Genetic Distance Research Articles

Is the persistence of Listeria monocytogenes in food processing facilities and its resistance to pathogen intervention linked to its phylogeny?

The foodborne pathogen Listeria monocytogenes is differentiated into four distinct lineages which differ in their virulence. It remains unknown, however, whether the four lineages also differ with respect to their ability to persist in food processing facilities, their resistance to high pressure, a preservation method that is used commercially for Listeria control on ready-to-eat meats, and their ability to form biofilms. This study aimed to determine differences in the pressure resistance and biofilm formation of 59 isolates of L. monocytogenes representing lineages I and II. Furthermore, the genetic similarity of 9 isolates of L. monocytogenes that were obtained from a meat processing facility over a period of 1 year and of 20 isolates of L. monocytogenes from food processing facilities was analyzed to assess whether the ability of the lineages of L. monocytogenes to persist in these facilities differs. Analysis of 386 genomes with respect to the source of isolation revealed that genomes of lineage II are over-represented in meat isolates when compared with clinical isolates. Of the 38 strains of Lm. monocytogenes that persisted in food processing facilities (this study or published studies), 31 were assigned to lineage II. Isolates of lineage I were more resistant to treatments at 400 to 600 MPa. The thickness of biofilms did not differ between lineages. In conclusion, strains of lineage II are more likely to persist in food processing facilities while strains of lineage I are more resistant to high pressure.IMPORTANCEListeria monocytogenes substantially contributes to the mortality of foodborne disease in developed countries. The virulence of strains of four lineages of L. monocytogenes differs, indicating that risks associated with the presence of L. monocytogenes are lineage specific. Our study extends the current knowledge by documentation that the lineage-level phylogeny of L. monocytogenes plays a role in the source of isolation, in the persistence in food processing facilities, and in the resistance to pathogen intervention technologies. In short, the control of risks associated with the presence of L. monocytogenes in food is also lineage specific. Understanding the route of contamination L. monocytogenes is an important factor to consider when designing improved control measures.

Genetic Characterization of Endangered Sterlet (Acipenser ruthenus, Linnaeus 1758) Gene Bank Broodstock, Natural and Cultured Populations in Hungary

The sterlet (Acipenser ruthenus) is the smallest-bodied endangered species among the six native sturgeon species of the Danube River, and self-sustaining populations still inhabit the Hungarian section of the Danube River and its largest tributary, the Tisza River. Their populations are drastically decreasing; however, they still have natural reproduction in these habitats. For the genetic conservation of the species, an ex situ gene bank is maintained in Hungary. The present study aimed to analyze the genetic resources of a gene bank with a near 40-year history and to compare it with natural populations and farmed stocks. Twelve microsatellites were used for population genetics analyses and individual genotyping of 268 specimens from two natural habitats (Danube and Tisza Rivers) and three captive stocks (a gene bank broodstock and two farms). Microsatellites revealed similar patterns among wild populations and gene bank stocks and did not show genetic differentiation (FST: 0.016–0.017) among them. These results confirmed that the gene bank broodstock properly represents the genetic background of the Danube and Tisza populations and is suitable as a source of breeding materials for the restocking programs. Negative trends were detected in the farmed stocks, reflected in reduced polymorphism at a few loci. The results of the principal component analyses indicate the farm stocks’ separation from the wild and gene bank stocks. The present genetic characterization study reveals a valuable captive stock of the endangered sterlet populations and provides unique information about the genetic similarities and differences among farms and wild stocks in Hungary. Our results provide information that contributes to preserving the genetic structure and variability in sterlet populations and supports the management of gene bank broodstock—avoiding inbreeding and preserving the unique genetic background of the Carpathian basin.

