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With just over 2000 species, Begonia is one of the largest vascular plant genera. The vast morphological diversity, detailed phylogeny and extensive distribution data makes it an ideal model to study the evolution of diversity in tropical herbaceous plants. Specifically, their diverse leaf morphology allows them to be excellent subjects for studying the drivers of leaf shape variation in a non-model system. Studies in a range of model plants and crops have identified the key genes regulating leaf shape and shown them to be largely conserved across angiosperms (with a number of interesting exceptions). This study describes the genetic and evolutionary patterns observed in leaf form across Begonia. I have used a morphometric approach to quantify leaf shape in Begonia and subsequently plotted shape metrics across the phylogeny to identify patterns across the different clades and sections. I showed that although establishing metrics to quantify all species of Begonia collectively proved to be a challenging task, Elliptical Fourier Analysis (EFA) was adequate in scoring smaller clades and identifying patterns of change within these sections. Genome mining was then done to obtain orthologs for key leaf developmental genes in 11 Begoniaceae genomes. The expression patterns of these orthologous genes in six different tissues from B. conchifolia and B. plebeja were plotted to predict whether changes in function may have occurred. The drastic expansion of gene copy number and the variation in DGE expression patterns suggest that novel morphologies may have risen as the result of key leaf developmental gene regulators being altered. QTL analysis of leaf shape trait genes identified a number of candidates for asymmetry, dissection index (a CUC-like gene on chromosome 3) and EFA PCs. The nature of genetic differences between sister species in generating morphological differences was then analysed in B. luxurians and B. parviflora. The range of changes that can occur from gene sequence variation, copy number, expression patterns are also present in this sister pair of species. The search for candidate genes responsible for the compound leaf form in B. luxurians identified changes in hormone signalling genes, NAC TFs, an AS1-like gene. Interestingly, KNOX I expression was not observed. The development of ectopic leaflets was linked to the downregulation of a trichome inhibitor and the upregulation of key meristem and polarity genes.

SDR (Short-chain Dehydrogenases/Reductases) are one of the oldest and heterogeneous superfamily of proteins, whose classification is problematic because of the low percent identity, even within families. To get clearer insights into SDR molecular evolution, we explored the splicing site organization of the 75 human SDR genes across their vertebrate and invertebrate orthologs. We found anomalous gene structures in members of the human SDR7C and SDR42E families that provide clues of retrogene properties and independent evolutionary trajectories from a common invertebrate ancestor. The same analyses revealed that the identity value between human and invertebrate non-allelic variants is not necessarily associated with the homologous gene structure. Accordingly, a revision of the SDR nomenclature is proposed by including the human SDR40C1 and SDR7C gene in the same family.

Metschnikowia pulcherrima is an important yeast species that is attracting increased interest thanks to its biotechnological potential, especially in agri-food applications. Phylogenetically related species of the so-called ‘pulcherrima clade’ were first described and then reclassified in one single species, which makes the identification an intriguing issue. Starting from the whole-genome sequencing of the protechnological strain Metschnikowia sp. DBT012, this study applied comparative genomics to calculate similarity with the M. pulcherrima clade publicly available genomes with the aim to verify if novel single-copy putative phylogenetic markers could be selected, in comparison with the commonly used primary and secondary barcodes. The genome-based bioinformatic analysis allowed the identification of 85 consensus single-copy orthologs, which were reduced to three after split decomposition analysis. However, wet-lab amplification of these three genes in nonsequenced type strains revealed the presence of multiple copies, which made them unsuitable as phylogenetic markers. Finally, average nucleotide identity (ANI) was calculated between strain DBT012 and available genome sequences of the M. pulcherrima clade, although the genome dataset is still rather limited. Presence of multiple copies of phylogenetic markers as well as ANI values were compatible with the recent reclassification of the clade, allowing the identification of strain DBT012 as M. pulcherrima.

Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.

Breeding miscanthus for biomass production and composition is essential for targeting high-yielding genotypes suited to different end-uses. Our objective was to understand the genetic determinism of these traits in M. sinensis, according to different plant ages and environmental conditions. A diploid population was established in two locations according to a staggered-start design, which made the “year” effect partitioned into “age” and “growing season” effects. An integrated genetic map of 2,602 SNP markers distributed across 19 LGs, was aligned with the M. sinensis reference genome and spanned 2,770 cM. The QTL mapping was based on Best Linear Unbiased Predictions estimated across three climatic conditions and at least three ages in both locations. 260 and 283 QTL were related to biomass production and composition traits, respectively. In each location, 40%-60% were related to biomass production traits and stable across different climatic conditions and ages, and 30% to biomass composition traits. Ten to fifteen% were stable for both trait types across locations. Twelve QTL clusters were established based on either biomass production or composition traits, and validated by high genetic correlations between the traits. Sixty-two putative M. sinensis genes, related to the cell-wall, were evidenced in the QTL clusters of biomass composition traits, and orthologous to those of sorghum and maize. Twelve of them were differentially expressed and belonged to gene families related to the cell-wall biosynthesis identified in other miscanthus studies. These stable QTL constitute new insights into Marker-Assisted Selection breeding while offering a joint improvement of biomass production or composition traits.

