De novo sequencing of the Hypericum perforatum L. flower transcriptome to identify potential genes that are related to plant reproduction sensu lato

Background: St. John's wort (Hypericum perforatum L.) is a medicinal plant that produces important metabolites with antidepressant and anticancer activities. Recently gained biological information has shown that this species is also an attractive model system for the study of a naturally occurring form of asexual reproduction called apomixis, which allows cloning plants through seeds. In aposporic gametogenesis, one or multiple somatic cells belonging to the ovule nucellus change their fate by dividing mitotically and developing functionally unreduced embryo sacs by mimicking sexual gametogenesis. Although the introduction of apomixis into agronomically important crops could have revolutionary implications for plant breeding, the genetic control of this mechanism of seed formation is still not well understood for most of the model species investigated so far. We used Roche 454 technology to sequence the entire H. perforatum flower transcriptome of whole flower buds and single flower verticils collected from obligately sexual and unrelated highly or facultatively apomictic genotypes, which enabled us to identify RNAs that are likely exclusive to flower organs (i.e., sepals, petals, stamens and carpels) or reproductive strategies (i.e., sexual vs. apomictic). Results: Here we sequenced and annotated the flower transcriptome of H. perforatum with particular reference to reproductive organs and processes. In particular, in our study we characterized approximately 37,000 transcripts found expressed in male and/or female reproductive organs, including tissues or cells of sexual and apomictic flower buds. Ontological annotation was applied to identify major biological processes and molecular functions involved in flower development and plant reproduction. Starting from this dataset, we were able to recover and annotate a large number of transcripts related to meiosis, gametophyte/gamete formation, and embryogenesis, as well as genes that are exclusively or preferentially expressed in sexual or apomictic libraries. Real-Time RT-qPCR assays on pistils and anthers collected at different developmental stages from accessions showing alternative modes of reproduction were used to identify potential genes that are related to plant reproduction sensu lato in H. perforatum. Conclusions: Our approach of sequencing flowers from two fully obligate sexual genotypes and two unrelated highly apomictic genotypes, in addition to different flower parts dissected from a facultatively apomictic accession, enabled us to analyze the complexity of the flower transcriptome according to its main reproductive organs as well as for alternative reproductive behaviors. Both annotation and expression data provided original results supporting the hypothesis that apomixis in H. perforatum relies upon spatial or temporal mis-expression of genes acting during female sexual reproduction. The present analyses aim to pave the way toward a better understanding of the molecular basis of flower development and plant reproduction, by identifying genes or RNAs that may differentiate or regulate the sexual and apomictic reproductive pathways in H. perforatum

Trade-offs between personal immunity and reproduction in the burying beetle, N. vespilloides

We know that parental investment and immune investment are costly processes, but it is unclear which trait will be prioritised when both may be required. Here we address this question using the burying beetle Nicrophorus vespilloides, carrion breeders that exhibit biparental care of young. Our results show that immunosuppression occurs during provision of parental care. We measured Phenoloxidase (PO) on Day 1-8 of the breeding bout and results show a clear decrease in PO immediately from presentation of the breeding resource onwards. Having established baseline immune investment during breeding we then manipulated immune investment at different times by applying a wounding challenge. Beetles were wounded prior to and during the parental care period and reproductive investment quantified. Different effects on reproductive output occur depending on the timing of wounding. Challenging the immune system with wounding prior to breeding does not affect reproductive output and subsequent Lifetime Reproductive Success (LRS). LRS is also unaffected by applying an immune elicitor prior to breeding, though different arms of the immune system are up/downregulated, perhaps indicating a trade-off between cellular and humoral immunity. In contrast, wounding during breeding reduces reproductive output and to the greatest extent if the challenge is applied early in the breeding bout. Despite being immunosuppressed, breeding beetles can still respond to wounding by increasing PO, albeit not to pre-breeding levels. This upregulation of PO during breeding may affect parental investment, resulting in a reduction in reproductive output. The potential role of juvenile hormone in controlling this trade-off is discussed

Bacterial feeding induces changes in immune-related gene expression and has trans-generational impacts in the cabbage looper (Trichoplusia ni)

<p>Abstract</p> <p>Background</p> <p>Poly- and oligophagous insects are able to feed on various host plants with a wide range of defense strategies. However, diverse food plants are also inhabited by microbiota differing in quality and quantity, posing a potential challenge for immune system mediated homeostasis in the herbivore. Recent studies highlight the complex interactions between environmentally encountered microorganisms and herbivorous insects, pointing to a potential adaptational alteration of the insects' physiology. We performed a differential gene expression analysis in whole larvae and eggs laid by parents grown on different diets to identify potential novel genes related to elevated microbial content in the caterpillars' food.</p> <p>Results</p> <p>We used GeneFishing, a novel differential display method, to study the effects of dietary bacteria on the general gene expression in different life stages and tissues of the cabbage looper (<it>Trichoplusia ni</it>). We were able to visualize several hundred transcripts on agarose gels, one fifth of which were differentially expressed between treatments. The largest number of differentially expressed genes was found in defense-related processes (13) and in recognition and metabolism (16). 21 genes were picked out and further tested for differential gene expression by an independent method (qRT-PCR) in various tissues of larvae grown on bacterial and bacteria-free diet, and also in adults. We detected a number of genes indicative of an altered physiological status of the insect, depending on the diet, developmental stage and tissue.</p> <p>Conclusion</p> <p>Changes in immune status are accompanied by specific changes in the transcript levels of genes connected to metabolism and homeostasis of the organism. Our findings show that larval feeding on bacteria-rich diet leads to substantial gene expression changes, potentially resulting in a reorganization of the insects' metabolism to maintain organismal homeostasis, not only in the larval but also in the adult stage. Furthermore, differences in gene expression levels can also be seen in the next generation, strongly influenced by parental diet.</p