The investigation of the role of oral-originated Prevotella-induced inflammation in childhood asthma

Background and objectivesThe oral and gut microbiota play significant roles in childhood asthma pathogenesis. However, the communication dynamics and pathogenic mechanisms by which oral microbiota influence gut microbiota and disease development remain incompletely understood. This study investigated potential mechanisms by which oral-originated gut microbiota, specifically Prevotella genus, may contribute to childhood asthma etiology.MethodsOral swab and fecal samples from 30 asthmatic children and 30 healthy controls were collected. Microbiome composition was characterized using 16S rRNA gene sequencing and metagenomics. Genetic distances identified potential oral-originated bacteria in asthmatic children. Functional validation assessed pro-inflammatory properties of in silico predicted microbial mimicry peptides from enriched asthma-associated species. Fecal metabolome profiling combined with metagenomic correlations explored links between gut microbiota and metabolism. HBE cells treated with Prevotella bivia culture supernatant were analyzed for lipid pathway impacts using UPLC-MS/MS.ResultsChildren with asthma exhibited distinct oral and gut microbiota structures. Prevotella bivia, P. disiens, P. oris and Bacteroides fragilis were enriched orally and intestinally in asthmatics, while Streptococcus thermophilus decreased. P. bivia, P. disiens and P. oris in asthmatic gut likely originated orally. Microbial peptides induced inflammatory cytokines from immune cells. Aberrant lipid pathways characterized asthmatic children. P. bivia increased pro-inflammatory and decreased anti-inflammatory lipid metabolites in HBE cells.ConclusionThis study provides evidence of Prevotella transfer from oral to gut microbiota in childhood asthma. Prevotella’s microbial mimicry peptides and effects on lipid metabolism contribute to disease pathogenesis by eliciting immune responses. Findings offer mechanistic insights into oral-gut connections in childhood asthma etiology.

Oxynoemacheilus fatmae, a new species from the Güzelhisar Stream in the Aegean Sea basin, Türkiye (Teleostei: Nemacheilidae).

Oxynoemacheilus fatmae, a new species, is found in the Güzelhisar Stream in the northern Aegean Sea basin. It is differentiated from all other species of Oxynoemacheilus in the northern Aegean Sea and adjacent basins by having four to eight irregularly shaped narrow black bars on the posterior part of flank, and anterior parts of the flank with a marbled pattern. O. fatmae is differentiated from the closest species Oxynoemacheilus theophilii by having 14 fixed diagnostic nucleotide substitution sites, and the pair-wise genetic distance is 2.22%. It further differs from O. theophilii by having a slenderer body (body at dorsal-fin origin: 15%-17% standard length [SL] vs. 17%-18%), a slenderer caudal peduncle (10%-12% SL vs. 12%-13%), a more forked caudal fin (length of middle caudal-fin lope: 16%-19% SL vs. 19%-23%), and the absence the dorsal and ventral adipose crests on the caudal peduncle behind the vertical of the posterior anal-fin base (vs. present). Three species delimitation tests (assemble species by automatic partitioning (ASAP), automatic barcode gap discovery (ABGD) and generalized mixed yule-coalescent (GMYC)) and phylogenetic analyses reinforce the validity of O. fatmae as a distinct species.

CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries.

Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Genetic diversity analysis using molecular markers and in vitro shoot regeneration of strawberry cultivars in Lam Dong

In the present study, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) molecular markers were used to study the genetic diversity of ten strawberry cultivars. In addition, shoot regeneration from in vitro leaf explants of ten commercial cultivars, i.e Aicyberry, Kayonoka, Tochiotome, Penchika, Amauo, Pajado, Selva, Monterey, Camarosa, and Albion, was also investigated. The result showed that a total of 9 SCoT primers and 9 CBDP primers detected genetic polymorphism among ten strawberry cultivars. Comparatively, SCoT markers proved to be more efficient than CBDP markers in terms of percentage polymorphism as the former detected an average of 74.49% and the latter at 71.15%. Meanwhile, the indices of genetic diversity from the aggregated data of two techniques SCoT and CBDP are as follows: expected heterozygosity (He) 0.2480, Shannon index (I) 0.3749, polymorphic band ratio 75.56%. The highest level of genetic similarity among the cultivars was 0.827 (between Aicyberry and Kayonoka varieties), the lowest was 0.586 (between Aicyberry and Selva varieties), and the average was 0.724. In addition, the results of shoot regeneration of strawberry varieties from leaf discs with different sizes were strongly dependent on the genotype and weakly on explant size. Leaf explants (3 mm in size) of Camarosa cultivar cultured on MS medium supplemented with 7 g/l agar, 30 g/l sucrose and 2 mg/l TDZ gave the best shoot regeneration.

