Number Of Repeats Research Articles

Insights into taxonomy and phylogenetic relationships of eleven Aristolochia species based on chloroplast genome.

The Aristolochia, as an important genus comprised of over 400 species, has attracted much interest because of its unique chemical and pharmacological properties. However, the intrageneric taxonomy and species identification within Aristolochia have long been difficult because of the complexity of their morphological variations and lack of high-resolution molecular markers. In this study, we sampled 11 species of Aristolochia collected from distinct habitats in China, and sequenced their complete chloroplast (cp) genomes. The 11 cp genomes of Aristolochia ranged in size from 159,375bp (A. tagala) to 160,626 bp (A. tubiflora), each containing a large single-copy (LSC) region (88,914-90,251 bp), a small single-copy (SSC) region (19,311-19,917 bp), and a pair of inverted repeats (IR) (25,175-25,698 bp). These cp genomes contained 130-131 genes each, including 85 protein-coding genes (CDS), 8 ribosomal RNA genes, and 37-38 transfer RNA genes. In addition, the four types of repeats (forward, palindromic, reverse, and complement repeats) were examined in Aristolochia species. A. littoralis had the highest number of repeats (168), while A. tagala had the lowest number (42). The total number of simple sequence repeats (SSRs) is at least 99 in A. kwangsiensis, and, at most, 161 in A. gigantea. Interestingly, we detected eleven highly mutational hotspot regions, including six gene regions (clpP, matK, ndhF, psbT, rps16, trnK-UUU) and five intergenic spacer regions (ccsA-ndhD, psbZ-trnG-GCC, rpl33-rps18, rps16-trnQ-UUG, trnS-GCU-trnG-UCC). The phylogenetic analysis based on the 72 protein-coding genes showed that 11 Aristolochia species were divided into two clades which strongly supported the generic segregates of the subgenus Aristolochia and Siphisia. This research will provide the basis for the classification, identification, and phylogeny of medicinal plants of Aristolochiaceae.

<i>Yersinia pestis</i> ssp. <i>pestis</i> Spatial MLVA25 Genotypic Structure in the Transboundary Saylyugem Natural Plague Focus

Advanced molecular-genetic methods for the diagnosis and typing of Yersinia pestis ssp. pestis in the field and clinical material are used for epidemiological surveillance of plague in the Saylyugem natural focus. The aim of the work was to study the spatial genotypic structure of Y. pestis ssp. pestis in the transboundary Saylyugem natural plague focus using MLVA25 typing. Materials and methods. The MLVA25 typing of 160 strains of Y. pestis ssp. Pestis isolated in the Saylyugem natural plague focus in 2012–2021 was carried out. Phylogenetic tree construction was performed with the help of UPGMA and MST methods. Results and discussion. The Y. pestis ssp. pestis strains isolated from the Saylyugem natural plague focus were differentiated into 15 MLVA types by the 25 VNTR loci cluster analysis. The studied strains form a homogeneous complex of MLVA25 types without marked geographical distribution across seven spatial groups. The analysis of the frequency of occurrence of the tandem repeats number for three variable loci of Y. pestis ssp. pestis strains shows the significant differences between the samples from the Mongolian and Russian parts of the Saylyugem natural plague focus. The most pronounced differences in spatial genotypic structure are traced through the yp4280ms62 locus.

Exploring nitric oxide as a crucial prognostic biomarker of coronary artery disease

