The general goal of this project was to use computational biology to understand signal transduction mechanisms in prokaryotes. Its specific focus was to characterize the cytoplasmic domain of methyl-accepting chemotaxis proteins (MCP_CD), a protein domain central to the function of chemotaxis, the most complex signaling network in prokaryotes. Chemotaxis enables cells to sense and respond to multiple external and internal stimuli by actively navigating to an optimal environment. MCP_CD is a central part of this circuit, but its coiled coil structure is difficult to analyze using traditional tools of computational biology. In this project, a new method for analysis of the domain was developed and used to gain insight into its function and evolution. Research advance 1: Characterization of the MCP_CD protein domain. Before this work, MCP_CD was known to have two distinct functional regions: the signaling region that activates the histidine kinase CheA and the methylation region where adaptation enzymes CheB and CheR store information about recent stimuli. The result of this project is classification of ~2000 MCP_CDs into twelve subfamilies. The unique mechanism of evolution of the domain has been clarified and precise boundaries of the adaptation and signaling regions determined. A new functional region, the flexible bundle subdomain, was identified and its contribution to the signaling mechanism elucidated by analysis of conserved sequence features. Conserved and variable sequence features in the adaptation and signaling subdomains led to a better understanding of the evolutionary history of the adaptation mechanism and of alternative higher-order arrangements of receptors within the membrane. Research advance 2: Development of a sensor / kinase correlation algorithm to couple diverse MCP_CD and kinase subfamilies. The receptor diversity discovered in this work is complemented by diversity in the kinases with which they interact. In this work, an algorithm was developed to associate receptor / kinase pairs which facilitated understanding of the function and evolution of chemotaxis. Research advance 3: Development of Cheops, a database of chemotaxis pathways. The Cheops (Chemotaxis operons) database presents the results of the sensor / kinase correlation algorithm and the information about receptor and kinase diversity in an integrated and intuitive way.

In the interest of understanding the genetic basis of adaption to environment, we developed F2 lines from an F1 interspecific cross between the rare serpentine endemic, Caulanthus amplexicaulis var. barbarae and the non-serpentine Caulanthus amplexicaulis var. amplexicaulis. Using genomic DNA from Caulanthus amplexicaulis var. barbarae, we developed a suite of microsatellite markers. In addition, we developed gene specific markers for genes known in Arabidopsis to be ecologically important. Our suite of markers was used to genotype 186 F2 plants, the basis for our F2 linkage map. In order to further resolve evolutionary relationships among related taxa, we constructed a molecular phylogeny for 52 taxa within the related genera Caulanthus, Guillenia, Sibaropsis, Streptanthella, and Streptanthus, using the sequences from the ribosomal ITS region and two chloroplast regions. To create a useful system to enable comparative genomics within the related taxa of the ecologically and morphologically diverse Streptanthoid Complex, we demonstrated that our molecular tools are portable across a large group of ecologically significant taxa. To use the significant genomic resources available in Arabidopsis, we constructed a collinear comparative map of Caulanthus and the model plant Arabidopsis thaliana based on ancestral linkage blocks with the Brassicaceae family. This comparative map acted as a guide for candidate gene selection in the mapping of sepal color. We identified a region of MYB transcription factors in an orthologous region of Arabidopsis. Sequence data from Caulanthus amplexicaulis var. barbarae and Caulanthus amplexicaulis var. amplexicaulis in this MYB region showed significant sequence divergence between the two taxa. To determine the genetic basis for the tolerance of high concentrations of magnesium in Caulanthus amplexicaulis var. barbarae, we phenotyped multiple individuals from 88 F2:3 families under two nutrient treatments, differing in the ratio of calcium to magnesium. Through QTL analysis, using our F2 linkage map as a framework for the analysis, we identified one major effect QTL on Caulanthus Linkage Group 8 and another QTL on Caulanthus Linkage Group 3. We identified candidate genes for the QTLs using our collinear comparative map to Arabidopsis.

