De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum)

<p>Abstract</p> <p>Background</p> <p>Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, <it>Fagopyrum esculentum </it>and <it>F. tataricum</it>, belong to the order Caryophyllales - a large group of flowering plants with uncertain evolutionary relationships. <it>F. esculentum </it>(common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations <it>Fagopyrum </it>species have not been the subject of large-scale sequencing projects.</p> <p>Results</p> <p>Normalized cDNA corresponding to genes expressed in flowers and inflorescences of <it>F. esculentum </it>and <it>F. tataricum </it>was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for <it>F. esculentum</it>) and 229 (<it>F. tataricum</it>) thousands of reads with average length of 341-349 nucleotides. <it>De novo </it>assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences.</p> <p>Conclusions</p> <p>454 transcriptome sequencing and <it>de novo </it>assembly was performed for two congeneric flowering plant species, <it>F. esculentum </it>and <it>F. tataricum</it>. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.</p

Transcriptome Analysis of the Oriental Fruit Fly (Bactrocera dorsalis)

The oriental fruit fly, Bactrocera dorsalis (Hendel), is one of the most economically important pests in the world, causing serious damage to fruit production. However, lack of genetic information on this organism is an obstacle to understanding the mechanisms behind its development and its ability to resist insecticides. Analysis of the B. dorsalis transcriptome and its expression profile data is essential to extending the genetic information resources on this species, providing a shortcut that will support studies on B. dorsalis.We performed de novo assembly of a transcriptome using short read sequencing technology (Illumina). The results generated 484,628 contigs, 70,640 scaffolds, and 49,804 unigenes. Of those unigenes, 27,455 (55.13%) matched known proteins in the NCBI database, as determined by BLAST search. Clusters of orthologous groups (COG), gene orthology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to better understand the functions of these unigenes. Genes related to insecticide resistance were analyzed in additional detail. Digital gene expression (DGE) libraries showed differences in gene expression profiles at different developmental stages (eggs, third-instar larvae, pupae, and adults). To confirm the DGE results, the expression profiles of six randomly selected genes were analyzed.This transcriptome greatly improves our genetic understanding of B. dorsalis and makes a huge number of gene sequences available for further study, including both genes of known importance and genes of unknown function. The DGE data provide comprehensive insight into gene expression profiles at different developmental stages. This facilitates the study of the role of each gene in the developmental process and in insecticide resistance

Adaptation and Convergent Evolution within the Jamesonia-Eriosorus Complex in High-Elevation Biodiverse Andean Hotspots

The recent uplift of the tropical Andes (since the late Pliocene or early Pleistocene) provided extensive ecological opportunity for evolutionary radiations. We test for phylogenetic and morphological evidence of adaptive radiation and convergent evolution to novel habitats (exposed, high-altitude páramo habitats) in the Andean fern genera Jamesonia and Eriosorus. We construct time-calibrated phylogenies for the Jamesonia-Eriosorus clade. We then use recent phylogenetic comparative methods to test for evolutionary transitions among habitats, associations between habitat and leaf morphology, and ecologically driven variation in the rate of morphological evolution. Páramo species (Jamesonia) display morphological adaptations consistent with convergent evolution in response to the demands of a highly exposed environment but these adaptations are associated with microhabitat use rather than the páramo per se. Species that are associated with exposed microhabitats (including Jamesonia and Eriorsorus) are characterized by many but short pinnae per frond whereas species occupying sheltered microhabitats (primarily Eriosorus) have few but long pinnae per frond. Pinnae length declines more rapidly with altitude in sheltered species. Rates of speciation are significantly higher among páramo than non-páramo lineages supporting the hypothesis of adaptation and divergence in the unique Páramo biodiversity hotspot

Deciduous Trees and the Application of Universal DNA Barcodes: A Case Study on the Circumpolar Fraxinus