PurposeThe study aimed to examine if the polymorphism of the endothelial nitric oxide synthase (eNOS) gene variable number of tandem repeats (VNTR) and the serum NO levels are associated with CAD. Materials/methodsCase-control study, 70 CAD and 30 control subjects were enrolled. The eNOS gene polymorphism was measured by polymerase chain reaction–agarose gel electrophoresis and the serum NO was assessed by using an ELISA plate and reader covering 540 nm. ResultsUncovering the area under curve (AUC) for serum NO, which was (0.6821), indicating that NO seemed to be a critical prognostic biomarker of CAD; also, glucose, serum creatinine and total bilirubin proved to be significant predictors of CAD with AUC (0.6793, 0.6717 and 0.6662) respectively. Furthermore, higher serum NO levels were associated with the eNOS (ab) genotype. Revealing the intron (a) allele was protective against CAD. Moreover, diminished levels of serum NO in CAD groups compared to controls (P < 0.05). Additionally, Multiple logistic regression analysis shows a significantly high Odds ratio associated with CAD in the Duhok population. ConclusionsThe eNOS (ab) variant seems to be a protective CAD factor for patients. Low serum NO levels are another risk factor for the advancement of CAD, suggesting their involvement in atherosclerosis. The (a) allele's protective effect is mediated through changes in eNOS promoter activity and higher NO levels.

Study of human ribosomal gene complex in cystic fibrosis

Increasing the life expectancy of patients with CF is an urgent healthcare task all over the world. According to the Register of patients with cystic fibrosis in the Russian Federation (2020), the number of patients over 18 years of age is 26.5%. Assumably, cystic fibrosis can be used as a model of accelerated aging to study the aging process in general.Aim of the study was to analyze the number of rDNA copies in a sample of cystic fibrosis patients at different ages and with lethal outcome in relation to lung function, complications, and respiratory tract infections.Methods. We studied DNA samples isolated by the standard method from peripheral blood leukocytes of 277 patients diagnosed with cystic fibrosis. 998 DNA samples from healthy volunteers were used as a control group.Results. The study showed that the genomes of patients with CF contain more rDNA copies than those of control patients. The greatest number of copies of ribosomal genes was observed in DNA samples from deceased patients (p &lt; 0.001) and was associated with more severe disease course. Among all CF patients, the largest number of rDNA copies in the genome was registered in patients with the lowest FEV1 values (less than 40%). It was found that patients with chronic Burkholderia cepacia complex infection had a significantly higher number of copies of ribosomal repeats than the total sample (p = 0.001) and the adults (p = 0.014). The number of ribosomal repeats did not differ between patients with other chronic respiratory tract infections.Conclusion. In the group of deceased patients, the patients with low respiratory function and Burkholderia cepacia complex infection had the highest number of rDNA copies in the genome, and the differences were significant. It can be assumed that the number of rDNA copies in the genome of CF patients is an additional prognostic marker that is associated with the patient’s life expectancy.

Complete mitochondrial genome of Thuja sutchuenensis and its implications on evolutionary analysis of complex mitogenome architecture in Cupressaceae

BackgroundThe complex physical structure and abundant repeat sequences make it difficult to assemble the mitogenomes of seed plants, especially gymnosperms. Only approximately 33 mitogenomes of gymnosperms have been reported. However, as the most widely distributed and the second largest family among gymnosperms, Cupressaceae has only six assembled mitogenomes, including five draft mitogenomes and one complete mitogenome, which has greatly hindered the understanding of mitogenome evolution within this large family, even gymnosperms.ResultsIn this study, we assembled and validated the complete mitogenome of Thuja sutchuenensis, with a size of 2.4 Mb. Multiple sequence units constituted its complex structure, which can be reduced to three linear contigs and one small circular contig. The analysis of repeat sequences indicated that the numbers of simple sequence repeats increased during the evolutionary history of gymnosperms, and the mitogenome of Thuja sutchuenensis harboured abundant extra-long repeats (more than 5 kb). Additionally, the longest repeat sequence identified in these seven gymnosperms also came from the mitogenome of Thuja sutchuenensis, with a length of up to 47 kb. The analysis of colinear blocks and gene clusters both revealed that the orders of mitochondrial genes within gymnosperms was not conserved. The comparative analysis showed that only four tRNAs were shared by seven gymnosperms, namely, trnD-GUC, trnE-UUC, trnI-CAU and trnY-GUA. Furthermore, four genes have undergone potential positive selection in most gymnosperm species, namely, atp8, ccmB, mttB and sdh4.ConclusionWe successfully assembled the second complete mitogenome within Cupressaceae and verified that it consisted of multiple sequence units. Our study also indicated that abundant long repeats may contribute to the generation of the complex conformation of the mitogenome of Thuja sutchuenensis. The investigation of Thuja sutchuenensis’s mitogenome in our study provides new insight into further understanding the complex mitogenome architecture within gymnosperms.

