Recombination Points Research Articles

Disruption of recombination machinery alters the mutational landscape in plant organellar genomes.

Land plant organellar genomes have extremely low rates of point mutation yet also experience high rates of recombination and genome instability. Characterizing the molecular machinery responsible for these patterns is critical for understanding the evolution of these genomes. While much progress has been made towards understanding recombination activity in land plant organellar genomes, the relationship between recombination pathways and point mutation rates remains uncertain. The organellar targeted mutS homolog MSH1 has previously been shown to suppress point mutations as well as non-allelic recombination between short repeats in Arabidopsis thaliana. We therefore implemented high-fidelity Duplex Sequencing to test if other genes that function in recombination and maintenance of genome stability also affect point mutation rates. We found small to moderate increases in the frequency of single nucleotide variants (SNVs) and indels in mitochondrial and/or plastid genomes of A. thaliana mutant lines lacking radA, recA1, or recA3. In contrast, osb2 and why2 mutants did not exhibit an increase in point mutations compared to wild type (WT) controls. In addition, we analyzed the distribution of SNVs in previously generated Duplex Sequencing data from A. thaliana organellar genomes and found unexpected strand asymmetries and large effects of flanking nucleotides on mutation rates in WT plants and msh1 mutants. Finally, using long-read Oxford Nanopore sequencing, we characterized structural variants in organellar genomes of the mutant lines and show that different short repeat sequences become recombinationally active in different mutant backgrounds. Together, these complementary sequencing approaches shed light on how recombination may impact the extraordinarily low point mutation rates in plant organellar genomes.

Molecular Characterization of the Chicken Parvovirus Based on VP1 Gene Circulating in Brazilian Chicken Flocks.

Parvovirus infection affects several animal species, especially young animals. In birds, parvovirus infection has been described in Muscovy ducks, turkeys, and chickens, all of which had enteric diseases characterized by diarrhea. Chicken parvovirus (ChPV) has been detected in poultry around the world in animals affected by enteric problems, showing dwarfism, cloacal pasting, and diarrhea. In Brazil, ChPV was detected in chickens affected by diarrhea fifteen years ago. However, the genetic characteristics of ChPV circulating in chicken flocks were not determined. Therefore, the aim of the present investigation was to determine the genetic characteristics of the VP1 gene from ChPV detected in chickens affected by enteric diseases in Brazil. For this purpose, a molecular approach was used. Specific primers were designed to flank the complete VP1 gene of ChPV and amplify it using PCR. The amplified products from samples of chickens with enteric diseases were sequenced, and 22 complete CDs of the VP1 gene were obtained. These samples, compared to the ABU-P1 sequence, showed 17 sequences with high nucleotide (NT) similarity of 92.7-97.4% and amino acid (AA) similarity of 94.8-99.5% associated with Runting and Stunting syndrome (RSS); there were also five samples associated with hens with diarrhea with unusual jejunal dilatation (JD) that had less similarity than the RSS sequences (NT of 86.5% and AA of 93-93.1%). The phylogenetic analysis determined four groups. Group I had sequences from Korea. The second group included sequences from Korea, China, and Brazil (not included in this work). The third group had studied RSS sequences grouped with the ABU-P1 strain and sequences from China and the United States. Finally, the sequences from JD were clustered in a separate group with a bootstrap of 100%, a group that was denoted as group IV, and included sequences from China. RDP4 and SimPlot analysis showed one point of recombination with the sequences of group III ChPV in the JD sequences. Herein, we show that circulating strains of ChPV exhibit genetic differences in the VP1 gene in Brazilian chicken flocks. Nevertheless, more studies are needed to determine the probability of a new genetic group of ChPV based on the analysis of the complete genome.

Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae

The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.

Prevalence of hepatitis E virus genotype 4 of probable human origin in Tibetan pigs from the Qinghai-Tibetan Plateau, China.

Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide. In 2018-2022, we investigated the presence of HEV RNA in 1233 stool samples collected in the Qinghai-Tibetan Plateau, including humans (16), Tibetan pigs (624), yaks (312), sheep (267), and dogs (14). HEV RNA was only detected in Tibetan pig faecal samples (18.27%, 114/624). To perform molecular characterization of HEV strains in Tibetan pigs, we obtained 21 complete HEV genome sequences between 2018 and 2022. Sequence comparisons showed that 21 HEV strains from Tibetan pigs shared the mean nucleotide identities with the reference HEV strains ranging between 82.9% and 94.9% and 89.3% and 92.1% similarities with human HEV strains. Phylogenetic analysis confirmed that all HEV strains were genotype 4, closely related to human HEV strains. Sequence recombinant analysis showed five potential recombinant strains identified in this study, of which SWU/D18/2018 (GenBank No. MK410044) was recombinant with human and swine HEV strains, located 6509-6878 nt from the recombination point. Based on the Bayesian evolutionary trees, we found that most HEV strains diverged later than human HEV (16 Tibetan pig HEV strains diverged later than 1979, and seven human HEV strains diverged earlier than 1979). Therefore, we speculated that the prevalence of HEV 4 in Tibetan pigs possibly originated from humans in the Qinghai-Tibetan Plateau.

Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants.

To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.

The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.

An Optimal Energy Absorption and Utilization Design for Deformable/Reconfigurable Modular Solar-Powered UAVs in Near Space

Maximizing the absorption and utilization of solar energy is a bottleneck issue and hot research concern for high-altitude long-endurance (HALE) solar-powered UAVs (SP-UAVs). This paper investigates the overall design and task optimization for a deformable/reconfigurable SP-UAV platform that utilizes its modular characteristics to optimize the overall solar absorption and structural weight while maximizing its mission utility. First, we establish the energy absorption/consumption model, the aerodynamic model, and the subsystem mass prediction model. Based on these models, the overall parameter design and optimization scheme of a modular SP-UAV is proposed by using heuristic intelligence algorithms. The results show that the loading ratio of the deformable modular SP-UAV increases from 8.2% to 9.8%. Then, the flight processes in both the deformed and the reconfigured cases are verified under task-oriented scenarios. Simulation results indicate that compared with comparable benchmarks with conventional layouts, deformable SP-UAVs are capable of increasing the feasible zone from 72 to 142 days. Additionally, the separation and recombination points are optimized and determined at specific latitudes and dates. A performance analysis shows that separation in the daytime can multiply, thereby increasing the flight range, although the feasible zone shrinks with increasing UAV unit number.

Blue emission and twin structure of p-type copper iodide thin films

Copper iodide is an attractive p-type transparent material suitable for optoelectronic applications. This work reports on the synthesis of copper iodide (CuI) by iodination of sputtered Cu films previously deposited on glass and silicon substrates. The crystalline phase and surface morphology were studied by X-ray diffraction (XRD) and scanning electron microscopy (SEM), respectively. The prepared CuI films crystallize in the zinc blende structure (γ-phase) at different amounts of iodine and exhibit preferential orientation along the <111> direction. Moreover, detailed investigation of the microstructure via high-resolution transmission electron microscopy (HR-TEM) revealed the presence and details of alternating twin crystallographic domains between adjacent grains. The electrical properties of the CuI films were characterized by Hall effect measurements and revealed a p-type carrier behavior for all films. The electrical behavior was discussed and attributed to the change in intrinsic point defects. In addition, the electronic bandgap and luminescence properties were investigated using optical transmission and photoluminescence (PL). The CuI films showed a wide band gap (about 3.05 eV) with an average transmittance of about (66 %) in the visible region. Moreover, the PL showed a blue emission ranging from 400 to 440 nm originating from the excitonic recombination and radiative point defects.