Colombia es el primer productor mundial de clavel y el patógeno, Fusarium oxysporum f.sp. dianthi (Fod) causa grandes pérdidas en el cultivo comercial de esta planta. La producción de variedades resistentes al hongo es una de las formas más efectivas para controlar los daños producidos por el parásito. A pesar de que se han realizado trabajos que han descrito el desarrollo de la enfermedad en clavel causadas por Fod, así como estudios sobre los cambios histológicos y bioquímicos en las variedades resistentes y susceptibles, los genes que gobiernan la respuesta de defensa en contra del ataque del patógeno no se han caracterizado aún. Sabemos por trabajos anteriores en nuestro grupo de investigación, que la resistencia del clavel a Fod esta mediada por tres pares de genes autosómicos con herencia simple y aditiva, pero es necesario reconocer estos genes de tal forma que se pueda utilizar este conocimiento para conducir apropiadamente los programas de mejoramiento del clavel comercial. En el presente trabajo se obtuvo el material biológico, usando células indiferenciadas de clavel y Fod cepa 2019, evaluado los oligos por amplificación por PCR en ADN genómico, posteriormente se evaluaron 22 parejas de oligos identificados en trabajos previos como housekeeping, genes relacionados con resistencia a parásitos y genes que codifican a proteínas relacionadas con patogenicidad mediante RT-qPCR, relacionados con la respuesta de defensa a Fod en las variedades resistentes UMNG395 y UMNGF1B2 y variedades susceptibles UMNGSH2 y UMNG6515 del programa de mejoramiento del clavel de la UMNG. Demostrando que la expresión unos genes en fenotipos resistentes no está asociado a la resistencia, sino que un conjunto de genes son parte de un metabolismo relacionado con la respuesta de defensa frente al patógeno, que abarca procesos de señalización, regulación, inducción, transcripción de genes. CAPÍTULO 1: REVISIÓN BIBLIOGRÁFICA 18 1. Clavel (Dianthus caryophyllus L.) 18 1.1. Importancia económica del clavel 19 1.2. Mejoramiento genético del clavel 20 2. Fusarium oxysporum 22 2.1. Fusarium oxysporum f.sp. dianthi (Fod) 23 2.2. Problemática causada por Fusarium oxysporum 23 2.3. Enfermedad causada por Fusarium oxysporum 24 2.4. Implicaciones en el cultivo de clavel 25 3. Manejo Enfermedad 27 3.1. Manejo tradicional de la enfermedad 27 3.2. Manejo biotecnológico de la enfermedad 28 4. Mecanismos de defensa Planta – Patógeno 29 4.1. Resistencia genética a Fusarium oxysporum 31 4.2. Mecanismos de regulación de la defensa vegetal contra factores de estrés 33 4.3. Algunas rutas de defensa en plantas, asociadas a metabolitos secundarios y dirigidas contra fitopatógenos 36 5. Uso de herramientas moleculares 37 CAPÍTULO II. ESCRITO TRABAJO DE GRADO 38 1. RESUMEN - ABSTRACT 39 2. INTRODUCCIÓN 39 3. OBJETIVOS 41 3.1. Objetivo general 42 3.2. Objetivos Específicos 42 4. MATERIALES Y MÉTODOS 42 4.1. Obtención del Material Biológico. 43 4.2. Propagación in vitro de células indiferenciadas (CIS) de variedades Resistentes y Susceptibles 43 4.3. Obtención de Fusarium oxysporum a partir de muestras de plantas infectadas. 44 4.4. Obtención de cultivos monospóricos de Fusarium oxysporum 44 4.5. Ensayo de reinfección y aislamiento de Fusarium oxysporum f.sp. dianthi (Fod) 45 4.6. Pruebas de Elicitación 45 4.7. Extracción y cuantificación de ADN de CIS 46 4.8. Extracción y cuantificación de ARN total de CIS. 46 4.9. Amplificación por PCR 47 4.10. RT-qPCR 48 4.10.1. Genes evaluados 49 4.11. Análisis de resultados de expresión 50 CAPÍTULO 3: RESULTADOS Y DISCUSIÓN 52 1. Obtención material biológico 52 1.1. Propagación in vitro de células indiferenciadas (CIS) de variedades resistentes y susceptibles 52 1.2. Obtención de Fusarium oxysporum a partir de muestras de plantas infectadas. 53 1.3. Caracterización morfológica 53 1.4. Obtención de cultivos monospóricos de Fusarium oxysporum 54 1.5. Ensayo de reinfección y aislamiento de Fusarium oxysporum f.sp. dianthi (Fod) 55 1.6. Ensayo de Elicitación 56 2. Evaluación material genético 58 2.1. Extracción y Cuantificación de ADN de CIS. 58 2.2. Amplificación por PCR de secuencias génicas 59 2.2.1. PCR de genes “Housekeeping” 59 2.2.2. PCR de genes asociados a la resistencia a parásitos 61 2.2.3. PCR de genes asociados con proteínas relacionadas con patogenicidad 63 2.3. Extracción y cuantificación de ARN total de CIS 67 3. Análisis de expresión 68 3.1. Genes “Housekeeping” 68 3.1.1. Alcohol deshidrogenasa 69 3.1.2. Arginina descarboxilasa 71 3.1.3. Tetrahidroxichalcona 2-glucosiltransferasa 72 3.1.4. “Ethylene Insensitive 3-like 2” 74 3.2. Genes relacionados con la resistencia a parásitos 76 3.2.1. Antranilato N-hidroxicinamoil / Benzoiltransferasa 77 3.2.2. Gen receptor de etileno 78 3.2.3. Flavonol 3-Glucosiltransferasa 79 3.2.4. Fenilalanina amonio liasa 81 3.2.5. Antocianidin sintasa 83 3.3. Genes relacionados con proteínas de patogenicidad 85 3.3.1. β-(1 3)-D-Glucanasa 86 3.3.2. Quitinasa 88 3.3.3. Hidrolasas de glucósido de β-glicosidasa 90 3.3.4. Aldosa 1-epimerasa 91 3.3.5. “Thaumatin Like Protein” 93 3.3.6. β- amilasa 95 3.3.7. Homólogo a peroxidasas 97 3.3.8. Catalasa 100 3.3.9. Malato deshidrogenasa 102 3.3.10. Vía de señalización mediada por ácido jasmonico 104 3.3.11. Proteína inhibidora de poligalacturonasas 106 3.3.12. Vía de señalización mediada por ácido salicílico 108 3.3.13. “Receptor- like Kinase” 111 4. CONCLUSIONES 113 5. BIBLIOGRAFÍA 114 6. ANEXOS 141 6.1. Gráficas análisis de expresión RT-qPCR 141 6.1.1. Gráficas RT-qPCR genes “Housekeeping” 141 6.1.2. Gráficas de RT-qPCR de Genes relacionados con resistencia a parásitos 146 6.1.3. Genes relacionados con proteínas de patogenicidad 151 6.1.4. Gráficas ecuación lineal genes 162 Colombia is the world's leading producer of carnation and the pathogen, Fusarium oxysporum f.sp. dianthi (Fod) causes great losses in the commercial cultivation of this plant. The production of varieties resistant to the fungus is one of the most effective ways to control the damage caused by the parasite. Although work has been done describing the development of the disease in carnation caused by Fod, as well as studies on the histological and biochemical changes in resistant and susceptible varieties, the genes that govern the defense response against the pathogen attack have not yet been characterized. We know from previous work in our research group that carnation resistance to Fod is mediated by three pairs of autosomal genes with simple and additive inheritance, but it is necessary to recognize these genes so that this knowledge can be used to properly conduct commercial carnation breeding programs. In the present work, biological material was obtained, using undifferentiated cells of carnation and Fod strain 2019, evaluated the oligos by PCR amplification in genomic DNA, then 22 pairs of oligos identified in previous works as housekeeping were evaluated, genes related to parasite resistance and genes encoding proteins related to pathogenicity were evaluated by RT-qPCR, related to the defense response to Fod in resistant varieties UMNG395 and UMNGF1B2 and susceptible varieties UMNGSH2 and UMNG6515 of the UMNG carnation breeding program. It shows that the expression of some genes in resistant phenotypes is not associated with resistance, but that a set of genes are part of metabolism related to the defense response against the pathogen, which includes processes of signaling, regulation, induction, and transcription of genes. Pregrado

Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

Proanthocyanidins (PAs) are a group of oligomers or polymers composed of monomeric flavanols. They offer many benefits for human fitness, such as antioxidant, anticancer, and anti-inflammatory activities. To date, three types of PA have been observed in nature: procyanidins, propelargonidins, and prodelphinidins. These are synthesized as some of the end-products of the flavonoid pathway by different consecutive enzymatic activities, from the same precursor—naringenin. Although the general biosynthetic pathways of PAs have been reported in a few model plant species, little is known about the species-specific pathways in major crops containing different types of PA. In the present study, we identified the species-specific pathways in 10 major crops, based on the presence/absence of flavanol-based intermediates in the metabolic pathway, and found 202 orthologous genes in the reference genomic database of each species, which may encode for key enzymes involved in the biosynthetic pathways of PAs. Parallel enzymatic reactions in the pathway are responsible for the ratio between PAs and anthocyanins, as well as among the three types of PAs. Our study suggests a promising strategy for molecular breeding, to regulate the content of PAs and anthocyanins and improve the nutritional quality of food sources globally.

