A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping

Holtgräwe D, Rosleff Soerensen T, Hausmann L, et al. A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock ‘Börner’ (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping. Frontiers in Plant Science. 2020;11: 156.Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar ‘Börner,’ carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of ‘Börner’ to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the ‘Börner’ genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5

Challenges in RNA virus bioinformatics

Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses. In contrast to many broad, established and well-organized bioinformatics communities (e.g. structural genomics, ontologies, next-generation sequencing, expression analysis), research groups focusing on viruses can probably be counted on the fingers of two hands. Results: The purpose of this review is to increase awareness among bioinformatics researchers about the pressing needs and unsolved problems of computational virology. We focus primarily on RNA viruses that pose problems to many standard bioinformatics analyses owing to their compact genome organization, fast mutation rate and low evolutionary conservation. We provide an overview of tools and algorithms for handling viral sequencing data, detecting functionally important RNA structures, classifying viral proteins into families and investigating the origin and evolution of viruses. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. The references for this article can be found in the Supplementary Materia

Magnetic and Cytotoxicity Properties of La1−xSrxMnO3(0 ≤ x ≤ 0.5) Nanoparticles Prepared by a Simple Thermal Hydro-Decomposition

This study reports the magnetic and cytotoxicity properties of magnetic nanoparticles of La1−xSrxMnO3(LSMO) withx = 0, 0.1, 0.2, 0.3, 0.4, and 0.5 by a simple thermal decomposition method by using acetate salts of La, Sr, and Mn as starting materials in aqueous solution. To obtain the LSMO nanoparticles, thermal decomposition of the precursor was carried out at the temperatures of 600, 700, 800, and 900 °C for 6 h. The synthesized LSMO nanoparticles were characterized by XRD, FT-IR, TEM, and SEM. Structural characterization shows that the prepared particles consist of two phases of LaMnO3(LMO) and LSMO with crystallite sizes ranging from 20 nm to 87 nm. All the prepared samples have a perovskite structure with transformation from cubic to rhombohedral at thermal decomposition temperature higher than 900 °C in LSMO samples ofx ≤ 0.3. Basic magnetic characteristics such as saturated magnetization (MS) and coercive field (HC) were evaluated by vibrating sample magnetometry at room temperature (20 °C). The samples show paramagnetic behavior for all the samples withx = 0 or LMO, and a superparamagnetic behavior for the other samples havingMSvalues of ~20–47 emu/g and theHCvalues of ~10–40 Oe, depending on the crystallite size and thermal decomposition temperature. Cytotoxicity of the synthesized LSMO nanoparticles was also evaluated with NIH 3T3 cells and the result shows that the synthesized nanoparticles were not toxic to the cells as determined from cell viability in response to the liquid extract of LSMO nanoparticles