Identifying SNP threshold from P2 sequences for investigating norovirus transmission

Noroviruses are a group of non-enveloped single-stranded positive-sense RNA virus belonging to Caliciviridae family. They can be transmitted by the fecal-oral route from contaminated food and water and cause mainly acute gastroenteritis. Outbreaks of norovirus infections could be difficult to detect and investigate. In this study, we developed a simple threshold detection approach based on variations of the P2 domain of the capsid protein. We obtained sequences from the norovirus hypervariable P2 region using Sanger sequencing, including 582 pairs of epidemiologically-related strains from 35 norovirus outbreaks and 6402 pairs of epidemiologically-unrelated strains during the four epidemic seasons. Genetic distances were calculated and a threshold was performed by adopting ROC (Receiver Operating Characteristic) curve which identified transmission clusters in all tested outbreaks with 80% sensitivity. In average, nucleotide diversity between outbreaks was 67.5 times greater than the diversity within outbreaks. Simple and accurate thresholds for detecting norovirus transmissions of three genotypes obtained here streamlines molecular investigation of norovirus outbreaks, thus enabling rapid and efficient responses for the control of norovirus.

Micropropagation of Al-Taif Rose: Effects of Medium Constituents and Light on In Vitro Rooting and Acclimatization

Micropropagation facilitates the rapid production of roses. Nevertheless, in vitro rhizogenesis of essential oil roses has presented significant challenges, primarily attributed to low rates of rooting and poorer acclimatization compared to ornamental rose varieties. This study reports the optimization of in vitro rooting of Al-Taif rose (Rosa damascena f. trigintipetala (Diek) R. Keller) microshoots with the aim of increasing survival rate during acclimatization. We also investigated the effects of various parameters, including type and concentration of auxin (i.e., 2,4-Dichlorophenoxyacetic acid (2,4-D), indole acetic acid (IAA), indole butyric acid (IBA), and naphthaleneacetic acid (NAA) at concentrations of 0, 0.05, 0.1, 0.2, and 0.4 mg/L), salt strength (i.e., full- and half-strength Murashige and Skoog (MS) medium), sucrose concentration (i.e., 20, 30, 40, 60, and 80 g/L), light spectra (a 2:1 or 1:2 blue/red spectral ratio, cool or warm white light at a 1:1 ratio, and fluorescent light), light intensity (photosynthetic photon flux density (PPFD) values of 25, 50, and 100 µmol·m−2·s−1), and activated charcoal (i.e., 0 and 0.5 g/L) on the rooting and growth of in vitro regenerated Al-Taif rose axillary shoots. We found that half-strength MS medium supplemented with 0.2 mg/L NAA, 80 g/L sucrose, 0.5 g/L activated charcoal, and 50 μmol·m−2·s−1 PPFD were the optimal conditions for 100% induction of adventitious roots. Next, micropropagated Al-Taif rose plantlets were successfully transferred to a potting medium containing perlite/peatmoss (in a 1:1 ratio). We found that 98% of plants survived ex vitro conditions. The genetic fidelity of micropropagated Al-Taif rose clones along with their mother plant was tested using the inter-simple sequence repeats (ISSR) molecular marker. The genetic similarity between the micropropagated plantlets and the mother plant of Al-Taif rose plants was 98.8%, revealing high uniformity and true-to-type regenerated plants. These findings may therefore contribute toward the commercial micropropagation of Al-Taif roses.

Bidirectional communication of the gut-brain axis: new findings in Parkinson’s disease and inflammatory bowel disease

Parkinson’s disease (PD) and inflammatory bowel disease (IBD) are the two chronic inflammatory diseases that are increasingly affecting millions of people worldwide, posing a major challenge to public health. PD and IBD show similarities in epidemiology, genetics, immune response, and gut microbiota. Here, we review the pathophysiology of these two diseases, including genetic factors, immune system imbalance, changes in gut microbial composition, and the effects of microbial metabolites (especially short-chain fatty acids). We elaborate on the gut–brain axis, focusing on role of gut microbiota in the pathogenesis of PD and IBD. In addition, we discuss several therapeutic strategies, including drug therapy, fecal microbiota transplantation, and probiotic supplementation, and their potential benefits in regulating intestinal microecology and relieving disease symptoms. Our analysis will provide a new understanding and scientific basis for the development of more effective therapeutic strategies for these diseases.

