Search

Background: TBX6, a member of the T-box gene family, encodes the transcription factor box 6 that is critical for somite segmentation in vertebrates. It is known that the compound heterozygosity of disruptive variants in trans with a common hypomorphic risk haplotype (T-C-A) in the TBX6 gene contribute to 10% of congenital scoliosis (CS) cases. The deletion of chromosome 17q12 is a rare cytogenetic abnormality, which often leads to renal cysts and diabetes mellitus. However, the affected individuals often exhibit clinical heterogeneity and incomplete penetrance. Methods: We here present a Chinese fetus who was shown to have CS by ultrasound examination at 17 weeks of gestation. Trio whole-exome sequencing (WES) was performed to investigate the underlying genetic defects of the fetus. In vitro functional experiments, including western-blotting and luciferase transactivation assay, were performed to determine the pathogenicity of the novel variant of TBX6. Results: WES revealed the fetus harbored a compound heterozygous variant of c.338_340del (p.Ile113del) and the common hypomorphic risk haplotype of the TBX6 gene. In vitro functional study showed the p.Ile113del variant had no impact on TBX6 expression, but almost led to complete loss of its transcriptional activity. In addition, we identified a 1.85 Mb deletion on 17q12 region in the fetus and the mother. Though there is currently no clinical phenotype associated with this copy number variation in the fetus, it can explain multiple renal cysts in the pregnant woman. Conclusions: This study is the first to report a Chinese fetus with a single amino acid deletion variant and a T-C-A haplotype of TBX6. The clinical heterogeneity of 17q12 microdeletion poses significant challenges for prenatal genetic counseling. Our results once again suggest the complexity of prenatal genetic diagnosis. [ABSTRACT FROM AUTHOR]

Background: The cashmere goat industry is one of the main pillars of animal husbandry in Inner Mongolia Autonomous Region, and plays an irreplaceable role in local economic development. With the change in feeding methods and environment, the cashmere produced by Inner Mongolia cashmere goats shows a tendency of coarser, and the cashmere yield can not meet the consumption demand of people. However, the genetic basis behind these changes is not fully understood. We measured cashmere traits, including cashmere yield (CY), cashmere diameter (CD), cashmere thickness (CT), and fleece length (FL) traits for four consecutive years, and utilized Genome-wide association study of four cashmere traits in Inner Mongolia cashmere goats was carried out using new genomics tools to infer genomic regions and functional loci associated with cashmere traits and to construct haplotypes that significantly affect cashmere traits. Results: We estimated the genetic parameters of cashmere traits in Inner Mongolia cashmere goats. The heritability of cashmere yield, cashmere diameter, and fleece length traits of Inner Mongolia cashmere goats were 0.229, 0.359, and 0.250, which belonged to the medium heritability traits (0.2 ~ 0.4). The cashmere thickness trait has a low heritability of 0.053. We detected 151 genome-wide significantly associated SNPs with four cashmere traits on different chromosomes, which were very close to the chromosomes of 392 genes (located within the gene or within ± 500 kb). Notch3, BMPR1B, and CCNA2 have direct functional associations with fibroblasts and follicle stem cells, which play important roles in hair follicle growth and development. Based on GO functional annotation and KEGG enrichment analysis, potential candidate genes were associated with pathways of hair follicle genesis and development (Notch, P13K-Akt, TGF-beta, Cell cycle, Wnt, MAPK). We calculated the effective allele number of the Inner Mongolia cashmere goat population to be 1.109–1.998, the dominant genotypes of most SNPs were wild-type, the polymorphic information content of 57 SNPs were low polymorphism (0 < PIC < 0.25), and the polymorphic information content of 79 SNPs were moderate polymorphism (0.25 < PIC < 0.50). We analyzed the association of SNPs with phenotypes and found that the homozygous mutant type of SNP1 and SNP3 was associated with the highest cashmere yield, the heterozygous mutant type of SNP30 was associated with the lowest cashmere thickness, the wild type of SNP76, SNP77, SNP78, SNP80, and SNP81 was associated with the highest cashmere thickness, and the wild type type of SNP137 was associated with the highest fleece length. 21 haplotype blocks and 68 haplotype combinations were constructed. Haplotypes A2A2, B2B2, C2C2, and D4D4 were associated with increased cashmere yield, haplotypes E2E2, F1F1, G5G5, and G1G5 were associated with decreased cashmere fineness, haplotypes H2H2 was associated with increased cashmere thickness, haplotypes I1I1, I1I2, J1J4, L5L3, N3N2, N3N3, O2O1, P2P2, and Q3Q3 were associated with increased cashmere length. We verified the polymorphism of 8 SNPs by KASP, and found that chr7_g.102631194A > G, chr10_g.82715068 T > C, chr1_g.124483769C > T, chr24_g.12811352C > T, chr6_g.114111249A > G, and chr6_g.115606026 T > C were significantly genotyped in verified populations (P < 0.05). Conclusions: In conclusion, the genetic effect of single SNP on phenotypes is small, and SNPs are more inclined to be inherited as a whole. By constructing haplotypes from SNPs that are significantly associated with cashmere traits, it will help to reveal the complex and potential causal variations in cashmere traits of Inner Mongolia cashmere goats. This will be a valuable resource for genomics and breeding of the cashmere goat. [ABSTRACT FROM AUTHOR]