Association of alcohol consumption with telomere length in humans: a systematic review

Telomeres are complex nucleoprotein structures with specific proteins of noncoding terminal regions of linear chromosomes of eukaryotic cells. Telomere DNA consists of a large number of short sequence repeats (TTAGGG in vertebrates). Telomeres protect chromosomes from their fusion and degradation, limit the proliferative potential of the cell, participate in the segregation of chromosomes during cell division, etc. Reduction of telomeres length is an important factor with significant impact on cell viability and function, aging, and leads to the development of various diseases including cancer.&#x0D; Alcohol abuse has a significant impact on a person's health. Ethanol consumption by a human potentially affects the length of chromosome telomeres on the cellular level.&#x0D; Current review represents systematic analysis of studies on the effect of alcohol consumption on telomere length in humans. PubMed and eLIBRARY.RU databases were explored for the combinations of the terms ("Ethanol" OR "Alcohol") AND "Telomer" with a limitation on the publication date until 01 January 2011. The search resulted in 269 studies. In accordance with the preset criteria, total 238 studies were excluded from the analysis, and 3 publications were excluded due to unavailability of full text. A total of 28 epidemiological and clinical studies were included for this study review.&#x0D; The association of alcohol consumption with shortening of telomeres was reported in 16 of the studies conducted with various populations and cohorts including individuals with alcohol abuse, alcohol dependence, and some genetic variants of alcohol metabolism enzymes. 12 studies reported alcohol consumption was not associated with change in telomere length.&#x0D; The analysis of reviewed studies allows to conclude that they are ambiguous and that there is further urgency to study the effect of alcohol on telomere length by engaging modern methods for its determination.

Подход к кластеризации пациентов по микрочиповым данным внутри отдельных локусов с использованием комбинаций вариантов

Fuchs' endothelial corneal dystrophy is a socially significant hereditary disease. More than a half of cases in the European population are caused by the increased number of trinucleotude repeats in the TCF4 gene. The study was aimed to develop and test the approach of dividing patients into groups based on the chip-based genotyping and genome-wide association study (GWAS) results. The analysis was conducted using FECD Genetics Multi-center Study and AREDs project datasets containing the data of 1721 clinical cases and 2408 control patients. When analyzing the GWAS results, the patients and the control group were divided into two groups by means of hierarchical clustering suggesting that patients with the increased number of repeats in the TCF4 gene are carriers of specific combinations of genomic variants (haplotypes). It was shown that individual variants cannot be used for the molecular genetic stratification of patients with the increased number of repeats in TCF4 due to inconsistent results obtained for the variants. Furthermore, the haplotype-based approach outperformed the SNPs in terms of odds ratio. The paper proposes a method that enables further search for the biologically relevant combinations of genomic variants.

Molecular Mechanisms to Optimize Gene Translation Elongation Differ Significantly in Bacteria with and without Nonribosomal Peptides

Nonribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes that form gene clusters in bacterial genomes. We hypothesized that the presence of nonribosomal peptide synthesis pathways is a specific feature of bacterial metabolism, which may affect other vital processes of the cell, including translational ones. This work was the first to show the relationship between the translation regulation mechanism of protein-coding genes in bacteria, which is largely determined by the efficiency of translation elongation, and the presence of gene clusters in the genomes for the biosynthesis of nonribosomal peptides. Bioinformatic analysis of the translation elongation efficiency of protein-coding genes was performed in 11679 bacterial genomes, some of which contained gene clusters of nonribosomal peptide biosynthesis and some of which did not. The analysis showed that bacteria whose genomes contained clusters of nonribosomal peptide biosynthetic genes and those without such gene clusters differ significantly in the molecular mechanisms that ensure translation efficiency. Thus, among microorganisms whose genomes contain gene clusters of nonribosomal peptide synthetases, a significantly smaller part of them is characterized by optimized regulation of the number of local inverted repeats, while most of them have genomes optimized by the averaged energy of inverted repeats studs in mRNA and additionally by codon composition. Our results suggest that the presence of nonribosomal peptide biosynthetic pathways in bacteria may influence the structure of the overall bacterial metabolism, which is also expressed in the specific mechanisms of ribosomal protein biosynthesis.