A comparative analysis reveals the genomic diversity among eight Muscovy duck populations.

The Muscovy duck (Cairina moschata) is a waterfowl indigenous to the neotropical regions of Central and South America. It has low demand for concentrated feed and strong adaptability to different rearing conditions. After being introduced to China through Eurasian commercial trade, Muscovy ducks have a domestication history of around 300 years in the Fujian Province of China. In the 1990s, the commodity Muscovy duck breed "Crimo", cultivated in Europe, entered the Chinese market for consumption and breeding purposes. Due to the different selective breeding processes, Muscovy ducks have various populational traits and lack transparency of their genetic background. To remove this burden in Muscovy duck breeding process, we analyzed genomic data from 8 populations totaling 83 individuals. We identify 11.24 million single nucleotide polymorphisms (SNPs) and categorized these individuals into the Fujian-bred and the Crimo populations according to phylogenetic analyses. We then delved deeper into their evolutionary relationships through assessing population structure, calculating fixation index (FST) values, as well as measuring genetic distances. Our exploration of runs of homozygosity (ROH) and homozygous-by-descent (HBD) uncovered genomic regions enriched for genes implicated in fatty acid metabolism, development and immunity pathways. Selective sweep analyses further indicated strong selective pressures exerted on genes including TECR, STAT2 and TRAF5. These findings provide insights into genetic variations of Muscovy ducks, thus offering valuable information regarding genetic diversity, population conservation, and genome-associated for the breeding of Muscovy ducks.

Characterizing the etiology of recurrent tuberculosis using whole genome sequencing-Alaska, USA, 2008-2020.

Understanding the etiology of recurrent tuberculosis (rTB) is important for effective TB control. Prior to the advent of whole genome sequencing (WGS), attributing rTB to relapse or reinfection using genetic information was complicated by the limited resolution of conventional genotyping methods. We applied a systematic method of evaluating whole genome single nucleotide polymorphism (wgSNP) distances and results of phylogenetic analyses to characterize the etiology of rTB in American Indian and Alaska Native (AIAN) persons in Alaska during 2008-2020. We contextualized our findings through descriptive analyses of surveillance data and results of a literature search for investigations that characterized rTB etiology using WGS. The percentage of TB cases in AIAN persons in Alaska classified as recurrent episodes (11.8%) was three times the national percentage (3.9%). Of 38 recurrent episodes included in genetic analyses, we attributed 25 (65.8%) to reinfection based on wgSNP distances and phylogenetic analyses; this proportion was the highest among 16 published point estimates identified through the literature search. By comparison, we attributed 11 of 38 (28.9%) and 6 of 38 (15.8%) recurrent episodes to reinfection based on wgSNP distances alone and on conventional genotyping methods, respectively. WGS and attribution criteria involving genetic distances and patterns of relatedness can provide an effective means of elucidating rTB etiology. Our findings indicate that rTB occurs at high proportions among AIAN persons in Alaska and is frequently attributable to reinfection, reinforcing the importance of active surveillance and control measures to limit the spread of TB disease in Alaskan AIAN communities.

Riverscape features determining the genetic structure of the Yellow‐Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia

AbstractLandscape characteristics can influence gene flow depending on the species ability to disperse. This imposes different levels of resistance to movement, determining the genetic structure and diversity of populations. Waterfalls and rapids in the Amazon basin have been suggested as contributing factors to the diversification and genetic structure of freshwater species, including turtles. Thus, along some main rivers of the Brazilian Amazon: Juruá, Madeira, Amazonas, Trombetas, Tapajós, Xingu, Tocantins, and Araguaia, we evaluated the spatial distribution of genetic diversity and characterized the population structure of Podocnemis unifilis, a widely distributed and endangered Amazonian turtle, using the mitochondrial DNA control region. We tested for isolation by geographic distance and by resistance models through an integrative approach using genetic, geographic, and ecological data, comparing these matrices with genetic distance. We found heterogeneous levels of genetic diversity and no spatial patterns. Results supported the isolation by resistance hypothesis, where the movement of individuals was influenced by freshwater, vegetational, climatological, and geomorphological variables, explaining the genetic distance of P. unifilis. Rapids and waterfalls impose greater resistance although they are barriers with different levels of permeability to the P. unifilis gene flow. Thus, the idiosyncrasies of each sub‐basin must be considered in the interpretation of the patterns found in assessing phylogeographic history.Abstract in Portuguese is available with online material.