The major histocompatibility complex region (MHC) is a multi gene family present in all jawed vertebrates, with a fundamental role in vertebrate immunity. More than two decades of studies have resulted in the characterization of over a dozen MHC regions, and models of evolution explaining that the MHC has gradually increased in size and gene content since its origins without addressing their genomic context or the environmental selective forces. Furthermore, a compelling reconstruction of the evolutionary history of the MHC has been hampered due to phylogenetic gaps and the absence of comparative phylogenetic methods applied to comparative genomics. Here I reconstruct 320 MY of MHC evolution using 42 amniote genomes using improved gene annotations, genomic alignments and phylogenetic algorithms to reconstruct the evolution of the MHC at three levels of phylogenetic resolution. The first one describes 25 MY of evolution of the primate MHC using eight Human and four non-Human primate MHC haplotypes. Results suggests that highly dense gene segments have a strikingly conserved gene organization, and six conserved and highly rearranging segments overlap genes that are most commonly associated to disease. Phylogenomic analysis implies that the MHC has remained stable in gene content and size, with significantly increased duplication rates in the primate ancestors. The second one describes 280 MY of MHC evolution through the first characterization of reptilian MHC region, which combines mammalian, reptilian, Bird and amphibian characteristics, which favors the hypothesis of the existence of a primordial MHC in which natural killer receptors, CD1 and lectin genes co-exist. The Anolis MHC expands our understanding of the origins of the exceptionally small Bird MHC regions and provides further information about the organization and size of the ancestral amniote MHC. The third one compares 42 amniote MHC regions and map gene duplications and losses to further evaluate the mode and tempo of the evolution of the region. Comparative phylogenetic methods imply that the genomic and environmental factors affect the diversification of MHC during 320 My of evolution.

A major obstacle to achieving commercially viable lignocellulosic biofuels through consolidated bioprocessing (CBP) is the lack of “industry-ready” microorganisms. Ideally, a CBP-relevant organism would achieve efficient and complete hydrolysis of lignocellulose, simultaneous utilization of the diverse hydrolysis products and high yields of the desired biofuel. To date, no single microbe has been identified that can perform all of these processes at industrially significant levels. As such, thermophilic decaying woodchip compost was investigated as a source of novel lignocellulolytic, biofuel producing bacteria. From a single sample, a collection of physiologically diverse strains were isolated, which displayed differences in substrate utilization and biofuel production capabilities. Molecular characterization of these isolates, and development of a genome relatedness prediction model based on the chaperonin-60 universal target sequence, identified these isolates as strains of Thermoanaerobacter thermohydrosulfuricus. Application of this model to other Thermoanaerobacter spp. further identified that these isolates belong to a divergent and lesser characterized lineage within the genus. Based on this, the CBP-potential of a single isolate, T. thermohydrosulfuricus WC1, was selected for further investigation through metabolic, genomic and proteomic analyses. Its ability to grow on polymeric xylan, potentially catalyzed by an endoxylanase found in only a few Thermoanaerobacter strains, distinguishes T. thermohydrosulfuricus WC1 from many other strains within the genus. The simultaneous consumption of two important lignocellulose constituent saccharides, cellobiose and xylose was also observed and represents a desirable phenotype in CBP-relevant organisms. However, at elevated sugar concentrations, T. thermohydrosulfuricus WC1 produces principally lactate, rather than the desired biofuel ethanol, as the major end-product. Proteomic analysis identified that all likely end-product forming proteins were expressed at high levels suggesting that the end-product distribution patterns in T. thermohydrosulfuricus WC1 are likely controlled via metabolite-based regulation or are constrained by metabolic bottlenecks. The xylanolytic and simultaneous substrate utilization capabilities of T. thermohydrosulfuricus WC1 identify it as a strain of interest for CBP. However, for its development into an “industry-ready” strain as a co-culture with a cellulolytic microorganism, improved biofuel producing capabilities are needed. The practical implications of CBP-relevant phenotypes in T. thermohydrosulfuricus WC1 in relation to other Thermoanaerobacter spp. will be discussed.

