Prediction of the CYP2D6 enzymatic activity based on investigating of the CYP2D6 genotypes around the vivax malaria patients in Yunnan Province, China

Background In recent years, the incidence rate of vivax malaria recurrence still had 3.1% in Yunnan Province population after eradication therapy using primaquine (PQ). In order to understand the specific failure reasons for preventing vivax malaria relapses, a preliminary exploration on the CYP2D6 enzyme activity was carried out in the vivax malaria patients in Yunnan Province population by analysing mutational polymorphism in the coding region of CYP2D6 gene. Methods Blood samples were collected from vivax malaria patients with suspected relapse (SR) and non-relapsed (NR) malaria in Yunnan Province. The DNA fragments containing 9 exons regions of human CYP2D6 gene were amplified by performing PCR and sequenced. The sequencing results were aligned by using DNAStar 11.0 to obtain the coding DNA sequence (CDS) of CYP2D6 gene. DnaSP 6.11.01 software was used to identify mutant polymorphisms and haplotypes of the CDS chain. The waterfall function of GenVisR package in R was utilized to visualize the mutational landscape. The alleles of CYP2D6 gene were identified according to the criteria prescribed by Human Cytochrome P450 (CYP) Allele Nomenclature Committee Database and the CYP2D6 enzyme activity was predicted based on diploid genotype. Results A total of 320 maternal CDS chains, including 63 from SR group and 257 from NR group, were obtained. Twelve mutant loci, including c.31 (rs769259), c.100 (rs1065852), c.271 (rs28371703), c.281 (rs28371704), c.294 (rs28371705), c.297 (rs200269944), c.336 (rs1081003), c.408 (rs1058164), c.505 (rs5030865), c.801 (rs28371718), c.886 (rs16947), and c.1,457 (rs1135840) were observed on the 640 CDS chains (including 320 maternal and 320 paternal chains). The high-frequency mutation at rs1135840 (0.703) and low-frequency mutation, such as rs28371703, were detected only in the SR group. The frequency of mutant rs1058164 and rs1135840 were significantly increased in the SR group ($${x}^{2}$$ x 2 = 4.468, 5.889, P < 0.05), as opposed to the NR group. Of the 23 haplotypes (from Hap_1 to Hap_23), the nomenclatures of 11 allelic forms could be found: Hap_3 was non-mutant, Hap_2 accounted for the highest frequency (36.9%, 236/640), and Hap_9 had the most complex sequence structure, containing 7 loci mutations. Allele *10 was the most frequent among these genotypes (0.423). Among the allele *10 standard named genotypes, *1/*10, *1/*1 and *2/*10 were significantly more frequent in the NR group ($${x}^{2}$$ x 2 = 3.911, P < 0.05) and all showed uncompromised enzyme activity; the impaired genotype *10/*39 was more frequent in the SR group ($${x}^{2}$$ x 2 = 10.050, P < 0.05), and genotype *4/*4was detected only in the SR group. Conclusion In the patients receiving PQ dosage in Yunnan Province population, both rs1135840 single nucleotide polymorphism and *10 allele form was common in the CYP2D6 gene. Low-frequency mutation sites, such as rs28371703, were only presented in patients with vivax malaria relapse.

Effect of Propagation Method and Ploidy Level of Various Rootstocks on the Response of the Common Clementine (Citrus clementina Hort. ex Tan) to a Mild Water Deficit

Current climatic upheavals reduce water availability which impacts the growth and fruit quality of plants. In citrus crops, scion/rootstock combinations are used to ensure high fruit production and quality and a stress tolerance/resistance. Our objective was to assess the effect on the clementine scion (C) under natural mild water deficit of (i) polyploid rootstocks by comparing the allotetraploid FlhorAG1 (C/4xFLs; trifoliate orange + Willowleaf mandarin) with its diploid parents, trifoliate orange (C/2xTOs), and Willowleaf mandarin (C/2xWLs), and with a diploid genotype used as reference (Carrizo citrange, C/2xCCs), (ii) rootstock propagation methods by comparing trifoliate orange seedling (C/2xTOs) with cutting (C/2xTOc). A mild water deficit observed under orchard conditions during the summer period (July–August) induced a significant change in yield (except in C/2xTOs), fruit size, and quality. C/2xCCs, C/2xTOs, and C/2xWLs appeared less affected by water deficit as indicated by their lower reduction of predawn leaf water potential (Ψpd), relative water content (RWC), transpiration (E), and photosynthetic parameters (Pnet and gs). Their greater redox balance was probably due to their better antioxidant efficiency. Seedling rootstocks lead to a better adaptation of clementine scions to water deficit than cutting or allotetraploid rootstock. Improving the tolerance to water deficit requires taking into consideration the rootstock genotype, propagation method, and ploidy level.

A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus (Carnegiea gigantea)

Genome sequence data are routinely being used to infer phylogenetic history within and between closely related diploid species, but few tree inference methods are specifically tailored to diploid genotype data. Here we re-examine the method of “polymorphism parsimony” (Inger 1967; Farris 1978; Felsenstein 1979), originally introduced to study morphological characters and chromosome inversion polymorphisms, to evaluate its utility for unphased diploid genotype data in large scale phylogenomic data sets. We show that it is equivalent to inferring species trees by minimizing deep coalescences—assuming an infinite sites model. Two potential advantages of this approach are scalability and estimation of a rooted tree. As with some other single nucleotide polymorphism (SNP) based methods, it requires thinning of data sets to statistically independent sites, and we describe a genotype-based test for phylogenetic independence. To evaluate this approach in genome scale data, we construct intraspecific phylogenies for 10 populations of the saguaro cactus using 200 Gbp of resequencing data, and then use these methods to test whether the population with highest genetic diversity corresponds to the root of the genotype trees. Results were highly congruent with the (unrooted) trees obtained using SVDquartets, a scalable alternative method of phylogenomic inference.