Geographic variation in genetic composition, sexual communication and mating compatibility of the False Codling Moth, Thaumatotibia leucotreta for optimisation of area-wide control

Intraspecific variation in sex pheromones is a driver of reproductive isolation and speciation in insects. The False Codling Moth (FCM) Thaumatotibia leucotreta (Lepidoptera: Tortricidae) is a quarantine pest endemic to sub-Saharan Africa (SSA). The currently available precision control measures for FCM use female sex pheromone components to lure males into traps. However, the existing data on the composition of the female sex pheromone, especially the isomer ratios of the main pheromone component (E/Z)-8-dodecenyl acetate, are inconsistent for populations in SSA. This inconsistency led to speculation about possible reproductive isolation between geographically separated FCM populations and the potential need for local adjustment of pheromone-based FCM control tools. This, however, requires a comparative evaluation of geographic variation in FCM sexual communication and inter-population mating compatibility. We therefore investigated genetic isolation and mating compatibility between five geographically isolated FCM populations in South Africa and analysed the ratio of (E)- and (Z)-8-dodecenyl acetate in females from these populations. The five studied populations were found to form three genetically distinct groups with high genetic distances between each other. Mating compatibility tests showed that mating is possible across these groups, however, males preferred females of their own population when given choices; without a choice, males successfully mated with and transferred spermatophores to females from all other populations. The ratio of (E)- and (Z)-8-dodecenyl acetate was similar (c. 4:1) across the populations, indicating that this main female pheromone component does not cause the observed intra-population mating preferences. It remains to be investigated if qualitative/quantitative variation in other sex pheromone components influences intra-population recognition in South African FCM, providing a base for the development of regionally-specific lures for area-wide control programmes.

Characteristics of sheep in the Near Arctic region by microsatellites and reproductive abilities

The microsatellites polymorphism was analyzed in ewe lambs obtained from intra-breed mating of the Pechora semifine-wool sheep and their littermates from crossing with the Kuibyshev rams. Genotyping of the population by STR loci was performed using the COrDIS Sheep reagent kit recommended by the International Society of Animal Genetics (ISAG). The age of the beginning of reproduction, fertility, milk yield, safety and growth intensity of the litter up to three months of age were taken into account in the ewe lambs. In the group of the Pechora sheep sows 74 alleles were detected, and 81 alleles were detected in the crossbred ones. INRA005 and INRA023 loci were the most polymorphic in both groups, while ETH152 was the least polymorphic. The mean genetic distance between the groups for the 12 STR loci was 0.019 ± 0.003. Pechora sheep (P) and their litters with the Kuibyshev rams (1/2 P + 1/2 K) differed significantly in the frequencies of some STR loci genes. Thus, the INRA023212 allele was found with a frequency of 0.174 in the group of P ewes and was absent in the 1/2 P + 1/2 K group, while the INRA172126 allele was found with a frequency of 0.326 and 0.122, respectively. The mean Fis values in both groups were close to zero. The groups did not differ significantly in the main genetic-population parameters. However, some advantage of the Pechora ewe sows in comparison with the crossbred sheep 1/2 P + 1/2 K on selective traits, apparently, is due to a higher genetic contribution to their heredity of the indigenous northern short-tailed sheep. According to the results of the study, it can be assumed that the age of onset of reproduction of the ewe lambs is related to the level of their heterozygosity for STR loci.

