De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Modification of Nanocrystalline Porous Cu_2-xSe Films during Argon Plasma Treatment

Cu2-xSe films were deposited on Corning glass substrates by radio frequency (RF) magnetron sputtering and annealed at 300 °C for 20 min under N2 gas ambient. The films had a thickness of 850–870 nm and a chemical composition of Cu1.75Se. The initial structure of the films was nanocrystalline with a complex architecture and pores. The investigated films were plasma treated with RF (13.56 MHz) high-density low-pressure inductively coupled argon plasma. The plasma treatment was conducted at average ion energies of 25 and 200 eV for durations of 30, 60, and 90 s. Notably, changes are evident in the surface morphology, and the chemical composition of the films changed from x = 0.25 to x = 0.10 to x = 0.00, respectively, after plasma treatment at average ion energies of 25 and 200 eV, respectively

Modification of Nanocrystalline Porous Cu2-xSe Films during Argon Plasma Treatment

Cu2-xSe films were deposited on Corning glass substrates by radio frequency (RF) magnetron sputtering and annealed at 300 °C for 20 min under N2 gas ambient. The films had a thickness of 850–870 nm and a chemical composition of Cu1.75Se. The initial structure of the films was nanocrystalline with a complex architecture and pores. The investigated films were plasma treated with RF (13.56 MHz) high-density low-pressure inductively coupled argon plasma. The plasma treatment was conducted at average ion energies of 25 and 200 eV for durations of 30, 60, and 90 s. Notably, changes are evident in the surface morphology, and the chemical composition of the films changed from x = 0.25 to x = 0.10 to x = 0.00, respectively, after plasma treatment at average ion energies of 25 and 200 eV, respectively

Variation of Surface Nanostructures on (100) PbS Single Crystals during Argon Plasma Treatment

The nanostructuring of the (100) PbS single crystal surface was studied under varying argon plasma treatment conditions. The initial PbS single crystals were grown by high-pressure vertical zone melting, cut into wafer samples, and polished. Subsequently, the PbS single crystals were treated with inductively coupled argon plasma under varying treatment parameters such as ion energy and sputtering time. Plasma treatment with ions at a minimum energy of 25 eV resulted in the formation of nanotips with heights of 30–50 nm. When the ion energy was increased to 75–200 eV, two types of structures formed on the surface: high submicron cones and arrays of nanostructures with various shapes. In particular, the 120 s plasma treatment formed specific cruciform nanostructures with lateral orthogonal elements oriented in four <100> directions. In contrast, plasma treatment with an ion energy of 75 eV for 180 s led to the formation of submicron quasi-spherical lead structures with diameters of 250–600 nm. The nanostructuring mechanisms included a surface micromasking mechanism with lead formation and the vapor–liquid–solid mechanism, with liquid lead droplets acting as self-forming micromasks and growth catalysts depending on the plasma treatment conditions (sputtering time and rate)

Variation of Surface Nanostructures on (100) PbS Single Crystals during Argon Plasma Treatment

The nanostructuring of the (100) PbS single crystal surface was studied under varying argon plasma treatment conditions. The initial PbS single crystals were grown by high-pressure vertical zone melting, cut into wafer samples, and polished. Subsequently, the PbS single crystals were treated with inductively coupled argon plasma under varying treatment parameters such as ion energy and sputtering time. Plasma treatment with ions at a minimum energy of 25 eV resulted in the formation of nanotips with heights of 30–50 nm. When the ion energy was increased to 75–200 eV, two types of structures formed on the surface: high submicron cones and arrays of nanostructures with various shapes. In particular, the 120 s plasma treatment formed specific cruciform nanostructures with lateral orthogonal elements oriented in four directions. In contrast, plasma treatment with an ion energy of 75 eV for 180 s led to the formation of submicron quasi-spherical lead structures with diameters of 250–600 nm. The nanostructuring mechanisms included a surface micromasking mechanism with lead formation and the vapor–liquid–solid mechanism, with liquid lead droplets acting as self-forming micromasks and growth catalysts depending on the plasma treatment conditions (sputtering time and rate)

A draft human pangenome reference

Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels. Based on alignments of the assemblies, we generate a draft pangenome that captures known variants and haplotypes and reveals new alleles at structurally complex loci. We also add 119 million base pairs of euchromatic polymorphic sequences and 1,115 gene duplications relative to the existing reference GRCh38. Roughly 90 million of the additional base pairs are derived from structural variation. Using our draft pangenome to analyse short-read data reduced small variant discovery errors by 34% and increased the number of structural variants detected per haplotype by 104% compared with GRCh38-based workflows, which enabled the typing of the vast majority of structural variant alleles per sample

De novo assembly of the cattle reference genome with single-molecule sequencing.

Major advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies. We present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use. We demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species