypotheses to explain how these genes are retained. / Thesis / Doctor of Philosophy (PhD)

Fungi play important roles in various environments. Some of them infect plants and cause economically important diseases. However, many fungal pathogens cause similar symptoms or are even spread asymptomatically, making it difficult to identify them morphologically. Therefore, culture-independent, sequence-based diagnostic methods that can detect and identify fungi independently of the symptoms that they cause are desirable. Whole genome metagenomic sequencing has the potential to enable rapid diagnosis of plant diseases without culturing pathogens and designing pathogen-specific probes. In my study, the MinION nanopore sequencer, a portable single‐molecule sequencing platform developed by Oxford Nanopore Technologies, was employed to detect the fungus Calonectria pseudonaviculata (Cps), the causal agent of the devastating boxwood blight disease of the popular ornamental boxwood (Buxus spp.). Various DNA extraction methods and computational tools were compared. Detection was sensitive with an extremely low false positive rate for most methods. Therefore, metagenomic sequencing is a promising technology that could be implemented in routine diagnostics of fungal diseases. Other fungi may play important roles in the atmosphere because of their ice nucleation activity (INA). INA is the capacity of some particles to induce ice formation above the temperature that pure water freezes (-38°C). Importantly, INPs affect the ratio of ice crystals to liquid droplets in clouds, which in turn affects Earth's radiation balance and the intensity and frequency of precipitation. A few fungal species can produce ice nucleating particles (INPs) that cause ice formation at temperatures ≥ –10°C and they may be present in clouds. Two such fungal genera are Fusarium and Mortierella but little is known about their INPs and the genetic basis of their INA. In my study, F. avenaceum and M. alpina were examined in detail. INPs of both species were characterized and it was found that strains within both species varied in regards to the strength of INA. Whole genome sequencing and comparative genomic studies were then performed to identify putative INA genes. Differential expression analyses at different growth temperatures were also performed. INP properties of the two species shared similarities, both appearing to consist of secreted aggregates larger than 30 kDa. Low temperatures induced INA in both species. Lists of candidate INA genes were identified based on their presence in the strains with the strongest INA and/or induction of their expression at low temperatures and because they either encode secreted proteins or enzymes that produce other molecules known to have INA in other organisms. These genes can now be characterized further to help identify the fungal INA genes in both species. This can be expected to help increase our understanding of the role of fungal INA in the atmosphere. / Doctor of Philosophy / Fungi are important to life on Earth and play roles in the environments that surround us. On the one hand, fungi can make plants sick and some plant diseases may even cause economic losses to farmers. If the cause of a disease can be identified accurately in an early stage before symptoms develop, disease transmission may be prevented and plants may be protected from disease. However, it is a challenge to find out which fungus causes which disease since symptoms of different fungal diseases look very similar. Typically, we have to wait for plants to become very sick or we have to isolate the fungus that causes a disease to identity it, which may be time-consuming and not lead to precise identification. DNA sequencing technologies have the potential to lead to more sensitive, faster, and more accurate disease diagnosis and, therefore, may help prevent disease outbreaks. In my study, the MinION nanopore sequencer, a small portable device, was used to detect the fungus causing boxwood blight on boxwood. By loading the DNA of unhealthy boxwood on the device, the boxwood blight pathogen was identified within a very short time. Thus, this method is a promising diagnostic method that may be applied to detect other plant fungal diseases as well. On the other hand, fungi may affect Earth's climate by affecting how many water droplets in clouds are frozen, which in turn affects Earth's temperature and how often and how much it rains and snows. Fungi may affect the freezing of water droplets in clouds since some of them have ice nucleation activity (INA), which is the capacity to catalyze ice formation at a higher temperature than the temperature at which pure water freezes (-38°C), and they may be present in clouds. So far, INA has only been found in a few fungi, including the species Fusarium avenaceum and Mortierella alpina, but the mechanism of their INA is poorly understood. In my study, multiple F. avenaceum and M. alpina strains were examined in detail. Two approaches were used. First, strains in each species were compared with each other to find out how strong their INA is. Once it was found that they differed in their strength of INA, their genomes were sequenced and compared to find genes present in the most active strains and missing from the least active strains since it is these genes that may contribute to INA. It was also found that both fungal species had stronger INA when they were grown at lower temperatures. Therefore, the expression of their genes between higher and lower temperatures was compared to find the genes that were more highly expressed at lower temperatures since it is these genes that may cause INA. Based on previous studies, fungal INPs may either consist of secreted proteins or be the products of biosynthetic gene clusters. Therefore, the list of potential genes was reduced by looking for genes encoding either secreted proteins or biosynthetic gene clusters. The list of these potential INA genes will make it easier to identify the INA genes in F. avenaceum and M. alpina and determine the role of fungi in affecting the weather and climate on Earth.

This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.