The viral family Herpesviridae consists of large double stranded DNA viruses including eight species that infect humans with varying pathology from benign rashes to cancerous cell transformation. From three subfamilies, alpha-, beta- and gammaherpes, the alphaherpes contains the genera iltovirus, mardivirus, varicellovirus and simplex, two of which, the human simplex viruses I and 2 (HSV) induce life-long infections that have appeared to have coevolved with their hosts from the origins of our species. Unique features of the simplex genus are latency, tropism in dorsal root ganglia neurons, extraordinary high GC content ranging from 65 to 77%, and nucleosome formation of their genomes within the host's nucleus without integration. Reviewing the basic molecular and genetic characteristics of herpes simplex will introduced in Chapter 1, followed by the introduction of a newly sequenced, de novo assembled and predicatively annotated herpes simplex virus, Leporid Herpes Virus-4 (LHV4). Isolated from a virulent outbreak in domesticated rabbits, LHV4 has the smallest reported simplex virus to date at roughly 125,600 base pairs and presents similar pathology seen in rabbit models infected with HSV. Comparative genomics revealed a high degree of sequence similarity and genome synteny between LHV4 and other simplex viruses. Four genes were not computationally predicted in our annotation and may be absent in the LHV4 genome. The absent proteins correspond to: UL56, ICP34.5, US5 and US12 and have postulated roles in membrane trafficking, neurovirulence, apoptotic control and MHC I presentation respectively. The solved genome structure leads to how this compacted genome functions with the noted absences to produce a similar pathology in rabbits to that of HSV and whether other biological correlates will continue to be found in in vitro and in vivo infection. The inverted repeat regions (IR), duplicated and inverted to simplex virus' two larger blocks of protein-coding regions are described in Chapter 3. The similarities and differences in critical genes from the IR that balance latency and replicative viral cycles are compared. A two-fold reduction in IR content indicates the ability for a simplex virus to maintain infectivity despite this large truncation. The appendix describes the eukaryotic phylogeny of two initiating proteins of the mismatch repair (MMR) pathway. MMR proteins are present in the replicative foci of productive herpes virus infection and this analysis may indicate adaptive pressures involved in both genomic fidelity and host tropism. The emerging era of state-of-the-art genome sequencing and computational power advances this newly characterized herpes virus, along with its model host organism, as excellent candidates for systems interaction, and experimental biology. / Graduation date: 2012