The linguistic, historical, and subsistent uniqueness of Hmong–Mien (HM) speakers offers a wonderful opportunity to investigate how these factors impact the genetic structure. The genetic differentiation among HM speakers and their population history are not well characterized. Here, we generate genome‐wide data from 65 Yao ethnicity samples and analyze them with published data, particularly by leveraging haplotype‐based methods. We determined that the fine‐scale genetic substructure of HM speakers corresponds better with linguistic classification than with geography. Particularly, parallels between serial founder events and language differentiations can be observed in West Hmongic speakers. Multiple lines of evidence indicate that ~500‐year‐old GaoHuaHua individuals are most closely related to West Hmongic‐speaking Bunu. The strong genetic bottleneck of some HM‐speaking groups, especially Bunu, could potentially be associated with their long‐term practice of swidden agriculture to some degree. The inferred admixture dates for most of the HM speakers overlap with the reign of the Ming dynasty (1368–1644 CE). Besides a common genetic origin for HM speakers, their genetic ancestry is shared primarily with neighboring Han Chinese and Tai‐Kadai speakers in south China. In conclusion, our analyses reveal that recent isolation and admixture events have contributed to the genetic population history of present‐day HM speakers. [ABSTRACT FROM AUTHOR]

The Yangtze River floodplain is an area with an extremely rich diversity of fish species. Poyang Lake, as an important part of this river–floodplain system, is a crucial habitat for the survival of fish. However, prolonged human activities, such as environmental pollution and hydroelectric development, have degraded the habitat in the Poyang Lake Basin, posing threats to fish populations. Understanding genetic diversity is crucial for maintaining fish populations and understanding their dynamics. The genetic diversity of Hemiculterella wui, an economically endemic species in China of subfamily Cultrinae (Cypriniformes: Cyprinidae), has been understudied. This study investigated the genetic diversity and structure of H. wui populations from the Ganjiang, Xinjiang, Fuhe, and Raohe rivers in the Poyang Lake Basin using mitochondrial Cytb gene analysis. Results showed high haplotype diversity but low nucleotide diversity in H. wui's Cytb sequences. Analysis of molecular variance (AMOVA) showed no significant geographic genetic structure among populations. Haplotype network analysis revealed no clear geographical clustering. Neutrality tests and haplotype nucleotide mismatch distribution indicated that all populations had experienced expansion events. These findings suggest that H. wui in Poyang Lake does not show a distinct geographic structure. However, it is still necessary to monitor the genetic characteristics of H. wui to maintain the genetic diversity of fishes in Poyang Basin, considering the threat of habitat loss and fragmentation to the population. [ABSTRACT FROM AUTHOR]

Background: The cestode Taenia hydatigena uses canids, primarily dogs, as definitive hosts, whereas the metacestode larval stage cysticercus infects a range of intermediate hosts, including domestic animals such as goats, sheep and pigs. Objectives: In this study, we aimed to determine the genetic differences and haplotypes of Cysticercus tenuicollis isolates obtained from sheep and goats slaughtered in the Bingol and Elazig provinces of Turkey. Methods: C. tenuicollis isolates were collected from 44 sheep and 26 goats slaughtered in slaughterhouses in Bingol and Elazig. After the isolation of total genomic DNA from C. tenuicollis isolates, the genetic characterization of the partial mitochondrial cytochrome oxidase 1 (CO1) gene region (866 bp) was amplified using specific primers by polymerase chain reaction (PCR), the products were then sequenced, and haplotype and genetic diversity analyses were carried out. Results: As a result of the haplotype network analyses, 34 different haplotypes were detected around the main haplotype (Hap02) arranged in a star‐like configuration and separated from other haplotypes by 1–28 mutation steps and covering 22.85% (16/70) of all isolates. Twenty‐seven polymorphic fields were detected, 77.77% (21/27) of which were parsimony‐informative, and secondary haplotype and nucleotide diversity were observed. Additionally, we detected high intraspecies haplotype diversity (hd: 0.933) and high nucleotide diversity (π: 0.00383), with 27 different nucleotide variation positions among the haplotypes of the isolates. Tajima's D value was negative, indicating population expansion and/or selection purification. The significantly negative Fu's Fs values indicated recent population expansion or the presence of expected rare haplotypes. Conclusion: The results of this study confirmed that C. tenuicollis isolates clustered in one lineage and were closely related to the relevant reference sequences in different countries, confirming the circulation of C. tenuicollis in different geographical regions. [ABSTRACT FROM AUTHOR]

Large sample datasets have been regarded as the primary basis for innovative discoveries and the solution to missing heritability in genome-wide association studies. However, their computational complexity cannot consider all comprehensive effects and all polygenic backgrounds, which reduces the effectiveness of large datasets. To address these challenges, we included all effects and polygenic backgrounds in a mixed logistic model for binary traits and compressed four variance components into two. The compressed model combined three computational algorithms to develop an innovative method, called FastBiCmrMLM, for large data analysis. These algorithms were tailored to sample size, computational speed, and reduced memory requirements. To mine additional genes, linkage disequilibrium markers were replaced by bin-based haplotypes, which are analyzed by FastBiCmrMLM, named FastBiCmrMLM-Hap. Simulation studies highlighted the superiority of FastBiCmrMLM over GMMAT, SAIGE and fastGWA-GLMM in identifying dominant, small α (allele substitution effect), and rare variants. In the UK Biobank-scale dataset, we demonstrated that FastBiCmrMLM could detect variants as small as 0.03% and with α ≈ 0. In re-analyses of seven diseases in the WTCCC datasets, 29 candidate genes, with both functional and TWAS evidence, around 36 variants identified only by the new methods, strongly validated the new methods. These methods offer a new way to decipher the genetic architecture of binary traits and address the challenges outlined above. [ABSTRACT FROM AUTHOR]