The Role of Alleles with Intermediate Numbers of Trinucleotide Repeats in Parkinson’s Disease and Other Neurodegenerative Diseases

The Role of Alleles with Intermediate Numbers of Trinucleotide Repeats in Parkinson’s Disease and Other Neurodegenerative Diseases

Effects of phosphorylation to the conformational space of C-terminal domain of RNA polymerase II.

Intrinsically disordered proteins (IDPs) are known as proteins without a defined secondary structure and linked with many neurological diseases. Exploring the conformational space of IDPs is one of the major challenges faced by the experimental and computational studies due to its disordered nature. Obtaining an accurate conformational space is very important to identify the structural properties of IDPs linked with these biological phenomena. RNA polymerase II (Pol II) C-terminal domain (CTD) is an intrinsically disordered low complexity domain that has a heptapeptide repeating sequence with number of repeats varies according to the organism. CTD was documented to undergo liquid-liquid phase separation, which is affected by its length and phosphorylation level. In this study, we investigated the conformational space of CTD and the effects of phosphorylation to its conformation using enhanced sampling molecular dynamics (MD) simulations. We used CTD models with two repeating units with non-phosphorylated and phosphorylated states. In addition, we study a longer synthetic CTD sequence, which has available experimental observables as a reference point to compare with the simulations. Our results suggested that phosphorylation has complex effects on the conformations of the CTD that depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination and interactions with the nearby residues. With this study we provide a detailed explanation of conformational changes of CTD models upon their phosphorylation.

IL-1 Polymorphism and Helicobacter pylori Infection Features: Highlighting VNTR’s Potential in Predicting the Susceptibility to Infection-Associated Disease Development

Genetic polymorphisms at the IL-1 cluster are associated with increased Helicobacter pylori (H. pylori)-associated disease risk in an ethnically dependent manner. Due to the corroborated role of IL-1β in H. pylori infection progression, our aim is to depict the impact of IL1B rs1143627 and rs16944 as well as the IL1RN variable number of identical tandem repeats (VNTR) on the clinical and biological features of Moroccan H. pylori-infected patients. A total of 58 patients with epigastralgic pain were referred to the gastroenterology department for histopathological and clinical analysis. DNA extraction from antrum and fundus biopsies and PCR-RFLP were performed to detect polymorphisms. As a result, VNTR was significantly associated with IL-1β antrum levels (p-value = 0.029), where the *1/*4 genotype showed a positive association with upregulated cytokine levels in the antrum and was clustered with H. pylori-infected patients' features and higher levels of IL-1β in the antrum and fundus. Likewise, *1/*1 genotype carriers clustered with severe gastritis activity and H. pylori density scores along with low levels of IL-1β in the antrum and fundus, while the *1/*2 genotype was clustered with non-infected-patient features and normal IL-1β levels. In conclusion, VNTR might be an interesting predictor to identify patients at risk of developing H. pylori-associated pathologies.

Genetic diversity of Candidatus Liberibacter asiaticus strains from the Central Pacific citrus region in Mexico