#1450 Polygenic risk score of native IgA nephropathy predicts risk of post-transplant disease recurrence

Abstract Background and Aims IgA nephropathy (IgAN) is a polygenic immune-mediated progressive glomerular disease. Recent GWAS reported that high genome-wide polygenic risk score (IgAN GPS), including 1 249 077 variants mapping to systemic immune pathways, was associated with risk of end stage kidney disease (ESKD). Post transplant (KTx) IgAN recurrence occurs in 30% of cases and it is a major cause of graft loss. Pathogenesis and predictors of IgAN recurrence are still not well defined. Herein, we studied the role of native IgAN GPS and clinical factors in predicting post-KTx IgAN recurrence and graft failure in a large cohort of KTx recipients. Method Four thousand one hundred eighty six KTx recipients from 6 sites were genome wide genotyped and imputed against multi-ancestry reference panels, retrieving >10 million variants. In each recipient, native IgAN GPS was computed and standard-normalized (i.e. expressed in units of standard deviations from the mean distribution in matched controls). Native kidney disease diagnosis, clinical parameters, and post-KTx outcome data were retrieved retrospectively from clinical charts. The IgAN GPS was tested as predictor of native IgAN in the entire KTx cohort in a logistic regression model adjusted for sex, age, recruitment site, and first 5 PCs. IgAN GPS was tested as predictor of age at transplantation (proxy for age at ESKD) among KTx recipients with native IgAN in a linear regression model adjusted for sex, recruitment site, and first 5 PCs. In recipients with native IgAN, recipient and donor parameters were individually tested as predictors for time to IgAN recurrence and time to graft failure in Cox proportional hazards models adjusted for recruitment site and first 5 PCs. Predictors with P-value < .1 were included in the multivariable models. Recipient IgAN GPS was added to the clinical models and tested for prediction of time-to IgAN recurrence, and, among KTx recipients with IgAN recurrence, of time-to subsequent graft failure. Results Three hundred sixty nine KTx recipients were affected by native IgAN, 271 were of male sex, median age at transplantation was 45 years, and 149 received a living donor KTx. Over a median follow-up time of 46 months, 96 IgAN recurrence events occurred, and, among KTx recipients with recurrent IgAN, 27 subsequent graft failure events occurred after 100 months post KTx. IgAN GPS significantly predicted native IgAN cases among all KTx recipients (OR [95% CI]: 1.95 [1.76,2.16], p = 5.60E-07, AUROC 0.73), and lower age at transplantation among recipients with native IgAN (beta [s.e.]: −1.11[0.55], p = 0.04). Clinical model for IgAN recurrence included age, sex, year of transplant, HLA mismatch, recruitment site, and first 5 PCs; clinical model for graft failure included age, sex, year of transplant, HLA mismatch, type of donation, donor age, sex, rejection events, recruitment site, and first 5 PCs. At the multivariable analysis, IgAN GPS, lower age at transplantation, lower HLA mismatch, and higher year of transplant were independently associated with time to IgAN recurrence (Fig. 1a). Among KTx recipients with recurrent IgAN, higher IgAN GPS predicted time-to graft failure independently from clinical factors (Fig. 1b), but not in non-recurrent cases. Conclusion In the KTx setting, IgAN GPS was an independent predictor of IgAN recurrence, suggesting shared genetic susceptibility between native and recurrent IgAN. In addition, associations of IgAN GPS with lower age at transplantation, and with graft failure among recurrent IgAN cases, suggest that IgAN GPS may be predictive of a more aggressive native as well as recurrent disease. Associations with lower HLA mismatch advocate donor-recipient genetic similarities as potential additional predictors of IgAN recurrence. These data, which need external validation, may provide potential new insights into the pathobiology and prediction of recurrent IgAN.

Complex genetic landscape revealed by a population in the eastern Tianshan Mountains of Xinjiang between the 8th and 11th centuries CE

AbstractThe eastern Tianshan Mountain (ETS) region in Xinjiang, China, has played a crucial role as a major highway for large‐scale human migrations and technological exchanges across Eurasia throughout history. Understanding the genetic makeup of past populations holds significant importance in comprehending human mobility in this region. Here, we report genome‐wide ancient DNA for the two individuals whose origins remain uncertain, found at the Dahe ancient city site in the ETS region. Our results indicate that although both individuals display a higher genetic affinity to Asian populations, one individual shows some genetic sharing with South Asians, while the other shares more affinity with populations from Northeastern Asia. Radiocarbon dating shows that the two human remains were not deposited simultaneously. Overall, the combined genetic, physical anthropology and radiocarbon evidence strongly suggests that the ETS region, situated at the heart of the Silk Road, has been a crossroads of diverse populations coexisting between the 8th and 11th centuries. Additionally, the genetic ancestry sharing with the Bronze Age Tarim mummies suggested a long‐term residual of indigenous ancestry in Xinjiang and showed that autochthonous deep Asian ancestry had left their genetic legacy into the historical populations of Xinjiang despite a spanning of over three millennia.

Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing

Optimization of genetic distance threshold for inferring the CRF01_AE molecular network based on next-generation sequencing

Phenotypic characterization of Guraghe and Jimma cattle breeds in Ethiopia: Implications for breed differentiation and in-situ conservation.

The aim of this study was to phenotypically characterize Guraghe and Jimma cattle breeds at the farm level and quantify the relationships between them. Eight morphometric measurements and sixteen morphological traits were recorded for a total of 313 (221 females and 92 males) randomly selected adult cattle from three purposively selected districts. Univariate and multivariate analysis procedures of Statistical Analysis Software (SAS 9.0) were used to analyze the data. Clear morphological and morphometric variations were not observed between the two cattle breeds. All of the studied cattle populations possessed straight-edged ears, a sloppy rump profile, and straight face and back profiles. Moreover, the majority of the studied cattle possess widely spaced curved horns, red-colored uniform body color patterns, and erected small humps located at the cervicothoracic position. In addition to their phenotypic similarities, multivariate analysis also failed to reveal significant differences between the two breeds. These results suggest the inseparable nature of the two cattle breeds. However, such similarities in phenotypic traits between the two cattle breeds do not necessarily indicate genetic similarities. Therefore, further genetic characterization is recommended to quantify the degree of genetic relationship between the breeds. In the meantime, it is recommended to design breed-specific in situ conservation as well as genetic improvement programs that consider cattle breeds as one. Furthermore, an inclusive and uniform breed name that can represent the two cattle populations is obtained from the country's steering committee for indigenous animal genetic resources.

The first mitogenomic phylogenetic framework of Dorcus sensu lato (Coleoptera: Lucanidae), with an emphasis on generic taxonomy in Eastern Asia

BackgroundDorcus stag beetles in broad sense are one of the most diverse group in Lucanidae and important saproxylic insects playing a crucial role in nutrient recycling and forest biomonitoring. However, the dazzling morphological differentiations have caused numerous systematic confusion within the big genus, especially the puzzlingly generic taxonomy. So far, there is lack of molecular phylogenetic study to address the chaotic situation. In this study, we undertook mitochondrial genome sequencing of 42 representative species including 18 newly-sequenced ones from Eastern Asia and reconstructed the phylogenetic framework of stag beetles in Dorcus sensu lato for the first time.ResultsThe mitogenome datasets of Dorcus species have indicated the variable mitogenomic lengths ranged from 15,785 to 19,813 bp. Each mitogenome contained 13 PCGs, 2 rRNAs, 22 tRNAs, and a control region, and all PCGs were under strong purifying selection (Ka/Ks < 1). Notably, we have identified the presence of a substantial intergenic spacer (IGS) between the trnAser (UCN) and NAD1 genes, with varying lengths ranging from 129 bp (in D. hansi) to 158 bp (in D. tityus). The mitogenomic phylogenetic analysis of 42 species showed that Eastern Asia Dorcus was monophyletic, and divided into eight clades with significant genetic distance. Four of them, Clade VIII, VII, VI and I are clustered by the representative species of Serrognathus Motschulsky, Kirchnerius Schenk, Falcicornis Séguy and Dorcus s.s. respectively, which supported their fully generic positions as the previous morphological study presented. The topology also showed the remaining clades were distinctly separated from the species of Dorcus sensu lato, which implied that each of them might demonstrate independent generic status. The Linnaeus nomenclatures were suggested as Eurydorcus Didier stat. res., Eurytrachellelus Didier stat. res., Hemisodorcus Thomson stat. res. and Velutinodorcus Maes stat. res. For Clade V, IV, III and II respectively.ConclusionThis study recognized the monophyly of Dorcus stag beetles and provided a framework for the molecular phylogeny of this group for the first time. The newly generated mitogenomic data serves as a valuable resource for future investigations on lucanid beetles. The generic relationship would facilitate the systematics of Dorcus stag beetles and thus be useful for exploring their evolutionary, ecological, and conservation aspects.