Salinity tolerance was studied in chickpea accessions from a germplasm collection and in cultivars from Kazakhstan. After NaCl treatment, significant differences were found between genotypes, which could be arranged into three groups. Those that performed poorest were found in group 1, comprising five ICC accessions with the lowest chlorophyll content, the highest leaf necrosis (LN), Na+ accumulation, malondialdehyde (MDA) content, and a low glutathione ratio GSH/GSSG. Two cultivars, Privo-1 and Tassay, representing group 2, were moderate in these traits, while the best performance was for group 3, containing two other cultivars, Krasnokutsky-123 and Looch, which were found to have mostly green plants and an exact opposite pattern of traits. Marker–trait association (MTA) between 6K DArT markers and four traits (LN, Na+, MDA, and GSH/GSSG) revealed the presence of four possible candidate genes in the chickpea genome that may be associated with the three groups. One gene, ATP-binding cassette, CaABCC6, was selected, and three haplotypes, A, D1, and D2, were identified in plants from the three groups. Two of the most salt-tolerant cultivars from group 3 were found to have haplotype D2 with a novel identified SNP. RT-qPCR analysis confirmed that this gene was strongly expressed after NaCl treatment in the parental- and breeding-line plants of haplotype D2. Mass spectrometry of seed proteins showed a higher accumulation of glutathione reductase and S-transferase, but not peroxidase, in the D2 haplotype. In conclusion, the CaABCC6 gene was hypothesized to be associated with a better response to oxidative stress via glutathione metabolism, while other candidate genes are likely involved in the control of chlorophyll content and Na+ accumulation. [ABSTRACT FROM AUTHOR]

Simple Summary: The global distribution of the genus Corbicula is driven by multiple hermaphroditic lineages. In Argentina, there remains a lack of comprehensive understanding of the current distribution, identity, and genetic relatedness of invasive Corbicula lineages. Reviewing 15 populations, we discriminate extant lineages based on both morphology and genetics in Argentina. We identified two lineages: AR morphotype (FW5 haplotype) and CS morphotype (FW17 haplotype). These lineages exhibited virtually segregated distributions, however, intermediate morphotypes found in northeastern Argentina suggest the presence of hybrids. Our study clarifies Corbicula identity and distribution, offering insights into invasion patterns in a wide geographic region. The broad global distribution of freshwater clams belonging to the genus Corbicula is driven by multiple hermaphroditic lineages. These lineages, characterized by shared morphological traits and phenotypic plasticity, pose challenges to morphological identification. Genetic markers, such as the mitochondrial COI gene, play a crucial role in delineating these lineages and their ranges. Morphotypes represent observed phenotypic variations, while lineages are defined based on genetic markers. Here, we comprehensively review Corbicula's distribution in Argentina, discriminate extant lineages based on both morphological and genetic (COI) data, and describe variations in internal and external morphologies using 15 Argentine populations. Genetic analyses identified two mitochondrial lineages: the AR morphotype (FW5 haplotype) and CS morphotype (FW17 haplotype). Strikingly, despite having similar vectors, origins, and invasive stages, Corbicula lineages exhibit virtually segregated distributions. However, mitochondrial haplotypes are found in sympatry mainly in northeastern Argentina where individuals with intermediate morphotypes exist, suggesting the presence of hybrids due to maternal genome retention. These findings contribute to the clarification of the identity and distribution of Corbicula lineages in Argentina, where the genus has been found for over half a century. Similar studies are needed in other areas to better understand the invasion patterns of this successful and adaptable group. [ABSTRACT FROM AUTHOR]

Background:DUOX2 is one of the major causative genes of congenital hypothyroidism (CH). Still, the mutation spectrum and clinical outcomes of biallelic DUOX2 variants are not fully understood. This study aimed to elucidate the molecular features and long-term clinical manifestations of CH caused by multiple pathogenic DUOX2 variants. Methods: A total of 255 patients with CH were screened for rare variants of 11 known causative genes. DUOX2 variants were classified according to their protein structure and residual activity. In vitro assays were performed for several variants of unknown functions. Clinical analyses were conducted for patients with multiple pathogenic variants of DUOX2 but not of other genes. Results: We identified 24 pathogenic variants of DUOX2, together with two benign variants and seven variants of uncertain significance, in 63 patients. The pathogenic variants included three missense substitutions and one frameshift variant that have not yet been linked to CH. Twenty-one patients carried multiple pathogenic DUOX2 variants without any other pathogenic gene variants. Three of the 21 patients harbored homozygous variants. Family analysis, long-read amplicon sequencing, and haplotype phasing confirmed compound heterozygosity of the DUOX2 variants in 14 patients, whereas the allelic positions of the variants in the remaining four patients could not be determined. Of the 21 patients, 19 were treated with levothyroxine; their ages at drug withdrawal ranged from 9 months to 21.4 years. Three patients required retreatment after drug-free intervals of 6 months, 8 months, and 10 years. There were no differences in clinical severity among patients with DUOX2 amorphic/amorphic, amorphic/hypomorphic, and hypomorphic/hypomorphic variants. Conclusions: These results broaden the mutational spectrum of DUOX2. Furthermore, our data imply that patients with multiple pathogenic DUOX2 variants typically exhibit transient CH without significant genotype–phenotype correlations. Most importantly, this study demonstrated for the first time that these patients are at risk of developing recurrent hypothyroidism after a long drug-free interval. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Ornithology is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Sequencing of a partial fragment of the mitochondrial ND5–cytb genes (1553 bp) and its nuclear copies in Phylloscopus borealis sensu lato (s.l.) individuals, belonging to different taxonomic groups from different parts of the range was carried out. The identity of the majority of taxon-specific and unique mitochondrial substitutions in examinandus and xanthodryas forms to those in nuclear copies of borealis mtDNA was demonstrated. Differences between the examinandus mitochondrial haplotypes and nuclear copies of borealis mtDNA were low (P = 0.02), and the genetic divergence in borealis–examinandus, borealis–xanthodryas, and examinandus–xanthodryas mtDNA itself considerably exceeded these values (P = 0.035, 0.044, and 0.046, respectively). For the first time, nuclear copy of the mitochondrial haplotype of the easternmost xanthodryas form was found in nuclear genome of one borealis individual from the western part of the breeding range (Komi Republic), and nuclear copies of xanthodryas mtDNA from Toyama Prefecture (Japan) were found to be close to the borealis mitochondrial haplotypes from Kytlym (Sverdlovsk oblast) (P = 0.018). Thus, the source of most substitutions in the mitochondrial DNA of the studied forms are mutations that arose in nuclear copies of mitochondrial genes. The origin of examinandus and xanthodryas mitochondrial haplotypes from nuclear copies of borealis mtDNA and close similarity of their nuclear genomes give reason to consider mitogenomes of these forms as haplotype variants of a single species, Ph. borealis s. l. With high degree of probability, it can be argued that the haplotype divergence time of the analyzed forms is considerably lower than 2.5–3 million years, as previously hypothesized by a number of authors, and the "molecular clock," which does not take into account recombination events between nuclear and mitochondrial genomes, cannot be used in this case. [ABSTRACT FROM AUTHOR]