The detection of non-protein-coding RNA (ncRNA) genes in bacteria and their diverse regulatory mode of action moved the experimental and bio-computational analysis of ncRNAs into the focus of attention. Regulatory ncRNA transcripts are not translated to proteins but function directly on the RNA level. These typically small RNAs have been found to be involved in diverse processes such as (post-)transcriptional regulation and modification, translation, protein translocation, protein degradation and sequestration. Bacterial ncRNAs either arise from independent primary transcripts or their mature sequence is generated via processing from a precursor. Besides these autonomous transcripts, RNA regulators (e.g. riboswitches and RNA thermometers) also form chimera with protein-coding sequences. These structured regulatory elements are encoded within the messenger RNA and directly regulate the expression of their “host” gene. The quality and completeness of genome annotation is essential for all subsequent analyses. In contrast to protein-coding genes ncRNAs lack clear statistical signals on the sequence level. Thus, sophisticated tools have been developed to automatically identify ncRNA genes. Unfortunately, these tools are not part of generic genome annotation pipelines and therefore computational searches for known ncRNA genes are the starting point of each study. Moreover, prokaryotic genome annotation lacks essential features of protein-coding genes. Many known ncRNAs regulate translation via base-pairing to the 5’ UTR (untranslated region) of mRNA transcripts. Eukaryotic 5’ UTRs have been routinely annotated by sequencing of ESTs (expressed sequence tags) for more than a decade. Only recently, experimental setups have been developed to systematically identify these elements on a genome-wide scale in prokaryotes. The first part of this thesis, describes three experimental surveys of exploratory field studies to analyze transcript organization in pathogenic bacteria. To identify ncRNAs in Pseudomonas aeruginosa we used a combination of an experimental RNomics approach and ncRNA prediction. Besides already known ncRNAs we identified and validated the expression of six novel RNA genes. Global detection of transcripts by next generation RNA sequencing techniques unraveled an unexpectedly complex transcript organization in many bacteria. These ultra high-throughput methods give us the appealing opportunity to analyze the complete RNA output of any species at once. The development of the differential RNA sequencing (dRNA-seq) approach enabled us to analyze the primary transcriptome of Helicobacter pylori and Xanthomonas campestris. For the first time we generated a comprehensive and precise transcription start site (TSS) map for both species and provide a general framework for the analysis of dRNA-seq data. Focusing on computer-aided analysis we developed new tools to annotate TSS, detect small protein-coding genes and to infer homology of newly detected transcripts. We discovered hundreds of TSS in intergenic regions, upstream of protein-coding genes, within operons and antisense to annotated genes. Analysis of 5’ UTRs (spanning from the TSS to the start codon of the adjacent protein-coding gene) revealed an unexpected size diversity ranging from zero to several hundred nucleotides. We identified and validated the expression of about 60 and about 20 ncRNA candidates in Helicobacter and Xanthomonas, respectively. Among these ncRNA candidates we found several small protein-coding genes that have previously evaded annotation in both species. We showed that the combination of dRNA-seq and computational analysis is a powerful method to examine prokaryotic transcriptomes. Experimental setups are time consuming and often combined with huge costs. Another limitation of experimental approaches is that genes which are expressed in specific developmental stages or stress conditions are likely to be missed. Bioinformatic tools build an alternative to overcome such restraints. General approaches usually depend on comparative genomic data and evolutionary signatures are used to analyze the (non-)coding potential of multiple sequence alignments. In the second part of my thesis we present our major update of the widely used ncRNA gene finder RNAz and introduce RNAcode, an efficient tool to asses local protein-coding potential of genomic regions. RNAz has been successfully used to identify structured RNA elements in all domains of life. However, our own experience and the user feedback not only demonstrated the applicability of the RNAz approach, but also helped us to identify limitations of the current implementation. Using a much larger training set and a new classification model we significantly improved the prediction accuracy of RNAz. During transcriptome analysis we repeatedly identified small protein-coding genes that have not been annotated so far. Only a few of those genes are known to date and standard proteincoding gene finding tools suffer from the lack of training data. To avoid an excess of false positive predictions, gene finding software is usually run with an arbitrary cutoff of 40-50 amino acids and therefore misses the small sized protein-coding genes. We have implemented RNAcode which is optimized for emerging applications not covered by standard protein-coding gene annotation software. In addition to complementing classical protein gene annotation, a major field of application of RNAcode is the functional classification of transcribed regions. RNA sequencing analyses are likely to falsely report transcript fragments (e.g. mRNA degradation products) as non-coding. Hence, an evaluation of the protein-coding potential of these fragments is an essential task. RNAcode reports local regions of high coding potential instead of complete protein-coding genes. A training on known protein-coding sequences is not necessary and RNAcode can therefore be applied to any species. We showed this with our analysis of the Escherichia coli genome where the current annotation could be accurately reproduced. We furthermore identified novel small protein-coding genes with RNAcode in this extensively studied genome. Using transcriptome and proteome data we found compelling evidence that several of the identified candidates are bona fide proteins. In summary, this thesis clearly demonstrates that bioinformatic methods are mandatory to analyze the huge amount of transcriptome data and to identify novel (non-)coding RNA genes. With the major update of RNAz and the implementation of RNAcode we contributed to complete the repertoire of gene finding software which will help to unearth hidden treasures of the RNA World.

Microsatellites are strings of short DNA motifs (≤6 bp) repeated in tandem across genomes of both prokaryotes and eukaryotes. In 20 years, they became popular genetic markers, successfully employed in the field of genetic mapping and gene hunting, as well as to address various biological questions at the individual, family, population and species level. However, evolutionary and demographic inferences from microsatellite polymorphism are hampered by controversy and ambiguity in the mutational processes of microsatellite sequences. Drawing on new data from genome projects, I review in Chapter 1 the concept of a microsatellite life cycle, which hypothesizes that microsatellites follow a life cycle from birth, through expansion, contraction, death and potentially resurrection. To document and understand this integrative concept of evolution, which could help improve current models of microsatellite evolution, there is an implicit need to study the evolution of microsatellites above the species level. A prerequisite of such comparative studies is therefore to find microsatellite loci that are conserved between different species. The near or full completion of many vertebrate genomes and their alignment against one another offer the ultimate approach to find genomic elements conserved over a large evolutionary scale. In Chapter 2, I present a new comprehensive method to find conserved microsatellites in whole genomes. Using the multiple-alignment of the human genome against those of 11 mammalian and five non-mammalian vertebrates, I examine the genomewide conservation of microsatellites, and challenge the general assumption that microsatellites are too labile to be maintained in distant species. In Chapter 3, I present similar results using the alignment of the newly sequenced platypus genome against those of three mammals, the chicken and the lizard, and incorporate these data into the framework created by the 17-genome analysis. This enlarged dataset was ground for attempting to reconstruct a vertebrate phylogeny from the presence/absence of microsatellites in the different genomes. Maximum parsimony analyses resulted in a tree much similar to that of the current view of the vertebrate phylogeny, while Bayesian analyses showed some discrepancies. This work opens a way for novel theoretical developments regarding the inference of ancestral states of microsatellites. In Chapter 4, I show how knowledge on conserved microsatellite sites can help for the development of a set of comparative primers useful across the Mammalia; implementing a similar protocol, nine conserved dinucleotide repeats were genotyped in 20 unrelated individuals of 18 species (nine sister species) encompassing the mammalian phylogeny, including marsupials and monotremes, and four microsatellites were sequenced in 4 individuals per species. My results emphasize conserved microsatellites as a new resource for genetic mapping and population studies. Finally, in Chapter 5, I recount the unexpected extent of structural change among mammalian orthologous microsatellites, including change of complexity, motif replacement and overall length variability. Altogether, these findings provide a comprehensive framework that may help in many areas of research, including molecular ecology, genome mapping, population genetics, and genome and microsatellite evolution.