InGAP-family: Accurate Detection of Meiotic Recombination Loci and Causal Mutations by Filtering Out Artificial Variants due to Genome Complexities

Accurately identifying DNA polymorphisms can bridge the gap between phenotypes and genotypes and is essential for molecular marker assisted genetic studies. Genome complexities, including large-scale structural variations, bring great challenges to bioinformatic analysis for obtaining high-confidence genomic variants, as sequence differences between non-allelic loci of two or more genomes can be misinterpreted as polymorphisms. It is important to correctly filter out artificial variants to avoid false genotyping or estimation of allele frequencies. Here, we present an efficient and effective framework, inGAP-family, to discover, filter, and visualize DNA polymorphisms and structural variants (SVs) from alignment of short reads. Applying this method to polymorphism detection on real datasets shows that elimination of artificial variants greatly facilitates the precise identification of meiotic recombination points as well as causal mutations in mutant genomes or quantitative trait loci. In addition, inGAP-family provides a user-friendly graphical interface for detecting polymorphisms and SVs, further evaluating predicted variants and identifying mutations related to genotypes. It is accessible at https://sourceforge.net/projects/ingap-family/.

Prevalence and phylogenetic analysis of spike gene of porcine epidemic diarrhea virus in Henan province, China in 2015-2019.

Porcine epidemic diarrhea virus (PEDV) causes diarrhea, dehydration and a high morbidity and mortality in piglets. To investigate the prevalence and molecular characteristics of the spike (S) gene of the PEDV strains, 575 faecal and intestinal samples were collected from individual pigs with diarrhea in 18 regions in Henan, China from April 2015 to March 2019. The detection results showed that PEDV infection was high up to 51.65% in Henan pigs. The PEDV positive rate in suckling piglets was the highest (60.47%), and it existed widely both in PEDV-vaccine immunized (25.00%) and non-immunized pigs (62.29%). The complete S gene of twenty-two representative PEDV strains were sequenced and analyzed. Phylogenetic analysis based on the S gene sequences revealed that the sixteen of the sequenced PEDV Henan strains were located in the G2-a clade and more related to the PEDV variant strains. The other six of the sequenced PEDV strains were closely related to S-INDEL strains and grouped within in the G1-b clade. The Recombinant Identification Program (RIP) and Simplot analysis showed PEDV Henan strains were evolved from the epidemic variant strains and there existed potential recombinant points in the S genome. Furthermore, the deduced amino acid sequences analysis of the S protein showed that there existed multiple amino acid mutations in the S protein of PEDV Henan strains, including the neutralizing epitope CO-26K equivalent (COE) and SS6 when compared with the CV777-based vaccine strain. These amino acid mutations in the S protein may change the antigenicity in the PEDV Henan variants, leading to the failure of immunization with the traditional vaccine based on the CV777 strain. These results would support the understanding of the prevalence and evolution characteristics of PEDV in China and promote the development of novel vaccines based on the current prevalence variant strains.

Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites.

The presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multibasic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences from documented cases of MBCS insertion due to recombination, we show that such recombination with host RNAs is most likely to occur at particular hotspots in ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and viral RNAs. The locations of these hotspots in highly abundant RNAs indicate that RNA recombination is facilitated by the binding of small nucleolar RNA (snoRNA) near the recombination points.

Representative Genotyping, Recombination and Evolutionary Dynamics Analysis of TSA56 Gene Segment of Orientia tsutsugamushi.

Scrub typhus is a zoonotic disease caused by Orientia tsutsugamushi (O. tsutsugamushi). Orientia tsutsugamushi has various genotypes and more new strains with difference in sequences increasingly appeared. Whether the accurateness of one special nested PCR method which amplifies segment instead of entire open reading frame (ORF) sequence meets the current work of identifying new strains and classifying genotypes remains to be confirmed. And the origins and evolution of this organism have not been thoroughly elucidated. Accordingly, in this study, segments and the entire ORF of the 56-kDa type-specific antigen (TSA56) gene of O. tsutsugamushi were collected, including 209 clinically isolated strains in Guangzhou, China from 2012 to 2016 and 139 reference strains worldwide. By performing phylogenetic analysis, we proved that the accurateness of the particular PCR method which almost met detection need. This re-grouping result showed that segments perfectly represented and identified strains of Karp, Boryong, Gilliam, TA763, Kawasaki and part of Kato genotype, and this accuracy is not restricted by region and time. Sequence diversification of Shimokoshi and some Kato strains made their genotyping need to consider entire ORF sequences, but their weak recognition might not be due to recombination. The frequent genetic recombination and high point mutations contributed to genetic diversification of the TSA56 gene. Major overlapping regions of most recombination events occurred between strains of the same genotype, especially Karp and Kato genotype. And cross-genotype overlapping events occurred between Karp and Boryong/Gilliam/TA763/Kato, Kato and Kawasaki/Gilliam/TA686, Boryong and TA686, and Gilliam and Kawasaki. But Segment has quite low recombination frequency and stable mutation trend from 1943 to 2016. So segment is a relatively conserved part of the TSA56 ORF as for its stable trend of genetic diversity, and it may anchor and represent the entire TSA56 ORF gene. And genetic diversity is rejected as one potential reason for the increased incidence of scrub typhus. But an occasional recombination event created an unrecognized genotype which might be due to the breakage of VD II and AD II. Additionally, strains in Guangzhou were homologous and Karp genotype was detected as a dominant.

