Analysis of the Rpv12 locus in a haplotype‑separated grapevine genome sequence

Plasmopara viticola, the grapevine downy mildew pathogen, causes severe losses in viticulture if not counteracted by fungicide sprays that need to be repeatedly applied during each growing season. To reduce the amount of plant protection, modern grapevine breeding generates fungus‑resistant grapevine cultivars by introgression of resistance loci from wild Vitis spec. sources. However, the presence of only a single resistance locus may provoke the emergence of pathogen races able to overcome the resistance trait of the host. Therefore, a combination of several, independently acting resistance loci is required for sustainable genetic resistance. Quite little is known about the resistance‑conferring genes within the various grapevine resistance loci. To ameliorate this situation and make stacking of resistance loci more efficient, the Rpv12 locus originating from the Asian Vitis amurensis was sequenced and characterized. The complete genome of breeding line Gf.99‑03, carrying Rpv12 in heterozygous state, was analyzed. Haplotypes were resolved by assigning the reads to one of the parents of Gf.99‑03 using trio binning. Annotation of the resulting genomic sequences was based on RNA-Seq data and predicted gene models. The haplotype carrying the Rpv12 locus, delimited by markers UDV‑014 and UDV‑370 on chromosome 14 (Venuti et al., 2013), diverges strongly from the susceptible haplotype as well as from the reference genome PN40024 12X.v2. It was found to contain two important gene clusters. One cluster includes pathogen-inducible genes similar to the gene ACCELERATED CELL DEATH 6 (A. thaliana) likely involved in hypersensitive response upon pathogen attack. The second cluster comprises positional resistance candidate genes corresponding to typical NLRs (nucleotide binding site, leucine rich repeats), hypothesized to be involved in pathogen perception and cellular defense signalling

Towards carbon nanotube growth into superconducting microwave resonator geometries

The in-place growth of suspended carbon nanotubes facilitates the observation of both unperturbed electronic transport spectra and high-Q vibrational modes. For complex structures integrating, e.g., superconducting rf elements on-chip, selection of a chemically and physically resistant material that survives the chemical vapor deposition (CVD) process provides a challenge. We demonstrate the implementation of molybdenum-rhenium coplanar waveguide resonators that exhibit clear resonant behaviour at cryogenic temperatures even after having been exposed to nanotube growth conditions. The properties of the MoRe devices before and after CVD are compared to a reference niobium device.Comment: 6 pages, 4 figures, IWEPNM conference proceedin

Long-read sequencing identifies a common transposition haplotype predisposing for CLCNKB deletions

BACKGROUND: Long-read sequencing is increasingly used to uncover structural variants in the human genome, both functionally neutral and deleterious. Structural variants occur more frequently in regions with a high homology or repetitive segments, and one rearrangement may predispose to additional events. Bartter syndrome type 3 (BS 3) is a monogenic tubulopathy caused by deleterious variants in the chloride channel gene CLCNKB, a high proportion of these being large gene deletions. Multiplex ligation-dependent probe amplification, the current diagnostic gold standard for this type of mutation, will indicate a simple homozygous gene deletion in biallelic deletion carriers. However, since the phenotypic spectrum of BS 3 is broad even among biallelic deletion carriers, we undertook a more detailed analysis of precise breakpoint regions and genomic structure. METHODS: Structural variants in 32 BS 3 patients from 29 families and one BS4b patient with CLCNKB deletions were investigated using long-read and synthetic long-read sequencing, as well as targeted long-read sequencing approaches. RESULTS: We report a ~3 kb duplication of 3'-UTR CLCNKB material transposed to the corresponding locus of the neighbouring CLCNKA gene, also found on ~50 % of alleles in healthy control individuals. This previously unknown common haplotype is significantly enriched in our cohort of patients with CLCNKB deletions (45 of 51 alleles with haplotype information, 2.2 kb and 3.0 kb transposition taken together, p=9.16×10-9). Breakpoint coordinates for the CLCNKB deletion were identifiable in 28 patients, with three being compound heterozygous. In total, eight different alleles were found, one of them a complex rearrangement with three breakpoint regions. Two patients had different CLCNKA/CLCNKB hybrid genes encoding a predicted CLCNKA/CLCNKB hybrid protein with likely residual function. CONCLUSIONS: The presence of multiple different deletion alleles in our cohort suggests that large CLCNKB gene deletions originated from many independently recurring genomic events clustered in a few hot spots. The uncovered associated sequence transposition haplotype apparently predisposes to these additional events. The spectrum of CLCNKB deletion alleles is broader than expected and likely still incomplete, but represents an obvious candidate for future genotype/phenotype association studies. We suggest a sensitive and cost-efficient approach, consisting of indirect sequence capture and long-read sequencing, to analyse disease-relevant structural variant hotspots in general