Background Auxins play an important role in plant growth and development; the auxins responsive gene; auxin/indole-3-acetic acid (Aux/IAA), small auxin-up RNAs (SAUR) and Gretchen Hagen3 (GH3) control their mechanisms. The GH3 genes function in homeostasis by the catalytic activities in auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. Results In our study, we identified the GH3 genes in three cotton species; Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, analyzed their chromosomal distribution, phylogenetic relationships, cis-regulatory element function and performed virus induced gene silencing of the novel Gh_A08G1120 (GH3.5) gene. The phylogenetic tree showed four clusters of genes with clade 1, 3 and 4 having mainly members of the GH3 of the cotton species while clade 2 was mainly members belonging to Arabidopsis. There were no paralogous genes, and few orthologous genes were observed between Gossypium and other species. All the GO terms were detected, but only 14 genes were found to have described GO terms in upland cotton, more biological functions were detected, as compared to the other functions. The GH3.17 subfamily harbored the highest number of the cis-regulatory elements, most having promoters towards dehydration-responsiveness. The RNA expression analysis revealed that 10 and 8 genes in drought and salinity stress conditions respectively were upregulated in G. hirsutum. All the genes that were upregulated in plants under salt stress conditions were also upregulated in drought stress; moreover, Gh_A08G1120 (GH3.5) exhibited a significant upregulation across the two stress factors. Functional characterization of Gh_A08G1120 (GH3.5) through virus-induced gene silencing (VIGS) revealed that the VIGS plants ability to tolerate drought and salt stresses was significantly reduced compared to the wild types. The chlorophyll content, relative leaf water content (RLWC), and superoxide dismutase (SOD) concentration level were reduced significantly while malondialdehyde concentration and ion leakage as a measure of cell membrane stability (CMS) increased in VIGS plants under drought and salt stress conditions. Conclusion This study revealed the significance of the GH3 genes in enabling the plant’s adaptation to drought and salt stress conditions as evidenced by the VIGS results and RT-qPCR analysis. Electronic supplementary material The online version of this article (10.1186/s12863-019-0756-6) contains supplementary material, which is available to authorized users.

Made available in DSpace on 2019-10-06T16:35:19Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01. Added 1 bitstream(s) on 2019-10-09T18:35:28Z : No. of bitstreams: 1 S1415-47572019000100145.pdf: 1807906 bytes, checksum: 429de26cfda2d5142dade2f2716528e9 (MD5) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) The filter cake from sugar cane processing is rich in organic matter and nutrients, which favors the proliferation of microorganisms with potential to deconstruct plant biomass. From the metagenomic data of this material, we assembled a draft genome that was phylogenetically related to Thermomonospora curvata DSM 43183, which shows the functional and ecological importance of this bacterium in the filter cake. Thermomonospora is a gram-positive bacterium that produces cellulases in compost, and it can survive temperatures of 60 ºC. We identified a complete set of biomass depolymerizing enzymes in the draft genome of Thermomonospora sp. CIT 1, such as α-amylase, catalase-peroxidases, β-mannanase, and arabinanase, demonstrating the potential of this bacterium to deconstruct the components of starch, lignin, and hemicellulose. In addition, the draft genome of Thermomonospora sp. CIT 1 contains 18 genes that do not share identity with five other species of Thermomonospora, suggesting that this bacterium has different genetic characteristics than those present in genomes reported so far for this genus. These findings add a new dimension to the current understanding of the functional profile of this microorganism that inhabits agro-industrial waste, which may boost new gene discoveries and be of importance for application in the production of bioethanol. Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Departamento de Tecnologia Laboratório de Bioinformática Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq) Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Departamento de Biologia Aplicada à Agropecuária Laboratório de Genética Aplicada Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Departamento de Tecnologia Laboratório de Bioinformática Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Laboratório Multiusuário Centralizado para Sequenciamento de DNA em Larga Escala e Análise de Expressão Gênica (LMSeq) Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP) Departamento de Biologia Aplicada à Agropecuária Laboratório de Genética Aplicada Faculdade de Ciências Agrárias e Veterinárias Universidade Estadual Paulista (UNESP)

The micronutrients iron (Fe) and zinc (Zn) are not only essential for plant survival and proliferation but are crucial for human health. Increasing Fe and Zn levels in edible parts of plants, known as biofortification, is seen a sustainable approach to alleviate micronutrient deficiency in humans. Wheat, as one of the leading staple foods worldwide, is recognized as a prioritized choice for Fe and Zn biofortification. However, to date, limited molecular and physiological mechanisms have been elucidated for Fe and Zn homeostasis in wheat. The expanding molecular understanding of Fe and Zn homeostasis in model plants is providing invaluable resources to biofortify wheat. Recent advancements in NGS (next generation sequencing) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms have initiated a revolution in resources and approaches for wheat genetic investigations and breeding. Here, we summarize molecular processes and genes involved in Fe and Zn homeostasis in the model plants Arabidopsis and rice, identify their orthologs in the wheat genome, and relate them to known wheat Fe/Zn QTL (quantitative trait locus/loci) based on physical positions. The current study provides the first inventory of the genes regulating grain Fe and Zn homeostasis in wheat, which will benefit gene discovery and breeding, and thereby accelerate the release of Fe- and Zn-enriched wheats.

Background The circadian clock drives endogenous 24-h rhythms that allow organisms to adapt and prepare for predictable and repeated changes in their environment throughout the day-night (diurnal) cycle. Many components of the circadian clock in Arabidopsis thaliana have been functionally characterized, but comparatively little is known about circadian clocks in grass species including major crops like maize and sorghum. Results Comparative research based on protein homology and diurnal gene expression patterns suggests the function of some predicted clock components in grasses is conserved with their Arabidopsis counterparts, while others have diverged in function. Our analysis of diurnal gene expression in three panicoid grasses sorghum, maize, and foxtail millet revealed conserved and divergent evolution of expression for core circadian clock genes and for the overall transcriptome. We find that several classes of core circadian clock genes in these grasses differ in copy number compared to Arabidopsis, but mostly exhibit conservation of both protein sequence and diurnal expression pattern with the notable exception of maize paralogous genes. We predict conserved cis-regulatory motifs shared between maize, sorghum, and foxtail millet through identification of diurnal co-expression clusters for a subset of 27,196 orthologous syntenic genes. In this analysis, a Cochran–Mantel–Haenszel based method to control for background variation identified significant enrichment for both expected and novel 6–8 nucleotide motifs in the promoter regions of genes with shared diurnal regulation predicted to function in common physiological activities. Conclusions This study illustrates the divergence and conservation of circadian clocks and diurnal regulatory networks across syntenic orthologous genes in panacoid grass species. Further, conserved local regulatory sequences contribute to the architecture of these diurnal regulatory networks that produce conserved patterns of diurnal gene expression.

We consider how the orthology/paralogy information can be corrected in order to represent a gene tree, a problem that has recently gained interest in phylogenomics. Interestingly, the problem is related to the Minimum CoGraph Editing problem on the relation graph that represents orthology/paralogy information, where we want to minimize the number of edit operations on the given relation graph in order to obtain a cograph. In this paper we provide both theoretical and experimental results on the Minimum CoGraph Editing problem. On the theoretical side, we provide approximation algorithms for bounded degree relation graphs, for the general problem and for the problem restricted to deletion of edges. On the experimental side, we present a genetic algorithm for Minimum CoGraph Editing and we provide an experimental evaluation of the genetic algorithm on synthetic data.