Fitness Cost and Competitive Ability to Different Ploidy Levels in Ryegrass Genotypes

ABSTRACT: The intergenotypic competition of tetraploid ryegrass with natural diploid population may be a tool to reduce the frequency of resistant individuals in an area. This study aimed to identify and compare the phenological development, fitness cost, and competitive ability between diploid and tetraploid ryegrass genotypes. Genotypes were grown in pots, and the morphological variables of genotype growth were assessed every 15 days up to 120 days after emergence to evaluate the fitness cost. Phenological development and seed yield components were measured in a single time together with the fitness cost. Competitive ability was determined in a replacement-series experiment with proportions of tetraploid and diploid ryegrass, in which the number of tillers, plant height, leaf area, and shoot dry weight were assessed at 50 days after emergence. The results of fitness cost showed that the number of tillers, leaf area, root dry weight, and the number of seeds were higher for tetraploid ryegrass, which presented a higher competitive ability than the diploid genotype regardless of the tested proportions. Tetraploid ryegrass may be useful for reducing the frequency of herbicide-resistant diploid ryegrass because of its higher competitive potential.

Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing

ABSTRACTOxford Nanopore Technologies’ MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunological compatibility between organ donors and recipients, but the platform’s high error rate makes it challenging to type alleles with clinical-grade accuracy. Here, we developed and validated Athlon, an algorithm that iteratively scores nanopore reads mapped to a hierarchical database of HLA alleles to arrive at a consensus diploid genotype; Athlon achieved a 100% accuracy in class I HLA typing at high resolution.

Estimating Genetic Kin Relationships in Prehistoric Populations

Archaeogenomic research has proven to be a valuable tool to trace migrations of historic and prehistoric individuals and groups, whereas relationships within a group or burial site have not been investigated to a large extent. Knowing the genetic kinship of historic and prehistoric individuals would give important insights into social structures of ancient and historic cultures. Most archaeogenetic research concerning kinship has been restricted to uniparental markers, while studies using genome-wide information were mainly focused on comparisons between populations. Applications which infer the degree of relationship based on modern-day DNA information typically require diploid genotype data. Low concentration of endogenous DNA, fragmentation and other post-mortem damage to ancient DNA (aDNA) makes the application of such tools unfeasible for most archaeological samples. To infer family relationships for degraded samples, we developed the software READ (Relationship Estimation from Ancient DNA). We show that our heuristic approach can successfully infer up to second degree relationships with as little as 0.1x shotgun coverage per genome for pairs of individuals. We uncover previously unknown relationships among prehistoric individuals by applying READ to published aDNA data from several human remains excavated from different cultural contexts. In particular, we find a group of five closely related males from the same Corded Ware culture site in modern-day Germany, suggesting patrilocality, which highlights the possibility to uncover social structures of ancient populations by applying READ to genome-wide aDNA data.

A protocol for sonication-assisted Agrobacterium rhizogenes-mediated transformation of haploid and diploid sugar beet (Beta vulgaris L.) explants.

Hairy root cultures obtained after Agrobacterium rhizogenes-mediated genetic transformation can serve as a model system for studying plant metabolism and physiology, or can be utilized for the production of secondary metabolites. So far no efficient protocol of hairy root development in sugar beet has been publically released. In this work, two A. rhizogenes strains (A4T and LBA1334) carrying a binary vector pBIN-m-gfp5-ER or pCAMBIA1301 possessing gfp and uidA reporter genes were used to transform petiole explants of haploid and diploid sugar beet genotypes. Five treatment combinations of sonicated-assisted Agrobacterium-mediated transformation were compared. Hairy roots appeared on 0% to 54% of explants depending on the treatment combination used. The highest frequency was achieved when explants of a diploid genotype were sonicated for 15 s in the inoculum containing A. rhizogenes of OD600=0.5 and then co-cultured for three days. Using the same treatment combinations the explants of haploid genotypes developed hairy roots with the frequency ranging from 10% to 36%. Transformation efficiency was independent on the bacterial strain used. The results indicate that haploid sugar beet explants are amenable to transformation using A. rhizogenes, and that the efficiency of that process can be increased by applying short ultrasound treatment.

Uneven Distribution of Mating Types among Genotypes of Candida glabrata Isolates from Clinical Samples

ABSTRACT In order to shed light on its basic biology, we initiated a population genetic analysis of Candida glabrata, an emerging pathogenic yeast with no sexual stage yet recognized. A worldwide collection of clinical strains was subjected to analysis using variable number of tandem repeats (VNTR) at nine loci. The clustering of strains obtained with this method was congruent with that obtained using sequence polymorphism of the NMT1 gene, a locus previously proposed for lineage assignment. Linkage disequilibrium supported the hypothesis of a mainly clonal reproduction. No heterozygous diploid genotype was found. Minimum-spanning tree analysis of VNTR data revealed clonal expansions and associated genotypic diversification. Mating type analysis revealed that 80% of the strains examined are MAT a and 20% MATα and that the two alleles are not evenly distributed. The MAT a genotype dominated within large clonal groups that contained only one or a few MATα types. In contrast, two groups were dominated by MATα strains. Our data are consistent with rare independent mating type switching events occurring preferentially from type a to α, although the alternative possibility of selection favoring type a isolates cannot be excluded.