In Indonesia, the sand crab Albunea symmysta distribution includes Java, Sumatra, and Moluccas. Populations are assumed to be differentiated between western and eastern Indonesia due to the Wallace line; however, no information on the genetic diversity and differentiation of A symmysta in Indonesia is available. This study was conducted to clarify the genetic diversity and differentiation of A. symmysta in Indonesia. During the sampling campaign, A. symmysta specimens were found only in Java and Papua. Genetic analysis based on the 643-bp fragment of the partial COI gene from 32 individuals revealed significant genetic differentiation between the Java and Papua populations (FST = 0.94, p < 0.005). The haplotype connectivity of the five A. symmysta sampling sites revealed a two-clade network. Based on analysis of molecular variance, most of the variation was found among populations (94.21%) rather than within populations (5.79%). Tajima's D and Fu's FS values indicated a population expansion. Overall, the findings support a high level of differentiation between the Java and Papua A. symmysta populations, suggesting the separation of population stocks due to low connectivity. [ABSTRACT FROM AUTHOR]

Honey bee Apis cerana is widely distributed in Asia and the Indonesian archipelago, including Sumatra. We studied the molecular variations of A. cerana using cytochrome c oxidase subunits 1 and 2 genes (cox1 and cox2) and the cox1/cox2 intergenic spacers (igs) in several altitudes in the six provinces of Sumatra. We explored the haplotype distributions of those three mtDNA markers for A. cerana in the low-, mid-, and highlands of Sumatra. We also analyzed their relationship with A. cerana in Sundaland and Asia using those markers. Our study revealed 12 new haplotypes of A. cerana cox1 in Sumatra, while nine and eight new haplotypes for cox2 and igs, respectively. Apis cerana in North Sumatra, Lampung, and South Sumatra had the three highest haplotype variations. Most of the specific haplotypes of inter-colony A. cerana from Sumatra were found in the lowlands, while most were in the highlands for intra-colony variations. We found low gene flow among populations of A. cerana in Sumatra. One haplotype, Sumatra4 cox2 from North Sumatra, was the same as Java3 haplotype, presumably due to anthropogenic impact. The molecular phylogenetic tree of A. cerana in the Sundaland revealed that A. cerana from Sumatra has a close relationship to those of Borneo compared to Java. [ABSTRACT FROM AUTHOR]

Low temperature severely affects rice development and yield. Ethylene signal is essential for plant development and stress response. Here, we reported that the OsEIN2‐OsEIL1/2 pathway reduced OsICE1‐dependent chilling tolerance in rice. The overexpressing plants of OsEIN2, OsEIL1 and OsEIL2 exhibited severe stress symptoms with excessive reactive oxygen species (ROS) accumulation under chilling, while the mutants (osein2 and oseil1) and OsEIL2‐RNA interference plants (OsEIL2‐Ri) showed the enhanced chilling tolerance. We validated that OsEIL1 and OsEIL2 could form a heterxodimer and synergistically repressed OsICE1 expression by binding to its promoter. The expression of OsICE1 target genes, ROS scavenging‐ and photosynthesis‐related genes were downregulated by OsEIN2 and OsEIL1/2, which were activated by OsICE1, suggesting that OsEIN2‐OsEIL1/2 pathway might mediate ROS accumulation and photosynthetic capacity under chilling by attenuating OsICE1 function. Moreover, the association analysis of the seedling chilling tolerance with the haplotype showed that the lower expression of OsEIL1 and OsEIL2 caused by natural variation might confer chilling tolerance on rice seedlings. Finally, we generated OsEIL2‐edited rice with an enhanced chilling tolerance. Taken together, our findings reveal a possible mechanism integrating OsEIN2‐OsEIL1/2 pathway with OsICE1‐dependent cascade in regulating chilling tolerance, providing a practical strategy for breeding chilling‐tolerant rice. Summary Statement: The OsEIN2‐OsEIL1/2 ethylene pathway has negative effect on rice tolerance to low temperature stress through transcriptionally repressing OsICE1‐mediated chilling response. [ABSTRACT FROM AUTHOR]