Significance This work represents a large, order-wide evolutionary analysis of the order Chiroptera (bats). Our pipeline for assembling sequence data and curating orthologous multiple sequence alignments includes methods for improving results when combining genomic and transcriptomic data sources. The resulting phylogenetic tree divides the order Chiroptera into Yinpterochiroptera and Yangochiroptera, in disagreement with the previous division into Megachiroptera and Microchiroptera and in agreement with some other recent molecular studies, and also provides evidence for other contested branch placements. We also performed a genome-wide analysis of positive selection and found 181 genes with signatures of positive selection. Enrichment analysis shows these positively selected genes to be primarily related to immune responses but also, surprisingly, collagen formation., Historically, the evolution of bats has been analyzed using a small number of genetic loci for many species or many genetic loci for a few species. Here we present a phylogeny of 18 bat species, each of which is represented in 1,107 orthologous gene alignments used to build the tree. We generated a transcriptome sequence of Hypsignathus monstrosus, the African hammer-headed bat, and additional transcriptome sequence for Rousettus aegyptiacus, the Egyptian fruit bat. We then combined these data with existing genomic and transcriptomic data from 16 other bat species. In the analysis of such datasets, there is no clear consensus on the most reliable computational methods for the curation of quality multiple sequence alignments since these public datasets represent multiple investigators and methods, including different source materials (chromosomal DNA or expressed RNA). Here we lay out a systematic analysis of parameters and produce an advanced pipeline for curating orthologous gene alignments from combined transcriptomic and genomic data, including a software package: the Mismatching Isoform eXon Remover (MIXR). Using this method, we created alignments of 11,677 bat genes, 1,107 of which contain orthologs from all 18 species. Using the orthologous gene alignments created, we assessed bat phylogeny and also performed a holistic analysis of positive selection acting in bat genomes. We found that 181 genes have been subject to positive natural selection. This list is dominated by genes involved in immune responses and genes involved in the production of collagens.

Stomatal abundance determines the maximum potential for gas exchange between the plant and the atmosphere. In Arabidopsis, it is set during organ development through complex genetic networks linking epidermal differentiation programs with environmental response circuits. Three related bHLH transcription factors, SPCH, MUTE, and FAMA, act as positive drivers of stomata differentiation. Mutant alleles of some of these genes sustain different stomatal numbers in the mature organs and have potential to modify plant performance under different environmental conditions. However, knowledge about stomatal genes in dicotyledoneous crops is scarce. In this work, we identified the Solanum lycopersicum putative orthologs of these three master regulators and assessed their functional orthology by their ability to complement Arabidopsis loss-of-function mutants, the epidermal phenotypes elicited by their conditional overexpression, and the expression patterns of their promoter regions in Arabidopsis. Our results indicate that the tomato proteins are functionally equivalent to their Arabidopsis counterparts and that the tomato putative promoter regions display temporal and spatial expression domains similar to those reported for the Arabidopsis genes. In vivo tracking of tomato stomatal lineages in developing cotyledons revealed cell division and differentiation histories similar to those of Arabidopsis. Interestingly, the S. lycopersicum genome harbors a FAMA-like gene, expressed in leaves but functionally distinct from the true FAMA orthologue. Thus, the basic program for stomatal development in S. lycopersicum uses key conserved genetic determinants. This opens the possibility of modifying stomatal abundance in tomato through previously tested Arabidopsis alleles conferring altered stomata abundance phenotypes that correlate with physiological traits related to water status, leaf cooling, or photosynthesis.

Especially in low income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, which are: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'. This article is protected by copyright. All rights reserved.

Background High-throughput techniques bring novel tools and also statistical challenges to genomic research. Identifying genes with differential expression between different species is an effective way to discover evolutionarily conserved transcriptional responses. To remove systematic variation between different species for a fair comparison, normalization serves as a crucial pre-processing step that adjusts for the varying sample sequencing depths and other confounding technical effects. Results In this paper, we propose a scale based normalization (SCBN) method by taking into account the available knowledge of conserved orthologous genes and by using the hypothesis testing framework. Considering the different gene lengths and unmapped genes between different species, we formulate the problem from the perspective of hypothesis testing and search for the optimal scaling factor that minimizes the deviation between the empirical and nominal type I errors. Conclusions Simulation studies show that the proposed method performs significantly better than the existing competitor in a wide range of settings. An RNA-seq dataset of different species is also analyzed and it coincides with the conclusion that the proposed method outperforms the existing method. For practical applications, we have also developed an R package named “SCBN”, which is freely available at http://www.bioconductor.org/packages/devel/bioc/html/SCBN.html. Electronic supplementary material The online version of this article (10.1186/s12859-019-2745-1) contains supplementary material, which is available to authorized users.

International audience; Plant cell walls play a fundamental role in several plant traits and also influence crop use as livestock nutrition or biofuel production. The Glycosyltransferase family 61 (GT61) is involved in the synthesis of cell wall xylans. In grasses (Poaceae), a copy number expansion was reported for the GT61 family, and raised the question of the evolutionary history of this gene family in a broader taxonomic context. A phylogenetic study was performed on GT61 members from 13 species representing the major angiosperm clades, in order to classify the genes, reconstruct the evolutionary history of this gene family and study its expansion in monocots. Four orthogroups (OG) were identified in angiosperms with two of them displaying a copy number expansion in monocots. These copy number expansions resulted from both tandem and segmental duplications during the genome evolution of monocot lineages. Positive selection footprints were detected on the ancestral branch leading to one of the orthogroups suggesting that the gene number expansion was accompanied by functional diversification, at least partially. We propose an OG-based classification framework for the GT61 genes at different taxonomic levels of the angiosperm useful for any further functional or translational biology study.

This contribution contains data associated to the research article entitled “Exploring the genes of yerba mate (Ilex paraguariensis A. St.-Hil.) by NGS and de novo transcriptome assembly” (Debat et al., 2014) [1]. By means of a bioinformatic approach involving extensive NGS data analyses, we provide a resource encompassing the full transcriptome assembly of yerba mate, the first available reference for the Ilex L. genus. This dataset (Supplementary files 1 and 2) consolidates the transcriptome-wide assembled sequences of I. paraguariensis with further comprehensive annotation of the protein coding genes of yerba mate via the integration of Arabidopsis thaliana databases. The generated data is pivotal for the characterization of agronomical relevant genes in the tree crop yerba mate -a non-model species- and related taxa in Ilex. The raw sequencing data dissected here is available at DDBJ/ENA/GenBank (NCBI Resource Coordinators, 2016) [2] Sequence Read Archive (SRA) under the accession SRP043293 and the assembled sequences have been deposited at the Transcriptome Shotgun Assembly Sequence Database (TSA) under the accession GFHV00000000. Fil: Aguilera, Patricia Mabel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina Fil: Debat, Humberto Julio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina Fil: Grabiele, Mauro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Universidad Nacional de Misiones. Instituto de Biología Subtropical; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigaciones Agropecuarias. Instituto de Patología Vegetal; Argentina

Background Polyploidy is considered a major driving force in genome expansion, yielding duplicated genes whose expression may be conserved or divergence as a consequence of polyploidization. Results We compared the genome sequences of tetraploid cotton (Gossypium hirsutum) and its two diploid progenitors, G. arboreum and G. raimondii, and found that the bHLH genes were conserved over the polyploidization. Oppositely, the expression of the homeolgous gene pairs was diversified. The biased homeologous proportion for bHLH family is significantly higher (64.6%) than the genome wide homeologous expression bias (40%). Compared with cacao (T. cacao), orthologous genes only accounted for a small proportion (41.7%) of whole cotton bHLHs family. The further Ks analysis indicated that bHLH genes underwent at least two distinct episodes of whole genome duplication: a recent duplication (1.0–60.0 million years ago, MYA, 0.005 60.0 MYA, 0.312