The utility of DNA barcoding for identifying representative specimens of the circumpolar tree genus Fraxinus (56 species) was investigated. We examined the genetic variability of several loci suggested in chloroplast DNA barcode protocols such as matK, rpoB, rpoC1 and trnH-psbA in a large worldwide sample of Fraxinus species. The chloroplast intergenic spacer rpl32-trnL was further assessed in search for a potentially variable and useful locus. The results of the study suggest that the proposed cpDNA loci, alone or in combination, cannot fully discriminate among species because of the generally low rates of substitution in the chloroplast genome of Fraxinus. The intergenic spacer trnH-psbA was the best performing locus, but genetic distance-based discrimination was moderately successful and only resulted in the separation of the samples at the subgenus level. Use of the BLAST approach was better than the neighbor-joining tree reconstruction method with pairwise Kimura's two-parameter rates of substitution, but allowed for the correct identification of only less than half of the species sampled. Such rates are substantially lower than the success rate required for a standardised barcoding approach. Consequently, the current cpDNA barcodes are inadequate to fully discriminate Fraxinus species. Given that a low rate of substitution is common among the plastid genomes of trees, the use of the plant cpDNA “universal” barcode may not be suitable for the safe identification of tree species below a generic or sectional level. Supplementary barcoding loci of the nuclear genome and alternative solutions are proposed and discussed

Solution for renewable future

Nowadays renewable energy sources are actively promoted as the most sustainable types of power to drive electricity generation of the future. Distributed generation with the use of wind turbines, solar panel, and biological fuel may become an answer to the numerous challenges which large power grids are facing. But integration of renewable energy based generation facilities requires not only availability of special technical means but also establishing of new types of trading patterns and platforms are necessary. This article provides the concept of smart billing system which allows to involve single households to the progressive type of energy consumption and generation and creates the new type of energy system and market participant – prosumer. Two types of billing approaches are suggested for households equipped with renewable energy sources based generation facilities. The first one implies that generated energy is consumed by the household itself and the second one implies that surplus of generated energy is sold to the grid. As calculation has shown the first pattern is beneficial for small facilities which in overall don’t have a large surplus in generation over consumption. And the second one is beneficial for those who generate more than they consume

HEART REMODELING IN OVERWEIGHT AND OBESITY WITH CARDIAC COMORBIDITIES

Aim. To assess structural geometric and functional disorders of the heart in males with coronary heart disease (CHD) comorbid with arterial hypertension (AH) and with visceral abdominal obesity, and to evaluate the grade of association of epicardial fat thickness (EFT) with cardiometabolic risk factors (RF).Material and methods. Totally, 90 in-patients included, males with AH and CHD and with metabolically unhealthy phenotype (MUP) at the age 61,2±1,7 y. o. with normal bodyweight (n=29) — 1 group, overweight (n=21) — 2 group, and obese (n=30) — 3 group, and 30 persons with metabolically healthy phenotype. All patients underwent anthropometric screening, calculation of visceral obesity index (VAI) and insulin resistance (HOMA-IR); lipid profile was assessed, and by the data from echocardiography the myocardial mas index (MMI) was evaluated, and EFT, the characteristics of the left ventricle hypertrophy (LVH) were counted and of diastolic dysfunction (DD).Results. The presence of obesity led to increase of metabolic RF in obese patients. Most informative were indexes as VAI (4,47±0,27; p&lt;0,001) and НОМА-IR (5,12±0,32; p&lt;0,001). In obese patients there was association of MMI and EFT (r=0,81, p&lt;0,001), predominance of concentric LVH with formation of restrictive DD. Regardless the level of abdominal obesity, there was increase of EFT in MUP patients, and the relation was confirmed to the main metabolic RF, as with structural geometric parameters of the heart.Conclusion. Cardiological patients with AH and CHD in MUP had increased levels of markers of anomalous phenotype, the values increased with obesity. In obese patinents (groups II, III) as a predominant trend there was concentric LVH, restrictive DD, significant increase of preload and left atrium volume. The significance of EFT was confirmed as a marker of visceral obesity. Study results show that obesity in comorbidity patients with cardiac pathology does influence the increase of cardiometabolic RF, worsens the remodeling of the heart and negatively influences cardiac muscle function