Huanglongbing (HLB) is associated with Candidatus Liberibacter asiaticus (CLas). It is a destructive disease of citrus. The objective of this study was to determine the genetic diversity of 90 strains of CLas infecting eight citrus species trees from the Central Pacific in Mexico. Genetic diversity among CLas was estimated by fourteen variable numbers of tandem repeat (VNTRs) loci. Three loci were polymorphic, SSR00 and SSR077 amplified four alleles each, while the locus SSR-A amplified two alleles, and the other loci only one allele per locus, resulting in a total of 21 alleles. Dendrogram analysis showed two clusters. No clear genetic structure was found in relation to geographical origin or host. The cluster I was mostly constituted by the majority of CLas strains (82%), but the cluster II comprised twelve strains of CLas collected in Tecoman location, State of Colima, and were obtained from different citrus hosts species. The frequency of 17 haplotypes among strains of CLas from the states of Nayarit, Jalisco, Colima and Michoacán was analyzed; in Colima 14 haplotypes were determinated, while in Michoacan all strains were identified in one haplotype. These results indicate a large genetic diversity among the strains of CLas present in the Central Pacific region in Mexico.

Versatile Biosynthetic Approach to Regioselective Enzyme Patterning for Direct Bioelectrocatalysis Application

AbstractDue to the outstanding attributes of oxidoreductases, they have been utilized as biomaterials for bioelectrocatalytic systems. Herein, a simple and versatile biosynthetic approach that can designate binding position of enzymes on electrode with their surface‐orientation is suggested. In this regard, material‐selective properties of gold‐binding peptide (GBP) are exploited and genetically fused GBP to enzyme. To optimize the design of synthetic enzyme, a variable repeat number of GBP are fused to flavin adenine dinucleotide‐dependent glucose dehydrogenase gamma‐alpha complex (GDHγα) and their catalytic and gold‐binding activities are determined. The substrate catalysis and direct electrocatalytic capability of selected construct, GDHγα with three GBP repeats (GDHγα‐3GBP), are investigated on electrode. In an inorganic‐binding characterization, GDHγα‐3GBP exhibits fourfold higher affinity on gold (Au) surface and 215‐fold lower binding affinity for silicon dioxide (SiO2) than wild‐type GDHγα. Utilizing those regioselective features, fusion GDHγα is incorporated into nanotemplates comprising Au nanopatterns and SiO2 background. Thereby, nanoscale patterned GDHγα‐3GBP molecules are successfully obtained with their binding locations controlled specifically by Au nanopatterns, not SiO2. The results reveal that genetic SBP fusions enable highly selective template‐based surface assembly of biomolecules with electrically intimate cofactor‐surface interfaces. The proposed technology has remarkable potential to fabricate small‐scale biochips applied for enzyme‐based bioelectronics.

Chloroplast genomes of four Carex species: Long repetitive sequences trigger dramatic changes in chloroplast genome structure.

The chloroplast genomes of angiosperms usually have a stable circular quadripartite structure that exhibits high consistency in genome size and gene order. As one of the most diverse genera of angiosperms, Carex is of great value for the study of evolutionary relationships and speciation within its genus, but the study of the structure of its chloroplast genome is limited due to its highly expanded and restructured genome with a large number of repeats. In this study, we provided a more detailed account of the chloroplast genomes of Carex using a hybrid assembly of second- and third-generation sequencing and examined structural variation within this genus. The study revealed that chloroplast genomes of four Carex species are significantly longer than that of most angiosperms and are characterized by high sequence rearrangement rates, low GC content and gene density, and increased repetitive sequences. The location of chloroplast genome structural variation in the species of Carex studied is closely related to the positions of long repeat sequences; this genus provides a typical example of chloroplast structural variation and expansion caused by long repeats. Phylogenetic relationships constructed based on the chloroplast protein-coding genes support the latest taxonomic system of Carex, while revealing that structural variation in the chloroplast genome of Carex may have some phylogenetic significance. Moreover, this study demonstrated a hybrid assembly approach based on long and short reads to analyze complex chloroplast genome assembly and also provided an important reference for the analysis of structural rearrangements of chloroplast genomes in other taxa.

