142 research outputs found
Evolutionary changes in the euglenoid chloroplast
No full textThe chloroplasts of three exemplar taxa of photosynthetic euglenoids, have been sequenced and compared, providing an overview of chloroplast evolution in this highly diverse group of organisms which acquired their chloroplast through secondary endosymbiosis. The use of synteny mapping has shown that the chloroplast genomes of euglenoids are not fully collinear, and significant gene rearrangements have occurred across the lineage. The gene rearrangements however, have occurred largely through the repositioning of conserved gene clusters. Gene content among the taxa was similar with only a few variations noted including rpl32, psaI, psaM, rrn5, rpoA and roaA genes. Comparisons between the euglenoid chloroplast genomes also highlighted significant differences in genome sizes, due mainly to expansion/shrinkage of intergenic space and an overall increase in intron number. Further comparisons with the chloroplast genome of Euglena gracilis and green algal taxa provided insight into chloroplast genome evolution within the Euglenophyta. Phylogenies based upon 55 chloroplast genes are nearly identical to those based on nuclear encoded genes, indicating similar evolutionary pathways. Sequence comparisons and phylogenetic analyses have also provided evidence that the putative green algal chloroplast donor lineage was a scaly green algal flagellate belonging to the Prasinophyceae and that the chloroplast was acquired through a single endosymbiotic event.Thesis (M.S.)--Michigan State University. Plant Biology, 2011Includes bibliographical references (pages 64-71
Extensive genome heterogeneity leads to preferential allele expression and copy number‐dependent expression in cultivated potato
No full textAdditional file 1: Figure S1. of Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.
No full textWork flow used for assemblies allowing incorporation of reads from all 5 tissue libraries while removing redundancy. Figure S2. Distributions of the number of isoforms for each transcript. Figure S3. SNP discovery pipeline with reads aligned to P. axillaris reference transcriptome assembly. Figure S4. Gene Ontology (GO) categories of the unigenes and unigenes with SNPs. Figure S5. Gene Ontology (GO) categories of the unigenes with more than ten SNPs. Distribution of the GO categories assigned to the unigenes were annotated in three categories: cellular components, molecular functions, and biological processes. Table S1. Primer sequences used for SNP validation by Sanger sequencing. Table S2. Primer sequences for CAPS markers developed from plastochron-related genes. (DOCX 782Â kb
Additional file 6: of Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.
No full textSupplemental Dataset 5. SSR primers derived from P. axillaris transcriptome. (XLSX 414Â kb
Additional file 4: of Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.
No full textSupplemental Dataset 3. Gene Ontology annotations of representative transcripts. (XLS 16720Â kb
Additional file 3: of Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.
No full textSupplemental Dataset 2. OrthoMCL clusters across three Petunia species. (XLSM 1433Â kb
Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides
No full textCalotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications
Continuous-time System Identification: A Bilinear Optimization Approach
No full textIn the noiseless case, the identification of a grey-box model can be posed as a feasibility problem, i.e. determining if existent - and if so - finding a parameter vector such that the parametric model equals the actual model (or its associated input-output data). Being that in this thesis we are interested in continuous-time grey-box identification, we shall be dealing with models that allow for forming a direct relationship with physical meaningful quantities. Such models include the state space representation and the matrix differential equation. In general, identifying such grey-box models turns out to be a non-convex problem. In this thesis, we initially review a framework which allows us to solve feasibility problems which have bilinear constraints. It turns out that most of the aforementioned non-convexities can be captured into a single bilinear matrix equation. However, the resulting feasibility problem, including the bilinear matrix equations, makes the overall search for the actual parameter vector NP-hard. In order to come up with numerical tractable algorithms, we use a heuristic known as Sequential Convex Relaxation to relax the bilinear equality constraints. This iterative scheme is flexible enough to allow for additional (in)equality constraints, possibly resembling any other physical constraints. We explore two different approaches to identify both the state space model and the matrix differential equation; one, by directly identifying the model from the given frequency response function; two, by first identifying a black-box model before performing a small scale optimization problem, transforming the black-box model such that it fits the grey-box parameterization. In addition, we present a novel method which uses the Power Spectral Density to estimate a 2nd order model. All methods are numerically validated.Mechanical Engineering | Systems and Contro
Genome Assembly and Annotation of the Medicinal Plant<i>Calotropis gigantea</i>, a Producer of Anticancer and Antimalarial Cardenolides
No full textAbstractCalotropis gigantea produces specialized secondary metabolites known as cardenolides, which have anticancer and antimalarial properties. Although transcriptomic studies have been conducted in other cardenolide-producing species, no nuclear genome assembly for an Asterid cardenolide-producing species has been reported to date. A high-quality de novo assembly was generated for C. gigantea, representing 157,284,427 bp with an N50 scaffold size of 805,959 bp, for which quality assessments indicated a near complete representation of the genic space. Transcriptome data in the form of RNA-sequencing libraries from a developmental tissue series was generated to aid the annotation and construction of a gene expression atlas. Using an ab initio and evidence-driven gene annotation pipeline, 18,197 high-confidence genes were annotated. Homologous and syntenic relationships between C. gigantea and other species within the Apocynaceae family confirmed previously identified evolutionary relationships, and suggest the emergence or loss of the specialized cardenolide metabolites after the divergence of the Apocynaceae subfamilies. The C. gigantea genome assembly, annotation, and RNA-sequencing data provide a novel resource to study the cardenolide biosynthesis pathway, especially for understanding the evolutionary origin of cardenolides and the engineering of cardenolide production in heterologous organisms for existing and novel pharmaceutical applications.</jats:p
Data from: De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin
No full textCamptotheca acuminata is 1 of a limited number of species that produce camptothecin, a pentacyclic quinoline alkaloid with anti-cancer activity due to its ability to inhibit DNA topoisomerase. While transcriptome studies have been performed previously with various camptothecin-producing species, no genome sequence for a camptothecin-producing species is available to date. We generated a high-quality de novo genome assembly for C. acuminata representing 403 174 860 bp on 1394 scaffolds with an N50 scaffold size of 1752 kbp. Quality assessments of the assembly revealed robust representation of the genome sequence including genic regions. Using a novel genome annotation method, we annotated 31 825 genes encoding 40 332 gene models. Based on sequence identity and orthology with validated genes from Catharanthus roseus as well as Pfam searches, we identified candidate orthologs for genes potentially involved in camptothecin biosynthesis. Extensive gene duplication including tandem duplication was widespread in the C. acuminata genome, with 2571 genes belonging to 997 tandem duplicated gene clusters. To our knowledge, this is the first genome sequence for a camptothecin-producing species, and access to the C. acuminata genome will permit not only discovery of genes encoding the camptothecin biosynthetic pathway but also reagents that can be used for heterologous expression of camptothecin and camptothecin analogs with novel pharmaceutical applications
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