Gene duplication is one of the major evolutionary mechanisms providing raw material for the generation of genes with new or modified functions. The yeast Saccharomyces cerevisiae originated after an allopolyploidization event, which involved mating between two different ancestral yeast species. ScALT1 and ScALT2 codify proteins with 65% identity, which were proposed to be paralogous alanine transaminases. Further analysis of their physiological role showed that while ScALT1 encodes an alanine transaminase which constitutes the main pathway for alanine biosynthesis and the sole pathway for alanine catabolism, ScAlt2 does not display alanine transaminase activity and is not involved in alanine metabolism. Moreover, phylogenetic studies have suggested that ScALT1 and ScALT2 come from each one of the two parental strains which gave rise to the ancestral hybrid. The present work has been aimed to the understanding of the properties of the ancestral type Lacchancea kluyveri LkALT1 and Kluyveromyces lactis KlALT1, alanine transaminases in order to better understand the ScALT1 and ScALT2 evolutionary history. These ancestral -type species were chosen since they harbor ALT1 genes, which are related to ScALT2. Presented results show that, although LkALT1 and KlALT1 constitute ScALT1 orthologous genes, encoding alanine transaminases, both yeasts display LkAlt1 and KlAlt1 independent alanine transaminase activity and additional unidentified alanine biosynthetic and catabolic pathway(s). Furthermore, phenotypic analysis of null mutants uncovered the fact that KlAlt1 and LkAlt1 have an additional role, not related to alanine metabolism but is necessary to achieve wild type growth rate. Our study shows that the ancestral alanine transaminase function has been retained by the ScALT1 encoded enzyme, which has specialized its catabolic character, while losing the alanine independent role observed in the ancestral type enzymes. The fact that ScAlt2 conserves 64% identity with LkAlt1 and 66% with KlAlt1, suggests that ScAlt2 diversified after the ancestral hybrid was formed. ScALT2 functional diversification resulted in loss of both alanine transaminase activity and the additional alanine-independent LkAlt1 function, since ScALT2 did not complement the Lkalt1Δ phenotype. It can be concluded that LkALT1 and KlLALT1 functional role as alanine transaminases was delegated to ScALT1, while ScALT2 lost this role during diversification.

WRKY transcription factors have been extensively characterized in the past 20 years, but in wheat, studies on WRKY genes and their function are lagging behind many other species. To explore the function of wheat WRKY genes, we identified a TaWRKY68 gene from a common wheat cultivar. It encodes a protein comprising 313 amino acids which harbors 19 conserved motifs or active sites. Gene expression patterns were determined by analyzing microarray data of TaWRKY68 in wheat and of orthologous genes from maize, rice and barley using Genevestigator. TaWRKY68 orthologs were identified and clustered using DELTA-BLAST and COBALT programs available at NCBI. The results showed that these genes, which are expressed in all tissues tested, had relatively higher levels in the roots and were up-regulated in response to biotic stresses. Bioinformatics results were confirmed by RT-PCR experiments using wheat plants infected by Agrobacterium tumefaciens and Blumeria graminis, or treated with Deoxynivalenol, a Fusarium graminearum-induced mycotoxin in wheat or barley. In summary, TaWRKY68 functions differ during plant developmental stages and might be representing a hub gene function in wheat responses to various biotic stresses. It was also found that including data from major cereal genes in the bioinformatics analysis gave more accurate and comprehensive predictions of wheat gene functions.

In this work we propose a simple method to obtain groups of homologous genes across multiple (k) organisms, called kGC. Our method takes as input all-against-all Blastp comparisons and produces groups of homologous sequences. First, homologies among groups of paralogs of all the k compared genomes are found, followed by homologies of groups among k - 1 genomes and so on, until groups belonging exclusively to only one genome, that is, groups of one genome not presenting strong similarities with any group of any other genome, are identified. We have used our method to determine homologous groups across six Actinobacterial complete genomes. To validate kGC, we first investigate the Pfam classification of the homologous groups, and after compare our results with those produced by OrthoMCL. Although kGC is much simpler than OrthoMCL it presented similar results with respect to Pfam classification.

Submitted by SILVAN GOMES DE BRITO null (gomesilvapb@hotmail.com) on 2016-08-15T13:40:13Z No. of bitstreams: 1 BRITO, SILVAN GOMES-Ver_Final.pdf: 2635186 bytes, checksum: 85043e51c1f988979dc82bbe50a8af96 (MD5) Approved for entry into archive by Ana Paula Grisoto (grisotoana@reitoria.unesp.br) on 2016-08-15T18:29:41Z (GMT) No. of bitstreams: 1 brito_sg_dr_jabo_par.pdf: 732534 bytes, checksum: 2b1e79b32cc0c34a955450d3cf67b772 (MD5) Made available in DSpace on 2016-08-15T18:29:41Z (GMT). No. of bitstreams: 1 brito_sg_dr_jabo_par.pdf: 732534 bytes, checksum: 2b1e79b32cc0c34a955450d3cf67b772 (MD5) Previous issue date: 2016-07-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) O genoma do sorgo tem sido utilizado como referência em estudos de genômica funcional e comparativa em cana-de-açúcar. A utilização do genoma do sorgo, em estudos de mapeamento comparativo, tem contribuído para auxiliar a detecção de QTL (locus de caracteres quantitativos) em cana-de-açúcar. Marcadores microssatélites de sorgo podem ser empregados no mapeamento comparativo com a cana-de-açúcar, assim como, o desenvolvimento de marcadores microssatélites a partir de sequências ortólogas conservadas (COS - Conserved Orthologous Sequences) podem servir de “marcadores âncoras” entre estas duas espécies. No presente trabalho, marcadores microssatélites de sorgo foram incorporados em um mapa prévio de ligação derivado do cruzamento entre o clone IACSP95-3018 e a cultivar IACSP93-3046, ambos do Programa de Melhoramento Genético de Cana-de-Açúcar do Instituto Agronômico de Campinas (IAC). Paralelamente, um conjunto de marcadores microssatélites obtidos a partir da identificação de sequências expressas ortólogas conservadas (COS) entre cana-de-açúcar e sorgo foram desenvolvidos e avaliados quanto ao seu potencial de polimorfismo e mapeamento em cana-de-açúcar. Os marcadores obtidos também foram utilizados para identificar associações putativas aos parâmetros de qualidade (Fibra% e Pol%Cana). Um total de 41 pares de microssatélites COS-EST-SSRs foi desenhado, dos quais 34 produziram amplicons em um grupo de 24 genótipos de Saccharum e Sorghum. O número de alelos variou de 2 a 15 com valor médio de PIC (conteúdo de informação de polimorfismo) de 0,71. Os 29 pares de primers de microssatélites de sorgo, juntamente com os 41 pares de primers COS-EST-SSRs genotipados na população de mapeamento produziram um total de 120 marcadores polimórficos, dos quais 92 segregaram em dose única. Destes 92, 52 (56,5%) foram incorporados ao mapa prévio originando 138 grupos de ligação agrupados em 12 grupos de homologia. A maioria das associações entre marcadores e o caractere Pol%Cana detectadas por meio da análise de marcas simples foram de efeito positivo contribuindo para o aumento deste caractere sendo apenas duas com contribuição negativa. De forma geral, os marcadores derivados de sorgo foram promissores no mapeamento da população aqui apresentada. Sorghum genome has been used as a reference in functional and comparative genomics studies of sugarcane. The sorghum genome has aided to colocalize QTL (quantitative trait locus) in sugarcane through comparative mapping approach. Sorghum microsatellite markers, as well as, the development of microsatellite markers derived from orthologous conserved sequences (COS) can serve as "anchors markers" in comparative mapping between these two species. In the present study, sorghum microsatellite markers were included in a previous map derived from a bi-parental cross between a clone (IACSP95-3018) and a sugarcane cultivar (IACSP93-3046) from the Instituto Agronômico de Campinas (IAC) sugarcane breeding program. A set of microsatellite markers derived from conserved orthologous (COS-EST-SSRs) sequences between sugarcane and sorghum was developed and evaluated for their polymorphism and mapping potential in sugarcane. These markers were also used to identify putative associations for sugarcane quality parameters (fiber% and Pol% Cane). A total of 41 COS-EST-SSRs primer pairs was designed, of which 34 produced amplicons in a group of 24 genotypes of Saccharum and Sorghum. The number of alleles ranged from 2 to 15 with an PIC (polymorphism information content) average value of 0.71. The 29 sorghum SSR primer pairs along with the 41 COS-EST-SSR primer pairs was genotyped in the mapping population and produced a total of 120 polymorphic markers, of which 92 were single dose markers. Of these, 52 (56.5%) were added to the previous map generating 138 linkage groups grouped into 12 homology groups. The majority of the single marker-trait associations detected for Pol% Cane showed positive effects contributing to increase this trait (only two showed negative contribution to Pol% Cane). In general, the sorghum derived markers were promising in the genetic mapping of the bi-parental population evaluated.

