Chromosome-level assembly of the common lizard (Zootoca vivipara) genome

Squamate reptiles exhibit high variation in their phenotypic traits and geographical distribution and are therefore fascinating taxa for evolutionary and ecological research. However, genomic resources are very limited for this group of species, consequently inhibiting research efforts. To address this gap, we assembled a high-quality genome of the common lizard, Zootoca vivipara (Lacertidae), using a combination of high coverage Illumina (shotgun and mate-pair) and PacBio sequencing data, coupled with RNAseq data and genetic linkage map generation. The 1.46 Gbp genome assembly has a scaffold N50 of 11.52 Mbp with N50 contig size of 220.4 Kbp and only 2.96% gaps. A BUSCO analysis indicates that 97.7% of the single-copy Tetrapoda orthologs were recovered in the assembly. In total 19,829 gene models were annotated to the genome using a combination of ab initio and homology-based methods. To improve the chromosome-level assembly, we generated a high-density linkage map from wild-caught families and developed a novel analytical pipeline to accommodate multiple paternity and unknown father genotypes. We successfully anchored and oriented almost 90% of the genome on 19 linkage groups. This annotated and oriented chromosome-level reference genome represents a valuable resource to facilitate evolutionary studies in squamate reptiles

First observation of electric-quadrupole infrared transitions in water vapour

Molecular absorption of infrared radiation is generally due to ro-vibrational electric-dipole transitions. Electric-quadrupole transitions may still occur, but they are typically a million times weaker than electric-dipole transitions, rendering their observation extremely challenging. In polyatomic or polar diatomic molecules, ro-vibrational quadrupole transitions have never been observed. Here, we report the first direct detection of quadrupole transitions in water vapor. The detected quadrupole lines have intensity largely above the standard dipole intensity cut-off of spectroscopic databases and thus are important for accurate atmospheric and astronomical remote sensing

Р-стереогенні діамандоїдні фосфіни

Despite diamondoid phosphines have found many synthetic applications and are even available commercially the chemistry of chiral diamondoid phosphines remains largely unexplored.Aim. To develop the convenient preparative method for the preparation of sterically-congested P-stereogenic secondary diamodoidyl phosphines as potential organocatalysts and ligands in the asymmetric synthesis.Results and discussion. A convenient method for the synthesis of P-stereogenic diamondoid phosphines with high yields through the phosphorylation of hydroxydiamondoids in trifluoroacetic acid followed by the reduction of the corresponding asymmetric chlorophosphonates has been proposed. The secondary phosphines obtained form stable complexes with borane that can be used to separate diamondoid phosphines into enantiomers.Experimental part. The experimental procedures for the preparation of 1- and 4-diamantyl-1-adamantyl- and phenylphosphines were developed; the structures of new compounds were confirmed by NMR and HRMS spectral data.Conclusions. A number of P-stereogenic mixed diamondoidylaryl phosphines and the secondary phosphines containing exclusively diamondoid substituents has been prepared. A degree of steric bulkiness is determined by the combination of diamondoid substituents around a phosphorus atom where 1-diamantyl derivatives are the most sterically-congested. The compounds obtained are potential ligands in asymmetric catalysis.Received: 31.03.2020Revised: 24.06.2020Accepted: 27.08.2020Незважаючи на те, що діамандоїдні фосфіни широко використовуються в органічному синтезі і навіть доступні комерційно, хімія хіральних діамандоїдних фосфінів залишається не дослідженою.Мета. Розробити зручний препаративний метод синтезу стереоускладнених Р-стереогенних вторинних діамандоїдних фосфінів, які можуть бути використані як ліганди в асиметричному синтезі, а також як органокаталізатори.Результати та їх обговорення. Запропоновано зручний метод синтезу P-стереогенних діамандоїдних фосфінів шляхом фосфорилювання гідроксипохідних діамандоїдів у трифтороцтовій кислоті з подальшим відновленням відповідних асиметричних хлорофосфонатів з високими виходами. Одержані таким чином фосфіни утворюють стійкі комплекси з бораном, які розглядаються як проміжні сполуки для подальшого розділення енантіомерів.Експериментальна частина. Був розроблений препаративний метод синтезу 1- і 4-діамантил-, 1-адамантил- і фенілфосфінів, структури яких підтверджено мас-спектрометричними і ЯМР-спектральними даними.Висновки. Одержано ряд Р-стереогенних змішаних діамандоїларилфосфінів та вторинних фосфінів, які містять виключно діамандоїдні замісники. Ступінь стеричного навантаження сполук визначається комбінацією діамандоїдних замісників навколо атома фосфору, де похідні 1-діамантилу найбільш стерично ускладнені. Одержані сполуки є потенційними лігандами в асиметричному каталізі.Received: 31.03.2020 Revised: 24.06.2020 Accepted: 27.08.202