Third-generation sequencing-based mapping and visualization of single nucleotide polymorphism, meiotic recombination, illegitimate mutation and repeat-induced point mutation.

Generation of new genetic diversity by crossover (CO) and non-crossover (NCO) is a fundamental process in eukaryotes. Fungi have played critical roles in studying this process because they permit tetrad analysis, which has been used by geneticists for several decades to determine meiotic recombination products. New genetic variations can also be generated in zygotes via illegitimate mutation (IM) and repeat-induced point mutation (RIP). RIP is a genome defense mechanism for preventing harmful expansion of transposable elements or duplicated sequences in filamentous fungi. Although the exact mechanism of RIP is unknown, the C:G to T:A mutations might result from DNA cytosine methylation. A comprehensive approach for understanding the molecular mechanisms underlying these important processes is to perform high-throughput mapping of CO, NCO, RIP and IM in zygotes bearing large numbers of heterozygous variant markers. To this aim, we developed ‘TSETA’, a versatile and user-friendly pipeline that utilizes high-quality and chromosome-level genome sequences involved in a single meiotic event of the industrial workhorse fungus Trichoderma reesei. TSETA not only can be applied to most sexual eukaryotes for genome-wide tetrad analysis, it also outcompetes most currently used methods for calling out single nucleotide polymorphisms between two or more intraspecies strains or isolates.

Sub-genotype change and recombination of coxsackievirus A6s may be the cause of it being the predominant pathogen for HFMD in children in Beijing, as revealed by analysis of complete genome sequences

ObjectivesTo investigate why coxsackievirus A6 (CVA6) has replaced enterovirus A71 (EV71) and coxsackievirus A16 (CVA16), which used to be the most predominant etiological agents, for hand, foot and mouth disease (HFMD) in children in Beijing, China. MethodsSixty-four CVA6-positive samples were identified from 2010 to 2016 and selected for whole genome sequence amplification and analysis. ResultsIt was demonstrated that the whole genome sequences of CVA6s in this study were 7432–7435 nucleotides in length, and the different lengths were only in the 5′UTR region. The phylogenetic tree analysis of the full-length VP1 region of CVA6s indicated that the prevalent CVA6s in Beijing changed from the previous D2 sub-genotype to the D3 sub-genotype in 2013. In this study, two recombinant forms (RFs)– RF-C and RF-D – of CVA6 mainly appeared in 2010 and 2011. Since 2013, three recombinant CVA6 variants – RF-A, J and L – have been prevalent in children with HFMD in Beijing. The recombination region of RF-J was located at the 2C region, while RF-L had a new recombination point in the 3D region. The recombination of prevalent CVA6s in Beijing from 2013 to 2016 occurred within non-capsid regions of the genome, especially the P2 and P3 regions. ConclusionsThe sub-genotype change and recombination of CVA6s indicated from this study may explain why CVA6 has become the predominant pathogen causing HFMD since 2013.

MoBPS - Modular Breeding Program Simulator.

The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays’ complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.