Transcriptome analysis of the sex pheromone gland of the noctuid moth Heliothis virescens

<p>Abstract</p> <p>Background</p> <p>The chemical components of sex pheromones have been determined for more than a thousand moth species, but so far only a handful of genes encoding enzymes responsible for the biosynthesis of these compounds have been identified. For understanding the evolution of moth sexual communication, it is essential to know which genes are involved in the production of specific pheromone components and what controls the variation in their relative frequencies in the pheromone blend. We used a transcriptomic approach to characterize the pheromone gland of the Noctuid moth <it>Heliothis virescens</it>, an important agricultural pest, in order to obtain substantial general sequence information and to identify a range of candidate genes involved in the pheromone biosynthetic pathway.</p> <p>Results</p> <p>To facilitate identifying sets of genes involved in a broad range of processes and to capture rare transcripts, we developed our majority of ESTs from a normalized cDNA library of <it>Heliothis virescens </it>pheromone glands (PG). Combining these with a non-normalized library yielded a total of 17,233 ESTs, which assembled into 2,082 contigs and 6,228 singletons. Using BLAST searches of the NR and Swissprot databases we were able to identify a large number of putative unique gene elements (unigenes), which we compared to those derived from previous transcriptomic surveys of the larval stage of <it>Heliothis virescens</it>. The distribution of unigenes among GO Biological Process functional groups shows an overall similarity between PG and larval transcriptomes, but with distinct enrichment of specific pathways in the PG. In addition, we identified a large number of candidate genes in the pheromone biosynthetic pathways.</p> <p>Conclusion</p> <p>These data constitute one of the first large-scale EST-projects for Noctuidae, a much-needed resource for exploring these pest species. Our analysis shows a surprisingly complex transcriptome and we identified a large number of potential pheromone biosynthetic pathway and immune-related genes that can be applied to population and systematic studies of <it>Heliothis virescens </it>and other Noctuidae.</p

Measuring the Overall Complexity of Graphical and Textual IEC 61131-3 Control Software

Software implements a significant proportion of functionality in factory automation. Thus, efficient development and the reuse of software parts, so-called units, enhance competitiveness. Thereby, complex control software units are more difficult to understand, leading to increased development, testing and maintenance costs. However, measuring complexity is challenging due to many different, subjective views on the topic. This paper compares different complexity definitions from literature and considers with a qualitative questionnaire study the complexity perception of domain experts, who confirm the importance of objective measures to compare complexity. The paper proposes a set of metrics that measure various classes of software complexity to identify the most complex software units as a prerequisite for refactoring. The metrics include complexity caused by size, data structure, control flow, information flow and lexical structure. Unlike most literature approaches, the metrics are compliant with graphical and textual languages from the IEC 61131-3 standard. Further, a concept for interpreting the metric results is presented. A comprehensive evaluation with industrial software from two German plant manufacturers validates the metrics' suitability to measure complexity.Comment: 8 pages, https://ieeexplore.ieee.org/abstract/document/9444196

Phylogenetic relatedness and host plant growth form influence gene expression of the polyphagous comma butterfly (Polygonia c-album)

<p>Abstract</p> <p>Background</p> <p>The mechanisms that shape the host plant range of herbivorous insect are to date not well understood but knowledge of these mechanisms and the selective forces that influence them can expand our understanding of the larger ecological interaction. Nevertheless, it is well established that chemical defenses of plants influence the host range of herbivorous insects. While host plant chemistry is influenced by phylogeny, also the growth forms of plants appear to influence the plant defense strategies as first postulated by Feeny (the "plant apparency" hypothesis). In the present study we aim to investigate the molecular basis of the diverse host plant range of the comma butterfly (<it>Polygonia c-album</it>) by testing differential gene expression in the caterpillars on three host plants that are either closely related or share the same growth form.</p> <p>Results</p> <p>In total 120 genes were identified to be differentially expressed in <it>P. c-album </it>after feeding on different host plants, 55 of them in the midgut and 65 in the restbody of the caterpillars. Expression patterns could be confirmed with an independent method for 14 of 27 tested genes. Pairwise similarities in upregulation in the midgut of the caterpillars were higher between plants that shared either growth form or were phylogenetically related. No known detoxifying enzymes were found to be differently regulated in the midgut after feeding on different host plants.</p> <p>Conclusion</p> <p>Our data suggest a complex picture of gene expression in response to host plant feeding. While each plant requires a unique gene regulation in the caterpillar, both phylogenetic relatedness and host plant growth form appear to influence the expression profile of the polyphagous comma butterfly, in agreement with phylogenetic studies of host plant utilization in butterflies.</p