Plastome evolution and phylogenomics of Impatiens (Balsaminaceae)

This study reported seven new plastomes from Impatiens and observed three highly variable regions for phylogeny and DNA barcoding, which resolved the relationships among sections of subgenus Impatiens. Impatiens L. (Balsaminaceae, Ericales) is one of the largest and most diverse genera of angiosperms, widely known for its taxonomic difficulty. In this study, we reevaluated the infrageneric relationships within the genus Impatiens, using complete plastome sequence data. Seven complete plastomes of Impatiens (representing 6 species) were newly sequenced and characterized along with 20 previously published plastomes of other Impatiens species, plus 2 plastomes of outgroups (Hydrocera triflora, Balsaminaceae; Marcgravia coriacea, Marcgraviaceae). The total size of these 29 plastomes ranged from 151,538bp to 152,917bp, except 2 samples of Impatiens morsei, which exhibited a shorter length and lost some genes encoding NADH dehydrogenase subunits. Moreover, the number of simple sequence repeats (SSRs) ranged from 51 to 113, and the number of long repeats from 17 to 26. In addition, three highly variable regions were identified (trnG-GCC (The previous one), ndhF-rpl32-trnL-UGA-ccsA, and ycf1). Our phylogenomic analysis based on 80 plastome-derived protein-coding genes strongly supported the monophyly of Impatiens and its two subgenera (Clavicarpa and Impatiens), and fully resolved relationships among the six (out of seven) sampled sections of subgenus Impatiens. Overall, the plastome DNA markers and phylogenetic results reported in this study will facilitate future identification, taxonomic and DNA barcoding studies in Impatiens as well as evolutionary studies in Balsaminaceae.

Staphylococcal Periscope proteins Aap, SasG, and Pls project noncanonical legume-like lectin adhesin domains from the bacterial surface

Staphylococcus aureus and Staphylococcus epidermidis are frequently associated with medical device infections that involve establishment of a bacterial biofilm on the device surface. Staphylococcal surface proteins Aap, SasG, and Pls are members of the Periscope Protein class and have been implicated in biofilm formation and host colonization; they comprise a repetitive region ("B region") and an N-terminal host colonization domain within the "A region," predicted to be a lectin domain. Repetitive E-G5 domains (as found in Aap, SasG, and Pls) form elongated "stalks" that would vary in length with repeat number, resulting in projection of the N-terminal A domain variable distances from the bacterial cell surface. Here, we present the structures of the lectin domains within A regions of SasG, Aap, and Pls and a structure of the Aap lectin domain attached to contiguous E-G5 repeats, suggesting the lectin domains will sit at the tip of the variable length rod. We demonstrate that these isolated domains (Aap, SasG) are sufficient to bind to human host desquamated nasal epithelial cells. Previously, proteolytic cleavage or a deletion within the A domain had been reported to induce biofilm formation; the structures suggest a potential link between these observations. Intriguingly, while the Aap, SasG, and Pls lectin domains bind a metal ion, they lack the nonproline cis peptide bond thought to be key for carbohydrate binding by the lectin fold. This suggestion of noncanonical ligand binding should be a key consideration when investigating the host cell interactions of these bacterial surface proteins.

Reduced volume of diabetic pancreatic islets in rodents detected by synchrotron X-ray phase-contrast microtomography and deep learning network

The pancreatic islet is a highly structured micro-organ that produces insulin in response to rising blood glucose. Here we develop a label-free and automatic imaging approach to visualize the islets in situ in diabetic rodents by the synchrotron radiation X-ray phase-contrast microtomography (SRμCT) at the ID17 station of the European Synchrotron Radiation Facility. The large-size images (3.2mm×15.97mm) were acquired in the pancreas in STZ-treated mice and diabetic GK rats. Each pancreas was dissected by 3000 reconstructed images. The image datasets were further analysed by a self-developed deep learning method, AA-Net. All islets in the pancreas were segmented and visualized by the three-dimension (3D) reconstruction. After quantifying the volumes of the islets, we found that the number of larger islets (=>1500 μm3) was reduced by 2-fold (wt 1004±94 vs GK 419±122, P<0.001) in chronically developed diabetic GK rat, while in STZ-treated diabetic mouse the large islets were decreased by half (189±33 vs 90±29, P<0.001) compared to the untreated mice. Our study provides a label-free tool for detecting and quantifying pancreatic islets in situ. It implies the possibility of monitoring the state of pancreatic islets in vivo diabetes without labelling.