Simple Summary: Currently, one of the most raised issues regarding the preservation of endemic honey bees is the importation of foreign subspecies, leading to genetic introgression and hybridization between subspecies. In Algeria, many beekeepers have reported importing foreign honey bees, notably the Italian Apis mellifera ligustica, for their high honey production. In order to provide a molecular characterization and a better knowledge of the genetic background of the Algerian honey bees subspecies A. m. intermissa and A. m. sahariensis, we analyzed the widely used COI-COII mitochondrial marker. In this study, we sequenced 139 drones of which 68 were from 20 regions in Algeria, and 71 individuals as a reference population, sampled in Europe, the South West Indian Ocean archipelagos, and Madagascar, representing the evolutionary lineages M, C, and A. As a result, we found that all Algerian samples belong to the African lineage A with the identification of 24 haplotypes, of which 16 are reported for the first time. The reference population shows ten different haplotypes distributed over the three lineages, with the identification of a new haplotype carried by two individuals sampled in France. The results of this survey show the absence of evidence of genetic introgression between Algerian and European honey bees. The practice of beekeeping in Algeria is of great cultural, social, and economic importance. However, the importation of non-local subspecies reported by beekeepers has disrupted the natural geographical distribution area and the genetic diversity of the native honey bees. To assess the genetic diversity of A. m. intermissa and A. m. sahariensis, and their relationships with African and European subspecies, the COI-COII intergenic region was analyzed in 335 individuals, 68 sampled in Algeria, 71 in Europe, Madagascar, and the South West Indian Ocean archipelagos, and 196 sequences recovered from GenBank. The results show the presence of the A lineage exclusively in Algerian samples with the identification of 24 haplotypes of which 16 are described for the first time. These haplotypes were found to be shared by both subspecies, with A74 being the most common haplotype in the population studied. The sequence comparison indicates the existence of three polymorphisms of the COI-COII marker: P0Q, P0QQ, and P0QQQ. One new haplotype was identified in the M lineage in samples from France. No evidence of genetic introgression within the Algerian honey bee population was detected. These data enhance our knowledge of the genetic diversity and emphasize the importance of protecting these local subspecies. [ABSTRACT FROM AUTHOR]

Simple Summary: Parasitic wasps are natural enemies of numerous significant agricultural and forestry pests and therefore play an important role in biological control. With the development of integrative taxonomy, a greater variety of techniques are being applied to species identification. Therefore, integrated taxonomy was utilized in this study to identify parasitic wasps. Xinjiang is the largest province in China in terms of land area. However, the resources and environmental adaptation characteristics of Chalcidoidea have been little researched. In this study, we utilized geometric morphometrics and COI gene haplotype analysis and found that the morphology and genetic differentiation of Chalcidoidea changed at different altitudes. Eulophidae and Pteromalidae are parasitic wasps with a global distribution and import for the biological control of pests. They can be distributed in different altitude regions, but their morphological and genetic adaptations to different altitudes are unclear. Here, we collected specimens that belong to Eulophidae and Pteromalidae from various altitudinal gradients, based on integrated taxonomic approaches to determine the species composition, and we analyzed their body shape and size from different altitudes using geometric morphometrics. Then, we performed an analysis of the D. isaea population's haplotype genes to illustrate their genetic diversity. As a result, eight species that belong to two genera, Diglyphus Walker (Eulophidae) and Pachyneuron Walker (Pteromalidae), were identified, including two newly recorded species from China (D. chabrias and D. sabulosus). Through a geometric morphometrics analysis of body shape, we found that a narrow forewing shape and a widened thorax are the significant characteristics of adaptation to high-altitude environments in D. isaea and P. aphidis. Additionally, the body size studies showed a principal relationship between centroid size and altitude; the size of the forewings and thorax increases at higher altitudes. Next, using haplotype analysis, 32 haplotypes were found in seven geographic populations with high genetic diversity of this species. Our research provides preliminary evidence for the morphological and genetic diversity adaptation of parasitic wasps to extreme environments, and these data can provide important references for investigations on the ecological adaptability of parasitic wasps. [ABSTRACT FROM AUTHOR]

Simple Summary: This research analyzed for the first time the diversity in the Czech population of the Western Honey Bee. It used two mitochondrial DNA markers to identify haplotypes. Sequencing revealed both common and novel haplotypes. The cox1 sequences showed more diversity than the tRNAleu-cox2 sequences. Most haplotypes belong to the C lineage. Some haplotypes showed links to the bees of African origin. No indigenous M lineage haplotype was found. Thus, the native population of the Dark Honey Bee, Apis mellifera mellifera, has been completely replaced by the C lineage. The haplotype networks and phylogenetic trees showed that some A and C lineage haplotypes were distinct. The haplotype diversity data indicate that there is ongoing population expansion and introgression. The Czech honeybee population is diverse, with different haplotypes in both tRNAleu-cox2 and cox1 sequences. The study aimed to analyze the genetic diversity in the Czech population of Apis mellifera using mitochondrial DNA markers, tRNAleu-cox2 intergenic region and cox1 gene. A total of 308 samples of bees were collected from the entire Czech Republic (from colonies and flowers in 13 different regions). Following sequencing, several polymorphisms and haplotypes were identified. Analysis of tRNAleu-cox2 sequences revealed three DraI haplotypes (C, A1, and A4). The tRNAleu-cox2 region yielded 10 C lineage haplotypes, one of which is a newly described variant. Three A lineage haplotypes were identified, two of which were novel. A similar analysis of cox1 sequences yielded 16 distinct haplotypes (7 new) within the population. The most prevalent tRNAleu-cox2 haplotype identified was C1a, followed by C2a, C2c, C2l, and C2d. For the cox1 locus, the most frequent haplotypes were HpB02, HpB01, HpB03, and HpB04. The haplotype and nucleotide diversity indices were high in both loci, in tRNAleu-cox2 with values of 0.682 and 0.00172, respectively, and in cox1 0.789 and 0.00203, respectively. The Tajima's D values were negative and lower in tRNAleu-cox2 than in cox1. The most frequent haplotypes were uniformly distributed across all regions of the Czech Republic. No haplotype of the indigenous M lineage was identified. High diversity and the occurrence of rare haplotypes indicate population expansion and continuous import of tribal material of the C lineage. [ABSTRACT FROM AUTHOR]