Semiconductor Spintronics

Spintronics refers commonly to phenomena in which the spin of electrons in a solid state environment plays the determining role. In a more narrow sense spintronics is an emerging research field of electronics: spintronics devices are based on a spin control of electronics, or on an electrical and optical control of spin or magnetism. This review presents selected themes of semiconductor spintronics, introducing important concepts in spin transport, spin injection, Silsbee-Johnson spin-charge coupling, and spindependent tunneling, as well as spin relaxation and spin dynamics. The most fundamental spin-dependent nteraction in nonmagnetic semiconductors is spin-orbit coupling. Depending on the crystal symmetries of the material, as well as on the structural properties of semiconductor based heterostructures, the spin-orbit coupling takes on different functional forms, giving a nice playground of effective spin-orbit Hamiltonians. The effective Hamiltonians for the most relevant classes of materials and heterostructures are derived here from realistic electronic band structure descriptions. Most semiconductor device systems are still theoretical concepts, waiting for experimental demonstrations. A review of selected proposed, and a few demonstrated devices is presented, with detailed description of two important classes: magnetic resonant tunnel structures and bipolar magnetic diodes and transistors. In most cases the presentation is of tutorial style, introducing the essential theoretical formalism at an accessible level, with case-study-like illustrations of actual experimental results, as well as with brief reviews of relevant recent achievements in the field.Comment: tutorial review; 342 pages, 132 figure

A fully phased interspecific grapevine rootstock genome sequence representing *V. riparia* and *V. cinerea* and allele-aware annotation of the phylloxera resistance locus *Rdv1*

Frommer B, Hausmann L, Holtgräwe D, et al. A fully phased interspecific grapevine rootstock genome sequence representing *V. riparia* and *V. cinerea* and allele-aware annotation of the phylloxera resistance locus *Rdv1*. bioRxiv. 2022.The phylloxera resistant rootstock cultivar ′Boerner′ is an interspecies hybrid derived from *Vitis riparia* and *V. cinerea* and a valuable resource for *Vitis* disease resistances. We created a fully phased, high-quality ′Boerner′ genome sequence named BoeRC using long PacBio reads. Comprehensive gene annotation of both ′Boerner′ haplotypes, designated BoeRip and BoeCin, was applied to describe the phylloxera resistance locus *Rdv1*. Using a mapping population derived from a sensitive *V. vinifera* cultivar and ′Boerner′, the *Rdv1* locus was further delimited. *Rdv1*, which is derived from *V. cinerea* and included in the haplotype BoeCin, was compared with sequences of phylloxera susceptible and phylloxera tolerant cultivars. Between flanking regions that display high synteny, we detected and precisely characterized a diverse sequence region that covers between 202 to 403 kbp in different haplotypes. In BoeCin, five putative disease resistance genes were identified that represent likely candidates for conferring resistance to phylloxera

Analysis of the Rpv12 locus in a haplotype‑separated grapevine genome sequence

Müllner S, Frommer B, Holtgräwe D, et al. Analysis of the Rpv12 locus in a haplotype‑separated grapevine genome sequence. VITIS Journal of Grapevine Research. 2023;62:77-80.*Plasmopara viticola*, the grapevine downy mildew pathogen, causes severe losses in viticulture if not counteracted by fungicide sprays that need to be repeatedly applied during each growing season. To reduce the amount of plant protection, modern grapevine breeding generates fungus‑resistant grapevine cultivars by introgression of resistance loci from wild *Vitis* spec. sources. However, the presence of only a single resistance locus may provoke the emergence of pathogen races able to overcome the resistance trait of the host. Therefore, a combination of several, independently acting resistance loci is required for sustainable genetic resistance. Quite little is known about the resistance‑conferring genes within the various grapevine resistance loci. To ameliorate this situation and make stacking of resistance loci more efficient, the *Rpv12* locus originating from the Asian *Vitis amurensis* was sequenced and characterized. The complete genome of breeding line Gf.99‑03, carrying *Rpv12* in heterozygous state, was analyzed. Haplotypes were resolved by assigning the reads to one of the parents of Gf.99‑03 using trio binning. Annotation of the resulting genomic sequences was based on RNA-Seq data and predicted gene models. The haplotype carrying the *Rpv12* locus, delimited by markers UDV‑014 and UDV‑370 on chromosome 14 (Venuti *et al*., 2013), diverges strongly from the susceptible haplotype as well as from the reference genome PN40024 12X.v2. It was found to contain two important gene clusters. One cluster includes pathogen-inducible genes similar to the gene *ACCELERATED CELL DEATH 6* (*A. thaliana*) likely involved in hypersensitive response upon pathogen attack. The second cluster comprises positional resistance candidate genes corresponding to typical NLRs (nucleotide binding site, leucine rich repeats), hypothesized to be involved in pathogen perception and cellular defense signalling

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

Background: Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non–genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step. Results: The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life. Conclusions: It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project

Draft genome of the aardaker (Lathyrus tuberosus\textit {Lathyrus tuberosus} L.), a tuberous legume

$\bf Objectives:$ $\textit {Lathyrus tuberosus}$ is a nitrogen-fixing member of the Fabaceae which forms protein-rich tubers. To aid future domestication programs for this legume plant and facilitate evolutionary studies of tuber formation, we have generated a draft genome assembly based on Pacific Biosciences sequence reads. $\textbf {Data description:}$ Genomic DNA from $\textit {L. tuberosus}$ was sequenced with PacBio's HiFi sequencing chemistry generating 12.8 million sequence reads with an average read length of 14 kb (approximately 180 Gb of sequence data). The reads were assembled to give a draft genome of 6.8 Gb in 1353 contigs with an N50 contig length of 11.1 Mb. The GC content of the genome assembly was 38.3%. BUSCO analysis of the genome assembly indicated a genome completeness of at least 96%. The genome sequence will be a valuable resource, for example, in assessing genomic consequences of domestication efforts and developing marker sets for breeding programs. The $\textit {L. tuberosus}$ genome will also aid in the analysis of the evolutionary history of plants within the nitrogen-fixing Fabaceae family and in understanding the molecular basis of tuber evolution