Molecular genetic aspects of Gilbert's syndrome, Crigler-Najjar syndromes types I and II

Variants of the UGT1A1 gene are associated with impaired bilirubin metabolism, which is clinically expressed in Gilbert's syndrome (GS), Crigler-Najjar syndrome types I and II, as well as increased toxicity intaking certain drugs (indinavir, irinotecan, atazanavir, sorafenib, tocilizumab, belinostat, and paracetamol). A common manifestation of these conditions is unconjugated hyperbilirubinemia. The most common variant in the UGT1A1 gene associated with GS (the most common pathology caused by UGT1A1 gene variants) is the UGT1A1*28 variant, which is an increased number of TA repeats in the promoter of the UGT1A1 gene up to 7. However, the UGT1A1*28 variant is not the only gene variant capable of causing unconjugated hyperbilirubinemia. It is known that the variants UGT1A*7, UGT1A*6, and UGT1A*27 were found in the Asian population, which also causes GS with a high frequency. For Caucasians, the UGT1A1*28 variant remains the only common variant that causes GS. At the same time, even the carriage of the UGT1A1*28 variant in the homozygous state does not always lead to the appearance of clinical symptoms. While in the heterozygous form of the UGT1A1*28 variant, high unconjugated hyperbilirubinemia can be observed. Thus, other molecular genetic markers probably explain the incomplete penetrance and variable expressivity of the clinical manifestations of the UGT1A1 gene variants

The genome of a Far Eastern isolate of Diaporthe caulivora, a soybean fungal pathogen.

Diaporthe caulivora is an economically important fungal pathogen and a causal agent of soybean stem canker and seed decay. Here, the genome of a Russian Far Eastern isolate of D. caulivora was sequenced, assembled, and announced. Assembly quality was enough for advanced annotation, including prediction of potential disease-related genes encoding virulence factors and molecular determinants contributing to pathogen-host selection, interactions, and adaptation. Comparative analysis of 15 Diaporthe species was conducted regarding general genome properties, collinearity, and proteomes, and included detailed investigation of interspersed repeats. A notable feature of this analysis is a high recombinant variability of Diaporthe genomes, determined by the number and distribution of interspersed repeats, which also proved to be responsible for the diversity of GC content and genome size. This variability is assumed the main determinant of the divergence of Diaporthe genomes. A Bayesian multi-gene phylogeny was inferred for the 15 Diaporthe species on the basis of twenty thousand polymorphic sites of > 100 orthologous genes using independently adjusted evolutionary models. This allowed for the most accurate determination of evolutionary relationships and species boundaries for effective reporting about these plant pathogens. The evidence, obtained by different genome analysis techniques, implies the host-independent evolution of Diaporthe species. KEY POINTS: • The genome of a Far Eastern isolate of D. caulivora was announced. • A high degree of recombinant variability determines genomic divergence in Diaporthe genus. • The multi-gene phylogeny implies host-independent evolution of Diaporthe species.

Natural variation of codon repeats in COLD11 endows rice with chilling resilience

Abnormal temperature caused by global climate change threatens the rice production. Defense signaling network for chilling has been uncovered in plants. However, less is known about repairing DNA damage produced from overwhelmed defense and its evolution during domestication. Here, we genetically identified a major QTL, COLD11, using the data-merging genome-wide association study based on an algorithm combining polarized data from two subspecies, indica and japonica, into one system. Rice loss-of-function mutations of COLD11 caused reduced chilling tolerance. Genome evolution analysis of representative rice germplasms suggested that numbers of GCG sequence repeats in the first exon of COLD11 were subjected to strong domestication selection during the northern expansion of rice planting. The repeat numbers affected the biochemical activity of DNA repair protein COLD11/RAD51A1 in renovating DNA damage under chilling stress. Our findings highlight a potential way to finely manipulate key genes in rice genome and effectively improve chilling tolerance through molecular designing.