Summary Shotgun metagenomics allows for direct analysis of microbial community genetics, but scalable computational methods for the recovery of bacterial strain genomes from microbiomes remains a key challenge. We introduce Floria, a novel method designed for rapid and accurate recovery of strain haplotypes from short and long-read metagenome sequencing data, based on minimum error correction (MEC) read clustering and a strain-preserving network flow model. Floria can function as a standalone haplotyping method, outputting alleles and reads that co-occur on the same strain, as well as an end-to-end read-to-assembly pipeline (Floria-PL) for strain-level assembly. Benchmarking evaluations on synthetic metagenomes show that Floria is   >   3 × faster and recovers 21% more strain content than base-level assembly methods (Strainberry) while being over an order of magnitude faster when only phasing is required. Applying Floria to a set of 109 deeply sequenced nanopore metagenomes took <20 min on average per sample and identified several species that have consistent strain heterogeneity. Applying Floria's short-read haplotyping to a longitudinal gut metagenomics dataset revealed a dynamic multi-strain Anaerostipes hadrus community with frequent strain loss and emergence events over 636 days. With Floria, accurate haplotyping of metagenomic datasets takes mere minutes on standard workstations, paving the way for extensive strain-level metagenomic analyses. Availability and implementation Floria is available at https://github.com/bluenote-1577/floria , and the Floria-PL pipeline is available at https://github.com/jsgounot/Floria%5fanalysis%5fworkflow along with code for reproducing the benchmarks. [ABSTRACT FROM AUTHOR]

Haplotype estimation, or phasing, has gained significant traction in large-scale projects due to its valuable contributions to population genetics, variant analysis, and the creation of reference panels for imputation and phasing of new samples. To scale with the growing number of samples, haplotype estimation methods designed for population scale rely on highly optimized statistical models to phase genotype data, and usually ignore read-level information. Statistical methods excel in resolving common variants, however, they still struggle at rare variants due to the lack of statistical information. In this study we introduce SAPPHIRE, a new method that leverages whole-genome sequencing data to enhance the precision of haplotype calls produced by statistical phasing. SAPPHIRE achieves this by refining haplotype estimates through the realignment of sequencing reads, particularly targeting low-confidence phase calls. Our findings demonstrate that SAPPHIRE significantly enhances the accuracy of haplotypes obtained from state of the art methods and also provides the subset of phase calls that are validated by sequencing reads. Finally, we show that our method scales to large data sets by its successful application to the extensive 3.6 Petabytes of sequencing data of the last UK Biobank 200,031 sample release. Author summary: Haplotype estimation, also known as phasing, is now applied to population scale projects, typically of hundreds of thousands of samples to millions of samples. Generally phasing relies on statistical methods as they provide very accurate results for common variations. However, for rare and very rare variants the lack of statistical power often results in poor phasing. The large amount of rare variations discovered with whole-genome sequencing as well as the number of samples makes it expensive to process. We have developed the SAPPHIRE method that leverages whole-genome sequencing data to verify and correct the phase at poorly phased variant loci. It does so by finding sequencing reads that contain both the poorly phased variant and an accurately phased common variant. SAPPHIRE scales with large data sets by specifically targeting variation where statistical phasing performed poorly, therefore it reduces the quantity of sequencing data to be processed and combines the advantages of both read-based and statistical approaches. We show the efficiency of SAPPHIRE by improving the estimated haplotypes for 200,031 samples in the UK Biobank. SAPPHIRE is free and available as open-source software. [ABSTRACT FROM AUTHOR]

Antagonistic selection has long been considered a major driver of the formation and expansion of sex chromosomes. For example, sexually antagonistic variation on an autosome can select for suppressed recombination between that autosome and the sex chromosome, leading to a neo-sex chromosome. Autosomal supergenes, chromosomal regions containing tightly linked variants affecting the same complex trait, share similarities with sex chromosomes, raising the possibility that sex chromosome evolution models can explain the evolution of genome structure and recombination in other contexts. We tested this premise in a Formica ant species, wherein we identified four supergene haplotypes on chromosome 3 underlying colony social organization and sex ratio. We discovered a novel rearranged supergene variant (9r) on chromosome 9 underlying queen miniaturization. The 9r is in strong linkage disequilibrium with one chromosome 3 haplotype (P2) found in multi-queen (polygyne) colonies. We suggest that queen miniaturization is strongly disfavored in the single-queen (monogyne) background and is thus socially antagonistic. As such, divergent selection experienced by ants living in alternative social "environments" (monogyne and polygyne) may have contributed to the emergence of a genetic polymorphism on chromosome 9 and associated queen-size dimorphism. Consequently, an ancestral polygyne-associated haplotype may have expanded to include the polymorphism on chromosome 9, resulting in a larger region of suppressed recombination spanning two chromosomes. This process is analogous to the formation of neo-sex chromosomes and consistent with models of expanding regions of suppressed recombination. We propose that miniaturized queens, 16%-20% smaller than queens without 9r, could be incipient intraspecific social parasites.

The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.

Long-read sequencing technologies substantially overcome the limitations of short-reads but have not been considered as a feasible replacement for population-scale projects, being a combination of too expensive, not scalable enough or too error-prone. Here we develop an efficient and scalable wet lab and computational protocol, Napu, for Oxford Nanopore Technologies long-read sequencing that seeks to address those limitations. We applied our protocol to cell lines and brain tissue samples as part of a pilot project for the National Institutes of Health Center for Alzheimer's and Related Dementias. Using a single PromethION flow cell, we can detect single nucleotide polymorphisms with F1-score comparable to Illumina short-read sequencing. Small indel calling remains difficult within homopolymers and tandem repeats, but achieves good concordance to Illumina indel calls elsewhere. Further, we can discover structural variants with F1-score on par with state-of-the-art de novo assembly methods. Our protocol phases small and structural variants at megabase scales and produces highly accurate, haplotype-specific methylation calls.

Abstract Background Aedes albopictus, commonly known as the Asian tiger mosquito, has become one of the most invasive mosquito species. Over the last 5 decades, it has been introduced and established in various tropical and temperate regions worldwide. First reported in Europe in 1979 in Albania and later in Italy in 1990, the species is now established in 13 European Union (EU)/European Economic Area (EEA) countries and 337 regions (2023). In Portugal, Ae. albopictus was first detected in the Algarve and Penafiel regions in 2017, followed by Alentejo in 2022 and Lisbon in 2023. This mosquito species poses a significant public health risk as a vector for numerous pathogenic viruses, including dengue, Zika, and chikungunya. Methods Aedes albopictus collected in Lisbon in 2023 were analyzed using cytochrome c oxidase I (COX) gene sequencing to understand their genetic relationships. Results Our data indicate that the Ae. albopictus mosquito populations detected in three locations in Lisbon in 2023 correspond to recent but distinct introduction events. Conclusions Although there has been no local transmission of Aedes-transmitted viruses in mainland Portugal to date, the spread of the mosquito and increased international travel increase the risk of Aedes-borne disease outbreaks. The ongoing spread of Ae. albopictus in the country and the confirmed multiple introductions in new locations raise awareness of the need to monitor mosquito vectors to control and prevent autochthonous Aedes-borne disease outbreaks. Graphical Abstract

Early pregnancy loss (EPL) is the most common pregnancy complication, found in approximately 15% of all clinically recognized pregnancy complications. Up to date, various maternal as well as fetal factors are reported as a cause of EPLs. However, in approximately 50% of EPL cases, the exact cause is not clearly identified and these cases are referred as idiopathic.

Abstract Background Phytosulfokine (PSK) functions as a plant peptide growth factor that plays important and diverse roles in plant development and stress responses. Nevertheless, PSKs have not been systematically analyzed in wheat. Results A genome-wide comparative analysis of PSK genes in wheat was conducted and 15 TaPSKs were identified and divided into four subgroups in the wheat genome based on sequence similarity. The examination of motif compositions of TaPSK genes revealed the presence of the YIYTQ signature motif in the C-terminus of all TaPSK polypeptide precursors, with a highly conserved feature across different species. Exogenous application of TaPSK peptide promoted root growth in wheat. Quantitative RT-PCR analysis revealed that the TaPSKs exhibited preferential or tissue-specific expression patterns in wheat. In particular, three homologs of the TaPSK1 genes were specifically expressed in grains, with the strongest expression observed in the developing grains at 15 days after anthesis. Compared with wild type, transgenic rice lines overexpressing TaPSK1-A exhibited larger grain size and higher thousand-grain weight. The promoter region and genomic sequence of the wheat TaPSK1-A gene were cloned. Sequence polymorphism showed that five single-nucleotide polymorphisms (SNPs) were identified in the promoter region of TaPSK1-A. A Kompetitive Allele-Specific PCR (KASP) marker was developed for TaPSK1-A based on –806 bp SNP (C/T transition), and two haplotypes, TaPSK1-A-HapI and TaPSK1-A-HapII were detected in 260 wheat accessions collected from different regions. The expression of TaPSK1-A, promoter activity, and thousand-grain weight (TGW) in the TaPSK1-A-HapII haplotype were higher than those in the TaPSK1-A-HapI haplotype. Furthermore, yeast one-hybrid assays revealed the binding of TaNF-YB1 and TaERF39 to the promoter regions of the TaPSK1-A gene, and TaMADS29 could bind to the promoters of TaPSK1-B and TaPSK1-D genes. Conclusions Comparative genome-wide analysis of TaPSK peptide family revealed that the TaPSK1 gene is involved in wheat grain development, and the developed TaPSK1-A-KASP marker could be utilized for marker-assisted selection breeding of wheat. Graphical Abstract

Abstract The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.

One of the urgent problems of medicine is to clarify the pathogenetic mechanisms of glomerulonephritis (GN) with refractory nephrotic syndrome (NS). In 30% of cases, refractory NS has a genetic nature. The role of human histocompatibility system (HLA) genes in the development of refractory NS has not been sufficiently studied. The purpose of this study was to study the association of two-locus haplotypes of HLA class II gene alleles with GN manifested by refractory NS. The typing of HLA class II genes in 136 patients with NS was performed by polymerase chain reaction (PCR), which included the identification of 13 alleles of the DRB1, 8 – DQA1, and 12 – DQB1 loci. The cohort of the examined patients was divided into two groups: a group of patients with refractory NS and a group of patients with rare relapses, with a lack of refractoriness to the therapy. Persons of Chuvash nationality were selected for the study. In the studied groups of patients, the values of the nonequilibrium coupling of alleles (D) were determined to identify characteristic two-locus haplotypes and their frequency according to the formulas of Piazza A. and coauthors. To assess the association of refractory NS with HLA haplotypes, relative risk values (RR) were calculated using the formula Woolf B. and Haldane J. The statistical significance of the association was assessed using the twosided Fisher exact method for four-field tables (PF). The highest value of RR was found in the haplotype HLA-DRB1*11(05)-DQA1*0301. Its value was 42.1 (PF = 0.005). Another statistically significant value was the RR value of the haplotype HLA-DRB1*15(02)-DQB1*0602-8, equal to 0.2 (PF = 0.004). As a result of the study, the haplotype DRB1*11(05)-DQA1*0301, associated with an increased risk of refractory NS, and the protective haplotype DRB1*15(02)-DQB1*0602-8, reducing the risk of refractory NS were found in the HLA genotype of individuals in the Chuvash population.