Identification and mapping of quantitative trait loci (QTL) and epistatic QTL for salinity tolerance at seedling stage in traditional aromatic short grain rice landrace Kolajoha (Oryza sativa L.) of Assam, India

Salinity stress is the most prominent stress impacting rice productivity worldwide. In the past, several quantitative trait loci (QTLs) for salinity tolerance had been identified in rice, however their utilization in rice breeding programs is largely confounded due to the unwanted linkage drag associated with the QTL region. Thus, it is strongly desirable to delimit the QTL region to a least possible chromosomal interval minimising any unwanted association. Addressing this, we have evaluated 68 recombinant inbred lines (RILs) derived from a cross between a salinity tolerant parent ‘Kolajoha’ and a salinity sensitive parent ‘Ranjit’ for identification of QTL(s) involved in imparting salinity tolerance at seedling stage. Genotyping by sequencing approach (GBS) was followed for SNP identification at genome wide scale. Around 3649 SNPs were identified by GBS method initially at 20% minor allele frequency. After filtering of SNPs with polymorphism with less than 10–15% of missing data, a total of 1248 SNPs were mapped to 1247 recombination points and the genetic map was constructed with a total map length of 1201.21 cM and resolution of 0.95 cM between markers. For 10 traits, a total of 23 additive QTLs were identified of which only 1 was a major QTL and 22 were minor QTLs. The average QTL interval size is about 2945 kb. Epistatic QTL mapping had identified one pair of QTLs that contribute significantly in the phenotypic variation of traits among the RILs. Total 1895 genes were identified in the QTL intervals, majority of them are located in Chr1 of rice genome between 22.09 and 38.29 Mb region. Although, this region is not very narrow, some of the genes falling in this region can be utilized for validation of QTLs in future. One differentially methylated region was found to be colocalized within the QTL intervals determined in Chr2 which indicates their potential role in epigenetic modifications in improving stress tolerance in rice.

Decreasing of the thermal conductivity of Si nanopillar/SiGe composite films investigated by using a piezoelectric photothermal spectroscopy

To investigate the decrease of thermal conductivity () of nanoscale Si materials, we conducted the piezoelectric photothermal (PPT) method for the highly periodic Si nanopillar arrays embedded in Si0.7Ge0.3. The PPT is an electrode free method that can measure a heat propagation in the parallel to the nanopillars direction. A distinctive dip was observed in the frequency-dependent PPT signal intensity. By focusing the dip frequency, was estimated from the comparison with the model analysis based on the one-dimensional multilayer thermal diffusion equation. The estimated was 0.19 ± 0.07 W m–1 K, in the parallel to the nanopillars direction. Since the considerable decrease of was confirmed from the non-radiative recombination point of view, we found the present non-destructive PPT method is very useful to estimate in the nanostructured devices for the thermoelectric application.

Phasing quality assessment in a brown layer population through family- and population-based software

BackgroundHaplotype data contains more information than genotype data and provides possibilities such as imputing low frequency variants, inferring points of recombination, detecting recurrent mutations, mapping linkage disequilibrium (LD), studying selection signatures, estimating IBD probabilities, etc. In addition, haplotype structure is used to assess genetic diversity and expected accuracy in genomic selection programs. Nevertheless, the quality and efficiency of phasing has rarely been a subject of thorough study but was assessed mainly as a by-product in imputation quality studies. Moreover, phasing studies based on data of a poultry population are non-existent. The aim of this study was to evaluate the phasing quality of FImpute and Beagle, two of the most used phasing software.ResultsWe simulated ten replicated samples of a layer population comprising 888 individuals from a real SNP dataset of 580 k and a pedigree of 12 generations. Chromosomes analyzed were 1, 7 and 20. We measured the percentage of SNPs that were phased equally between true and phased haplotypes (Eqp), proportion of individuals completely correctly phased, number of incorrectly phased SNPs or Breakpoints (Bkp) and the length of inverted haplotype segments. Results were obtained for three different groups of individuals, with no parents or offspring genotyped in the dataset, with only one parent, and with both parents, respectively. The phasing was performed with Beagle (v3.3 and v4.1) and FImpute v2.2 (with and without pedigree). Eqp values ranged from 88 to 100%, with the best results from haplotypes phased with Beagle v4.1 and FImpute with pedigree information and at least one parent genotyped. FImpute haplotypes showed a higher number of Bkp than Beagle. As a consequence, switched haplotype segments were longer for Beagle than for FImpute.ConclusionWe concluded that for the dataset applied in this study Beagle v4.1 or FImpute with pedigree information and at least one parent genotyped in the data set were the best alternatives for obtaining high quality phased haplotypes.