Analytical “Bake-Off” of Whole Genome Sequencing Quality for the Genome Russia Project Using a Small Cohort for Autoimmune Hepatitis

A comparative analysis of whole genome sequencing (WGS) and genotype calling was initiated for ten human genome samples sequenced by St. Petersburg State University Peterhof Sequencing Center and by three commercial sequencing centers outside of Russia. The sequence quality, efficiency of DNA variant and genotype calling were compared with each other and with DNA microarrays for each of ten study subjects. We assessed calling of SNPs, indels, copy number variation, and the speed of WGS throughput promised. Twenty separate QC analyses showed high similarities among the sequence quality and called genotypes. The ten genomes tested by the centers included eight American patients afflicted with autoimmune hepatitis (AIH), plus one case’s unaffected parents, in a prelude to discovering genetic influences in this rare disease of unknown etiology. The detailed internal replication and parallel analyses allowed the observation of two of eight AIH cases carrying a rare allele genotype for a previously described AIH-associated gene (FTCD), plus multiple occurrences of known HLA-DRB1 alleles associated with AIH (HLA-DRB1-03:01:01, 13:01:01 and 7:01:01). We also list putative SNVs in other genes as suggestive in AIH influence

Genotyping and Whole-Genome Resequencing of Welsh Sheep Breeds Reveal Candidate Genes and Variants for Adaptation to Local Environment and Socioeconomic Traits

BackgroundAdvances in genetic tools applied to livestock breeding has prompted research into the previously neglected breeds adapted to harsh local environments. One such group is the Welsh mountain sheep breeds, which can be farmed at altitudes of 300 m above sea level but are considered to have a low productive value because of their poor wool quality and small carcass size. This is contrary to the lowland breeds which are more suited to wool and meat production qualities, but do not fare well on upland pasture. Herein, medium-density genotyping data from 317 individuals representing 15 Welsh sheep breeds were used alongside the whole-genome resequencing data of 14 breeds from the same set to scan for the signatures of selection and candidate genetic variants using haplotype- and SNP-based approaches.ResultsHaplotype-based selection scan performed on the genotyping data pointed to a strong selection in the regions of GBA3, PPARGC1A, APOB, and PPP1R16B genes in the upland breeds, and RNF24, PANK2, and MUC15 in the lowland breeds. SNP-based selection scan performed on the resequencing data pointed to the missense mutations under putative selection relating to a local adaptation in the upland breeds with functions such as angiogenesis (VASH1), anti-oxidation (RWDD1), cell stress (HSPA5), membrane transport (ABCA13 and SLC22A7), and insulin signaling (PTPN1 and GIGFY1). By contrast, genes containing candidate missense mutations in the lowland breeds are related to cell cycle (CDK5RAP2), cell adhesion (CDHR3), and coat color (MC1R).ConclusionWe found new variants in genes with potentially functional consequences to the adaptation of local sheep to their environments in Wales. Knowledge of these variations is important for improving the adaptative qualities of UK and world sheep breeds through a marker-assisted selection

Phylogenomics revealed migration routes and adaptive radiation timing of holarctic malaria mosquito species of the Maculipennis group

BackgroundPhylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics.ResultsTo reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group.ConclusionsOur phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattle are widely studied, whereas our knowledge of the genetic mechanisms of adaptation to local environments is still scarce. To address this issue for cold climates we used an integrated approach for detecting genomic intervals related to body temperature maintenance under acute cold stress. Our approach combined genome-wide association studies (GWAS) and scans for signatures of selection applied to a cattle population (Hereford and Kazakh Whiteheaded beef breeds) bred in Siberia. We utilized the GGP HD150K DNA chip containing 139,376 single nucleotide polymorphism markers

Genomic Legacy of the African Cheetah, Acinonyx jubatus

Background Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one \u3e100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p\u3c0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah’s extremely high (\u3e80 %) pleiomorphic sperm. Conclusions The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition