Article Comparative Transcriptome Analyses Reveal Core Parasitism Genes and Suggest Gene Duplication and Repurposing as Sources of Structural Novelty

Abstract The origin of novel traits is recognized as an important process underlying many major evolutionary radiations. We studied the genetic basis for the evolution of haustoria, the novel feeding organs of parasitic flowering plants, using comparative transcriptome sequencing in three species of Orobanchaceae. Around 180 genes are upregulated during haustorial development following host attachment in at least two species, and these are enriched in proteases, cell wall modifying enzymes, and extracellular secretion proteins. Additionally, about 100 shared genes are upregulated in response to haustorium inducing factors prior to host attachment. Collectively, we refer to these newly identified genes as putative "parasitism genes." Most of these parasitism genes are derived from gene duplications in a common ancestor of Orobanchaceae and Mimulus guttatus, a related nonparasitic plant. Additionally, the signature of relaxed purifying selection and/or adaptive evolution at specific sites was detected in many haustorial genes, and may play an important role in parasite evolution. Comparative analysis of gene expression patterns in parasitic and nonparasitic angiosperms suggests that parasitism genes are derived primarily from root and floral tissues, but with some genes co-opted from other tissues. Gene duplication, often taking place in a nonparasitic ancestor of Orobanchaceae, followed by regulatory neofunctionalization, was an important process in the origin of parasitic haustoria

Factors affecting the efficiency of Rhizobium rhizogenes root transformation of the root parasitic plant Triphysaria versicolor and its host Arabidopsis thaliana

Abstract Background Rhizobium rhizogenes transformation is commonly used to generate transgenic roots traditionally called hairy roots, for both investigative and commercial applications. While fertile plants can be regenerated from transgenic roots, the transgenic roots are more typically used directly, either to investigate root biology or to produce valuable secondary metabolites. Hairy roots have been particularly useful for genetic studies of rhizosphere interactions; including the recognition of host plant roots by the roots of parasitic angiosperms. Results In this manuscript we analyzed various environmental, nutritional and procedural conditions for their effects on transformation of the model hemi-parasitic plant Triphysaria versicolor and Arabidopsis thaliana, one of its hosts. We first examined the effects of media, gelling agents and co-incubation times on Triphysaria root transformation and determined that while all three affected transformation rates, the media were the most significant. Once those primary conditions were fixed, we examined the roles of seedling age, explant type, acetosyringone, temperature and illumination on Triphysaria hairy root transformation rates. Using the optimized procedure approximately 70% of Triphysaria seedlings developed transgenic roots as judged by expression of YFP. These conditions were then used to transform Arabidopsis and similar transformation rates were obtained. Conclusions Analyses of root transformation factors provides a method recovering transgenic roots from both parasitic plants and their hosts at high frequency. In addition to providing an effective in vitro approach for genetic investigations of parasitic plant-host plant interactions, these results are applicable to genetic studies of non-parasitic plants as well

Internet of things (IoT) for smart agriculture: Assembling and assessment of a low-cost IoT system for polytunnels.

Internet of things (IoT) applications in smart agricultural systems vary from monitoring climate conditions, automating irrigation systems, greenhouse automation, crop monitoring and management, and crop prediction, up to end-to-end autonomous farm management systems. One of the main challenges to the advancement of IoT systems for the agricultural domain is the lack of training data under operational environmental conditions. Most of the current designs are based on simulations and artificially generated data. Therefore, the essential first step is studying and understanding the finely tuned and highly sensitive mechanism plants have developed to sense, respond, and adapt to changes in their environment, and their behavior under field and controlled systems. Therefore, this study was designed to achieve two specific objectives; to develop low-cost IoT components from basic building blocks, and to study the performance of the developed systems, and generate real-time experimental data, with and without plants. Low-cost IoT devices developed locally were used to convert existing basic polytunnels to semi-controlled and monitoring-only polytunnels. Their performances were analyzed and compared with each other based on several matrices while maintaining the planted tomato variety and agronomic practices similar. The developed system performed as expected suggesting the possibility of commercial applications and research purposes

Universal barcoding regions, rbcL, matK and trnH-psbA do not discriminate Cinnamomum species in Sri Lanka.

The genus Cinnamomum consists of about 250 species spread globally. Out of these, C. verum (C. zeylanicum), also known as true cinnamon or Ceylon cinnamon, has gained worldwide attention due to its culinary uses and medicinal values. Sri Lanka is the largest true cinnamon producer in the world and accounts for about 80-90% of global production. Other than the cultivated species, Sri Lankan natural vegetation is home to seven endemic wild species of the genus Cinnamomum. While these are underutilized, proper identification and characterization are essential steps in any sustainable conservation and utilization strategies. Currently, species identification is purely based on morphological traits, and intraspecific diversity has made it more challenging. In this study, all the eight Cinnamomum species found in Sri Lanka, C. capparu-coronde, C. citriodorum C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum, C. sinharajaense, and C. verum were collected in triplicates and identified using typical morphological traits. DNA extracted with the same collection was assessed with universal barcoding regions, rbcL, matK, and trnH-psbA. While no intraspecific sequence differences were observed in C. citriodorum, C. rivulorum, and C. verum, the others had polymorphic sites in one, two, or all regions assessed. Interestingly, two individuals of C. sinharajaense had identical barcodes to the cultivated species C. verum, while the other one had one variable cite in matK region and three cites in trnH-psbA reigon. Further, one C. dubium and one C. capparu-coronde accession each had identical, rbcL, and trnH-psbA sequences while those had only a single nucleotide variation observed in matK region. Overall, the phylogeny of Cinnamomum species found in Sri Lanka could not be completely resolved with DNA barcoding regions studied

Nucleotide diversity in ITS regions among 10 <i>Cinnamomum</i> species.

Nucleotide diversity in ITS regions among 10 Cinnamomum species.</p

The nucleotide diversity (Pi) calculated for the chloroplast genomes of <i>Cinnamomum</i> species.

The nucleotide diversity (Pi) calculated for the chloroplast genomes of Cinnamomum species.</p

SSR type, location in the genome, and the count among <i>Cinnamomum</i> species.

SSR type, location in the genome, and the count among Cinnamomum species.</p

Sequence variation in two parts of the <i>ycf1</i> gene among <i>Cinnamomum</i> species.

Sequence variation in two parts of the ycf1 gene among Cinnamomum species.</p

Primers used to amplify highly varying regions of the chloroplast genome.

Primers used to amplify highly varying regions of the chloroplast genome.</p