Genome-Wide Analyses Reveal Footprints of Divergent Selection and Drought Adaptive Traits in Synthetic-Derived Wheats.

Crop-wild introgressions have long been exploited without knowing the favorable recombination points. Synthetic hexaploid wheats are one of the most exploited genetic resources for bread wheat improvement. However, despite some QTL with major effects, much less is known about genome-wide patterns of introgressions and their effects on phenotypes. We used two genome-wide association approaches: SNP-GWAS and haplotype-GWAS to identify SNPs and haplotypes associated with productivity under water-limited conditions in a synthetic-derived wheat (SYN-DER) population. Haplotype-GWAS further enriched and identified 20 more genomic regions associated with drought adaptability that did not overlap with SNP-GWAS. Since GWAS is biased to the phenotypes in the study and may fail to detect important genetic diversity during breeding, we used five complementary analytical approaches (t-test, Tajima’s D, nucleotide diversity (π), Fst, and EigenGWAS) to identify divergent selections in SYN-DER compared to modern bread wheat. These approaches consistently pinpointed 89 ‘selective sweeps’, out of which 30 selection loci were identified on D-genome. These key selections co-localized with important functional genes of adaptive traits such as TaElf3-D1 (1D) for earliness per se (Eps), TaCKX-D1 (3D), TaGS1a (6D) and TaGS-D1 (7D) for grain size, weight and morphology, TaCwi-D1 (5D) influencing drought tolerance, and Vrn-D3 (7D) for vernalization. Furthermore, 55 SNPs and 23 haplotypes of agronomic and physiological importance such as grain yield, relative water content and thousand grain weight in SYN-DER, were among the top 5% of divergent selections contributed by synthetic hexaploid wheats. These divergent selections associated with improved agronomic performance carry new alleles that have been introduced to wheat. Our results demonstrated that GWAS and selection sweep analyses are powerful approaches for investigating favorable introgressions under strong selection pressure and the use of crop-wild hybridization to assist the improvement of wheat yield and productivity under moisture limiting environments.

Recombinant Variants of Hepatitis C Virus in Siberia

This review summarizes the results of a comprehensive multi-year molecular-epidemiological research on HCV (2001–2016) in Altai krai and Novosibirsk oblast. The first eight cases of infection with the CRF01_1b2k recombinant form of HCV were revealed during this research. The recombination point in the NS2 gene was confirmed for all CRF01_1b2k Siberian isolates, which agrees with the data on the previously identified recombinants of the same form in other regions of Russia and the rest of the world. An analysis of the nucleotide sequences of the Core, E1, NS2, and NS5b gene fragments in the genomes of eight recombinant isolates of the 2k/1b type identified in Siberia showed a close phylogenetic relationship between them, as well as with 27 recombinants described in St. Petersburg, Azerbaijan, Armenia, Estonia, The Netherlands, Ireland, France, and the United States. The levels of homology for the Core, Е1, NS2, and NS5b genes were 97, 94, 92, and 96%, respectively. Phylogenetic analysis of the genomes of recombinants indicated the common origin of isolates of the 2k/1b type and their broad circulation in the territory of Russia. Analysis of the 5'‑region of the genome of recombinant isolates of subtype 2k showed that, apart from Russia, the closest isolates of the 2k subtype were previously identified in Moldova and Uzbekistan in 1996–2013. The incidence of recombinant isolates in the Siberian region is estimated at 1%. The molecular clock method has shown that the most probable time of the appearance of the CRF01_1b2k recombinant form is between 1957 and 1970.