Ranunculus L. is an early diverging clade in the Angiosperm phylogeny. The split between terrestrial and aquatic/semi-aquatic lineages within the genus occurred within 20 Ma (Emadzade and Horandl, 2011), which is much younger than for some well-known aquatic lineages such as Ceratophyllum and Potamogeton. Ranunculus sceleratus Linn. is a semi-aquatic plant commonly found in paddy fields, streams and lakes in Asia, Europe and North America (eFlora of China, http://www.efloras.org/). The plant has also been studied for its unique toxicological and pharmacological properties (Prieto et al., 2003). Its karyotype is 2n = 32, x = 8 in mainland China (Yang, 2000). It usually roots in inundated soils, with stems and leaves emergent. The semi-aquatic R. sceleratus has been hypothesized to be an inter-mediate type in the transition from a terrestrial to aquatic habitat within the genus (Barrett et al., 1993; Prieto et al., 2003). In this study, we generated RNA-seq data of R. sceleratus and analyzed this in relation to the RNA-seq data of Ranunculus bungei Steud., Ranunculus cantoniensis DC., and Ranunculus brotherusii Freyn (Chen et al., 2015). Our aim was to generate RNA-seq data of R. sceleratus and identify the orthologous genes among the four species. Links to deposited data RNA-seq data of R. sceleratus was deposited at NCBI sequence Reads Archive (no. SRP072329). It is in SRA format. ITS sequence of R. sceleratus was deposited in GenBank (no. {"type":"entrez-nucleotide","attrs":{"text":"KT957621","term_id":"949478889","term_text":"KT957621"}}KT957621). All the unigenes of R. sceleratus, data matrices of ITS and chloroplast DNA, sequences of the 3455 putative orthologous clusters identified using the program OrthoMCL, and 884 clusters after filters were deposited in figshare (https://figshare.com/s/f40d8f9bd8f894f2d630; sequences in fasta format). These data can be used for further transcriptome assembly, selective pressure estimation, phylogenetic analyses, etc.

Helicobacter pylori è un batterio patogeno che infetta e abita lo stomaco umano. La sua diffusione è ubiquitaria nel mondo ed esso è responsabile di varie patologie, sia gastriche che extra-gastriche. Vista l’estrema ostilità del suo habitat, H. pylori necessita di specifici adattamenti che lo rendono unico nella sua capacità di tollerare l’estrema acidità dello stomaco umano, oltre ad evitare la risposta immunitaria dell’ospite. In questa tesi verranno adottati degli approcci bioinformatici per cercare di individuare quali possano essere gli adattamenti e le caratteristiche del genoma di questo batterio correlati con la sopravvivenza nell’ambiente gastrico e l’adattamento all’ospite umano.

Many important crops have received little attention by the scientific community, either because they are not considered economically important or due to their large and complex genomes. De novo transcriptome assembly, using next-generation sequencing data, is an attractive option for the study of these orphan crops. In spite of the large amount of sequencing data that can be generated, there is currently a lack of tools which can effectively help molecular breeders and biologists to mine this type of information. Our goal was to develop a tool that enables molecular breeders, without extensive bioinformatics knowledge, to efficiently study de novo transcriptome data from any orphan crop (http://www.bioinformatics.nl/denovobrowser/db/species/index). The Orphan Crops Browser has been designed to facilitate the following tasks (1) search and identification of candidate transcripts based on phylogenetic relationships between orthologous sequence data from a set of related species and (2) design specific and degenerate primers for expression studies in the orphan crop of interest. To demonstrate the usability and reliability of the browser, it was used to identify the putative orthologues of 17 known lignin biosynthetic genes from maize and sugarcane in the orphan crop Miscanthus sinensis. Expression studies in miscanthus stem internode tissue differing in maturation were subsequently carried out, to follow the expression of these genes during lignification. Our results showed a negative correlation between lignin content and gene expression. The present data are in agreement with recent findings in maize and other crops, and it is further discussed in this paper. Electronic supplementary material The online version of this article (doi:10.1007/s11032-015-0430-2) contains supplementary material, which is available to authorized users.

Odorant receptors (ORs) interface animals with airborne chemical signals. They are under strong selection pressure and are therefore highly divergent in different taxa. Yet, some OR orthologs are highly conserved. These ORs may be tuned to odorants of broad importance, across species boundaries. Two widely distributed lepidopteran herbivores, codling moth Cydia pomonella (Tortricidae) feeding in apples and pears, and the African cotton leafworm Spodoptera littoralis (Noctuidae), a moth feeding on foliage of a wide range of herbaceous plants, both express a receptor ortholog, OR19, which shares 58% amino acid identity and 69% amino acid similarity. Following heterologous expression in the empty neuron system of Drosophila melanogaster, we show by single sensillum recordings that CpomOR19 and SlitOR19 show similar affinity to several substituted indanes. Tests with a series of compounds structurally related to 1-indanone show that 2-methyl-1-indanone, 2-ethyl-1-indanone, 3-methyl-1-indanone and 1-indanone elicit a strong response from both ORs. A keto group in position 1 is essential for biological activity and so are both rings of the indane skeleton. However, there is an important difference in steric complementary of the indane rings and the receptor. Methyl substituents on the benzene ring largely suppressed the response. On the other hand, alkyl substituents at position 2 and 3 of the five-membered ring increased the response indicating a higher complementarity with the receptor cavity, in both CpomOR19 and SlitOR19. Our results demonstrate a conserved function of an odorant receptor in two moths that are phylogenetically and ecologically distant. It is conceivable that a conserved OR is tuned to signals that are relevant for both species, although their ecological roles are yet unknown. Our finding demonstrates that functional characterization of ORs leads to the discovery of novel semiochemicals that have not yet been found through chemical analysis of odorants from insects and their associated host plants.

Background and aims Arachis batizocoi is a wild relative of cultivated peanut (A. hypogaea), an allotetraploid with an AABB genome. Arachis batizocoi was once considered the ancestral donor of the peanut B genome, but cytogenetics and DNA phylogenies have indicated a new genome classification, 'K'. These observations seem inconsistent with genetic studies and breeding that have shown that A. batizocoi can behave as a B genome. Methods The genetic behaviour, genome composition and phylogenetic position of A. batizocoi were studied using controlled hybridizations, induced tetraploidy, whole-genome in situ fluorescent hybridization (GISH) and molecular phylogenetics. Key results Sterile diploid hybrids containing AK genomes were obtained using A. batizocoi and the A genome species A. duranensis, A. stenosperma, A. correntina or A. villosa. From these, three types of AAKK allotetraploids were obtained, each in multiple independent polyploidy events. Induced allotetraploids were vigorous and fertile, and were hybridized to A. hypogaea to produce F1 hybrids. Even with the same parental combination, fertility of these F1 hybrids varied greatly, suggesting the influence of stochastic genetic or epigenetic events. Interestingly, hybrids with A. hypogaea ssp. hypogaea were significantly more fertile than those with the subspecies fastigiata. GISH in cultivated × induced allotetraploids hybrids (harbouring AABK genomes) and a molecular phylogeny using 16 intron sequences showed that the K genome is distinct, but more closely related to the B than to the A genome. Conclusions The K genome of A. batizocoi is more related to B than to the A genome, but is distinct. As such, when incorporated in an induced allotetraploid (AAKK) it can behave as a B genome in crosses with peanut. However, the fertility of hybrids and their progeny depends upon the compatibility of the A genome interactions. The genetic distinctness of A. batizocoi makes it an important source of allelic diversity in itself, especially in crosses involving A. hypogaea ssp. hypogaea.

Odorant receptors (ORs) interface animals with airborne chemical signals. They are under strong selection pressure and are therefore highly divergent in different taxa. Yet, some OR orthologs are highly conserved. These ORs may be tuned to odorants of broad importance, across species boundaries. Two widely distributed lepidopteran herbivores, codling moth Cydia pomonella (Tortricidae) feeding in apples and pears, and the African cotton leafworm Spodoptera littoralis (Noctuidae), a moth feeding on foliage of a wide range of herbaceous plants, both express a receptor ortholog, OR19, which shares 58% amino acid identity and 69% amino acid similarity. Following heterologous expression in the empty neuron system of Drosophila melanogaster, we show by single sensillum recordings that CpomOR19 and SlitOR19 show similar affinity to several substituted indanes. Tests with a series of compounds structurally related to 1-indanone show that 2-methyl-1-indanone, 2-ethyl-1-indanone, 3-methyl-1-indanone, and 1-indanone elicit a strong response from both ORs. A keto group in position 1 is essential for biological activity and so are both rings of the indane skeleton. However, there is an important difference in steric complementary of the indane rings and the receptor. Methyl substituents on the benzene ring largely suppressed the response. On the other hand, alkyl substituents at position 2 and 3 of the five-membered ring increased the response indicating a higher complementarity with the receptor cavity, in both CpomOR19 and SlitOR19. Our results demonstrate a conserved function of an odorant receptor in two moths that are phylogenetically and ecologically distant. It is conceivable that a conserved OR is tuned to signals that are relevant for both species, although their ecological roles are yet unknown. Our finding demonstrates that functional characterization of ORs leads to the discovery of novel semiochemicals that have not yet been found through chemical analysis of odorants from insects and their associated host plants.

Most of the gene regulation pathways data from biochemical and molecular experiments are drawn from humans or from species commonly used as experimental animal models. Accordingly, the software packages to analyse these data on the basis of specific gene identification codes (IDs) or accession numbers (AN) are not easy to apply to other organisms that are less characterized at the genomic level. Here, we have developed the Gene2Path programme which automatically searches pathway databases to analyse microarray data in an independent, species-specific way. We have illustrated the method with data obtained from an immune targeted rainbow trout microarray to search for orthologous pathways defined for other well known biological species, such as zebrafish, although the software can be applied to any other case or species of interest. The scripts and programme are available and free at the “GENE2PATH” web site http://gene2path.no-ip.org/cgi-bin/gene2path/index.cgi. A user guide and examples are provided with the package. The Gene2Path software allows the automated searching of NCBI databases and the straightforward visualization of the data retrieved based on a graphic network environment., We thank Mario García-Lacoba for his advice and helpful comments. This work was funded by Consejo Superior de Investigaciones Cientificas (project 2010-20E084) and by Ministerio de Economia y Competitividad, (MINECO) project AGL2010- 18454 of Spain. N. Ballesteros wants to thank the MINECO for a PhD student fellowship

A gene order database of 32 completely sequenced plastid genomes was developed. The data structure is formally identical to that of the feature tables in the major GenBank/EMBL/DDBJ databases. The quality of annotations was largely improved. A normalizing gene-labeling system across the complete plastid genomes was developed so that comparative studies are made available without having to go back to sequence analysis. Many incorrect coordinates of tRNA-encoding regions found in the major databases were corrected. We attempted to distinctively label tRNA genes with the anticodon sequence CAT, which encodes either the initiator tRNA, elongator tRNA, or Ile-tRNA. The database is available at http://www.rs.noda.tus.ac.jp/~kunisawa.

The mammalian target of rapamycine (mTOR) pathway is a key regulator of cellular growth, development, and ageing, and unraveling its control is essential for understanding life and death of biological organisms. A motif-discovery workbench including nine tools was used to identify transcription factors involved in five basic (Insulin, MAPK, VEGF, Hypoxia, and mTOR core) activities of the mTOR pathway. Discovered transcription factors are classified as “process-specific” or “pathway-ubiquitous” with highlights toward their regulating/regulated activities within the mTOR pathway. Our transcription regulation results will facilitate further research on investigating the control mechanism in mTOR pathway.

Diatoms are among the most diverse groups of phytoplankton in the ocean. Despite their widely recognized influence on ocean ecosystems and global biogeochemistry, little is known about the impact of this diversity on large-scale processes. Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three diatoms —Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries —to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. The three species shared 5583 clusters of orthologous genes based on OrthoMCL clustering of publically available diatom genomes. These clusters represent 30–54% of the predicted genes in each diatom genome. Less than 5% of genes within these core clusters displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Characterization of these finely tuned responses will help to better predict which types of diatoms will bloom under which sets of environmental factors.

Background With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure. Results Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/. Conclusions PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.

A widespread bacterium Serratia marcescens (family Enterobacteriaceae) is an opportunistic pathogen and exhibits multiple drug resistance. Active removal of antibiotics and other antimicrobials from the cells by efflux systems is one of the mechanisms responsible for microbial resistance to these compounds. Among enterobacteria, efflux systems of Escherichia coli and Salmonella enterica ser. Typhimurium have been studied most extensively. Few efflux systems that belong to different families have been reported for S. marcescens. In this review, we analyzed available literature about S. marcescens efflux systems and carried out the comparative analysis of the genes encoding the RND type systems in different Serratia species and in other enterobacteria. Bioinformatical analysis of the S. marcescens genome allowed us to identify the previously unknown efflux systems based on their homology with the relevant E. coli genes. Identification of additional efflux systems in S. marcescens genome will promote our understanding of the physiology of these bacteria, will detect new molecular mechanisms of resistance, and will reveal their resistance potential. © 2013 Pleiades Publishing, Ltd.

A widespread bacterium Serratia marcescens (family Enterobacteriaceae) is an opportunistic pathogen and exhibits multiple drug resistance. Active removal of antibiotics and other antimicrobials from the cells by efflux systems is one of the mechanisms responsible for microbial resistance to these compounds. Among enterobacteria, efflux systems of Escherichia coli and Salmonella enterica ser. Typhimurium have been studied most extensively. Few efflux systems that belong to different families have been reported for S. marcescens. In this review, we analyzed available literature about S. marcescens efflux systems and carried out the comparative analysis of the genes encoding the RND type systems in different Serratia species and in other enterobacteria. Bioinformatical analysis of the S. marcescens genome allowed us to identify the previously unknown efflux systems based on their homology with the relevant E. coli genes. Identification of additional efflux systems in S. marcescens genome will promote our understanding of the physiology of these bacteria, will detect new molecular mechanisms of resistance, and will reveal their resistance potential. © 2013 Pleiades Publishing, Ltd.

Background Aspartic proteases (APs) are a large family of proteolytic enzymes found in almost all organisms. In plants, they are involved in many biological processes, such as senescence, stress responses, programmed cell death, and reproduction. Prior to the present study, no grape AP gene(s) had been reported, and their research on woody species was very limited. Results In this study, a total of 50 AP genes (VvAP) were identified in the grape genome, among which 30 contained the complete ASP domain. Synteny analysis within grape indicated that segmental and tandem duplication events contributed to the expansion of the grape AP family. Additional analysis between grape and Arabidopsis demonstrated that several grape AP genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes arose before the divergence of grape and Arabidopsis. Phylogenetic relationships of the 30 VvAPs with the complete ASP domain and their Arabidopsis orthologs, as well as their gene and protein features were analyzed and their cellular localization was predicted. Moreover, expression profiles of VvAP genes in six different tissues were determined, and their transcript abundance under various stresses and hormone treatments were measured. Twenty-seven VvAP genes were expressed in at least one of the six tissues examined; nineteen VvAPs responded to at least one abiotic stress, 12 VvAPs responded to powdery mildew infection, and most of the VvAPs responded to SA and ABA treatments. Furthermore, integrated synteny and phylogenetic analysis identified orthologous AP genes between grape and Arabidopsis, providing a unique starting point for investigating the function of grape AP genes. Conclusions The genome-wide identification, evolutionary and expression analyses of grape AP genes provide a framework for future analysis of AP genes in defining their roles during stress response. Integrated synteny and phylogenetic analyses provide novel insight into the functions of less well-studied genes using information from their better understood orthologs.

The relationship between genome characteristics and several human diseases has been a central research goal in genomics. Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering. published

Natural variants of cerato-platanin (CP), a pathogen associated molecular pattern (PAMP) protein produced by Ceratocystis platani (the causal agent of the plane canker stain), have been found to be produced by other four species of the genus Ceratocystis, including five clones of Ceratocystis fimbriata isolated from different hosts. All these fungal strains were known to be pathogenic to plants with considerable importance in agriculture, forestry, and as ornamental plants. The putative premature proteins were deduced on the basis of the nucleotide sequence of genes orthologous to the cp gene of C. platani; the deduced premature proteins of Ceratocystis populicola and Ceratocystis variospora reduced the total identity of all the others from 87.3% to 60.3%. Cerato-populin (Pop1), the CP-orthologous protein produced by C. populicola, was purified and characterized. Pop1 was a well-structured alfa/beta protein with a different percentage of the alfa-helix than CP, and it self-assembled in vitro in ordered aggregates. Moreover, Pop1 behaved as PAMP, since it stimulated poplar leaf tissues to activate defence responses able to reduce consistently the C. populicola growth.

Background A genome-wide comparative analysis of human and mouse gene expression patterns was performed in order to evaluate the evolutionary divergence of mammalian gene expression. Tissue-specific expression profiles were analyzed for 9,105 human-mouse orthologous gene pairs across 28 tissues. Expression profiles were resolved into species-specific coexpression networks, and the topological properties of the networks were compared between species. Results At the global level, the topological properties of the human and mouse gene coexpression networks are, essentially, identical. For instance, both networks have topologies with small-world and scale-free properties as well as closely similar average node degrees, clustering coefficients, and path lengths. However, the human and mouse coexpression networks are highly divergent at the local level: only a small fraction ( Conclusion The dissonance between global versus local network divergence suggests that the interspecies similarity of the global network properties is of limited biological significance, at best, and that the biologically relevant aspects of the architectures of gene coexpression are specific and particular, rather than universal. Nevertheless, there is substantial evolutionary conservation of the local network structure which is compatible with the notion that gene coexpression networks are subject to purifying selection.

Apresentação efectuada nas "11as Jornadas de Biologia de Leveduras Professor Nicolau van Uden", realizadas na Escola Superior Agrária de Bragança, em Maio de 2003., Glycerol, besides acting as compatible solute, accumulated by S. cerevisiae to counteract the low aw stress environments, is a key compound in the regulation of multiple metabolic pathways. Most of the genes involved in glycerol consumption and production are now available for this yeast. Furthermore, three genes had been described as involved in glycerol uptake as well as export, respectively, GUP1/21 and FPS123. Altogether, these genes regulate intracellular glycerol levels in a way not yet completely unveiled. Some of these mechanisms, like the stimulation of glycerol production and accumulation under stress growth conditions and the presence of constituvely active transport for glycerol, are common to a series of other yeasts4. Being so, we decided to search for some of the genes from glycerol uptake and metabolism in some of those yeasts. We began using the partial genome sequencing available for several yeasts from the Génolevures Program. Further ahead we included Candida albicans from Stanford Genome Sequencing Data Base. Our search focused on GUP1/2, FPS1, GPD1/2 (glycerol 3-P dehydrogenase) and GUT1 (glycerol kinase) genes. From this search we choosed the sequences with higher similarity, which were present in Candida tropicalis, Kluveryomyces marxianus, Kluveryomyces lactis, Kluveryomyces thermotolerans, Pichia angusta, Pichia sorbitophila and Zigossacharomyces rouxii, besides Candida albicans. The entire sequences of the genes were obtained using standard procedures, like primer walking sequencing and RACE (rapid amplification of cDNA ends). Genes were obtained by PCR and complementation analysis was done. Sequences were used to create/enlarge gene families, to explore the evolutionary relationship of these species and to establish the putative relation between sequence and function.

Finding orthologous genes among multiple sequenced genomes is a primary step in comparative genomics studies. With the number of sequenced genomes increasing exponentially, comparative genomics becomes more powerful than ever for genomic analysis. However, the very large number of genomes in need of analysis makes conventional orthology prediction methods incapable of this task. Thus, an ultrafast tool is urgently needed. Here, we present PorthoMCL, a fast tool for finding orthologous genes among a very large number of genomes. PorthoMCL can be run on a single machine or in parallel on computer clusters. We have demonstrated PorthoMCL’s capability by identifying orthologs in 2,758 prokaryotic genomes. The results are available for download at: http://ehsun.me/go/porthomcl/ . PorthoMCL is a fast and easy to run tool for identifying orthology among any number of genomes with minimal requirements. PorthoMCL will facilitate comparative genomics analysis with increasing number of available genomes thanks to the rapidly evolving sequencing technologies.