L'immense diversité génomique des microorganismes leur permet de vivre partout, même dans les environnements extrêmes tels que Ies sources hydrothermales profondes. Ces dernières, disséminées sur l’ensemble des fonds océaniques, sont un bon modèle pour étudier la biogéographie et la diversification des génomes. Une approche de génomique comparative a été employée sur des isolats du genre Thermococcus proches d'un point de vue évolutif. Ce travail visait à identifier des mécanismes ayant un rôle dans Ia diversification de ces génomes, et également d'identifier des gènes impliqués dans cette différenciation. A cette fin, deux groupes d'une vingtaine d'isolats ayant des origines géographiques diverses ont été sélectionnés et séquencés. L'éloignement géographique résultant de la colonisation de nouveaux systèmes hydrothermaux semble être un facteur de diversification et de spéciation pour certains isolats. Cependant, lorsque les sites hydrothermaux sont relativement proches, il semblerait qu'un transfert de gènes entre les isolats soit toujours possible. Dans ce cas, l’adaptation à de nouvelles niches écologiques serait un facteur de la diversification des génomes. L'approche de génomique comparative a permis d'identifier des gènes spécifiques à certains sous-groupes, apparentés à des espèces. Ces gènes sont notamment impliqués dans les métabolismes des acides aminés, de production d'énergie et de transport d'ions inorganiques. Ceci reflète les pressions de sélections que peuvent subir ces organismes dans ces environnements hostiles à de nombreuses formes de vie. / The immense genomic diversity of microorganisms allows them to live everywhere, even in extreme environments such as deep hydrothermal vents. Scattered over the seabed, these are a good model for studying the biogeography and genomes diversification. A comparative genomics approach has been used on closely related isolates, of the genus Thermococcus. This work aimed at identifying mechanisms that have a role in the diversification of these genomes, and also to identify genes involved in this differentiation. For this purpose, two groups of about 20 isolates with different geographical origins were selected and sequenced.The geographical isolation resulting from colonization of new hydrothermal systems is likely to be a diversification and speciation factor for some isolates. But when hydrothermal sites are relatively close, it would seem that gene transfer between isolates is still possible. In this case, adaptation to new ecological niches would be a factor contributing to the genomes diversification. The comparative genomics approach allowed highlighting genes specific to certain subgroups, related to species. These genes are involved in amino acid metabolism, energy production and the transport of inorganic ions. This reflects selection pressures that these organisms may experience in these environments, otherwise hostile to many forms of life.

It is known that chromosomal rearrangements play an important role in speciation by limiting gene flow within and between species. Furthermore, this effect may be enhanced by involvement of sex chromosomes that are known to undergo fast evolution compared to autosomes and play a special role in speciation due to their engagement in postzygotic reproductive isolation. The work presented in this study uses various molecular-genetic and cytogenetic techniques to describe karyotype and sex chromosome evolution of two groups of Lepidoptera, namely selected representatives of the family Tortricidae and Leptidea wood white butterflies of the family Pieridae. The acquired knowledge points to unexpected evolutionary dynamics of lepidopteran karyotypes including the presence of derived neo-sex chromosome systems that originated as a result of chromosomal rearrangements. We discuss the significance of these findings for radiation and subsequent speciation of both lepidopteran groups.

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.