Bertiella spp. is a mite-borne cestode parasite that inhabits the small intestine of wide range of mammals, including non-human primates. In the present study, the morphological and molecular analysis of Bertiella studeri recovered from the small intestine of a bonnet macaque (Macaca radiata) from Wayanad, Kerala (South India) was performed. Acetic alum carmine staining identified the cestode morphologically based on the characters like broader proglottids, which contain irregularly alternating genital pores, single set of reproductive organs, 280 testes and a tubular transverse uterus. Molecular characterization was done using 18SrRNA, ITS1-5.8S and COX1 genes. Phylogenetic trees were constructed using MEGA X based on the Maximum Likelihood (ML) method (Hasegawa-Kishino-Yano (HKY) model). Cytochrome oxidase I gene could detect the existence of genetic variation in the parasite from two different hosts viz., monkey (Kerala, Argentina, and Kenya) and human (Sri Lanka). A minimum spanning network of haplotypes was generated by the haplotype networking with the above sequences using the popARTv1.7. Haplotype analysis based on COX1 revealed that the parasite haplotype was different in each country with highest population frequency in Sri Lanka.

Background: The Murrah buffalo, pivotal in Asian agriculture, faces challenges in maximizing milk production despite significant breeding efforts. Recognizing its economic importance, this study investigates mtDNA D-loop variations in Murrah buffalo as potential indicators of milk production variability, addressing challenges in maximizing yield despite significant breeding efforts. Methods and results: Analyzing mtDNA D-loop sequences from 50 buffaloes, we categorized them into Low (Group 1), Medium (Group 2), and High ECM (Group 3) groups based on milk yields, fat and protein percentage of a 30-day period data. Somatic cell mtDNA D-loop analysis revealed distinct genetic variations, with significant differences among ECM groups. Group 2 showed higher SNP prevalence, group 3 had more insertions/deletions, and Group 1 exhibited the highest transition frequency. Notably, a consistent "C" deletion at the 714th position occurred in Groups 1 and 3, prevalent in 68% of Group 2. A G-A variation at the 93rd position was specific to the medium ECM group. Negative Tajima D values indicated unique variations in each group, with Group 1 having the highest number, and a specific SNP linked to Group 2 was identified. These SNPs in the D-loop region could impact mtDNA replication, influencing mitochondrial content among animals. Our results provide valuable insights into the role of mtDNA D-loop polymorphisms in milk production traits in Murrah buffalo. Conclusions: Our research highlights the potential for valuable markers of cellular energy efficiency in Murrah buffalo. Exploring diverse cytoplasmic backgrounds opens avenues for mtDNA-based selection strategies, enhancing milk production and optimizing genetic traits for the dairy industry. [ABSTRACT FROM AUTHOR]

In a year-long research study, we delved into the thermoregulation and performance of twenty-one honey bee colonies situated in three distinct landscape settings: 1- Urban, 2- Agricultural (AG), and 3- Non-agricultural (Non-AG) environments. All colonies, consistent in size, were equipped with sensors designed to record inner hive temperature and humidity. Additionally, colonies were placed on precision electronic scales for weight monitoring. Varroa mite infestations were documented at seven different time points throughout the experiment. Colonies were genetically analyzed for subspecies and haplotype identification using the in silico DraI mtDNA COI-COII test. Our results unveiled an overall significant (p < 0.001) weight gain (5.76 kg) in colonies located within the urban setting, in stark contrast to both AG and Non-AG locations. Notably, colonies situated in the natural refuge center (Non-AG) experienced a weight loss of −0.05 kg, signaling a lack of sustainable forage resources in such a setting. Similarly, the inner hive temperature was significantly (p < 0.001) higher in the urban area (33.65 °C) with a significantly lower relative humidity (61.2%) compared to both other locations. Among the locations, the temperature variable displayed the strongest significant correlation (p < 0.001) with a positive correlation coefficient (r = 0.95). Two distinct mtDNA haplotypes were identified: C1 and C2j, characterizing the ligustica and carnica maternal origin, respectively. These haplotypes consistently demonstrated significant differences in their thermoregulation and weight gain, irrespective of the landscape compositions. The C1 haplotype displayed significantly higher weight gain alongside lower inner hive temperature and humidity levels compared to the C2j haplotype. No differences in mite infestation were observed between the various locations or haplotypes. Our data underscores the substantial impact of landscape composition on honey bee performance. It also unveils significant variations in thermoregulation and adaptation between haplotypes, shedding light on the multifaceted relationship between environmental factors, genetics, and bee colony dynamics. [ABSTRACT FROM AUTHOR]

In recent years, several studies have highlighted the high resilience of zoantharians to ocean warming. In particular, populations of Palythoa caribaeorum are proliferating and beginning to dominate the coastal ecosystems of the Canary Islands. This expansion has been associated with increasing sea surface temperatures (SSTs). Here, we provide new insights into the endosymbiont-P. caribaeorum associations during and after a heat stress experiment to understand the processes underlying their high resilience to elevated temperatures. For this purpose, 61 colonies collected in the Canary Islands were exposed to an increasing temperature gradient (from 24 to 32 °C) to assess their heat tolerance, and then transferred back to the control temperature (24 °C) to evaluate their resilience. Colonies performance was assessed by comparing host color changes (bleaching degree), analyzing their Symbiodiniaceae morphological condition, and determining the dominant lineage of Symbiodiniaceae using the psbAncr molecular marker. All colonies showed signs of bleaching during heat stress, evidenced by color loss and a decrease in healthy Symbiodiniaceae content. Nevertheless, P. caribaeorum showed high resistance to heat stress, as all colonies kept up to 30 °C were able to survive and significantly recover. Furthermore, as the experimental temperature increased, a new haplotype of the Cladocopium C1 lineage, not detected in the control and wild samples, emerged and dominated most of the colonies (59.09%). Our study demonstrates the resilience of P. caribaeorum to heat stress in the Canary Islands, raising important ecological concerns about the future of native macroalgae ecosystems in an ocean warming scenario. [ABSTRACT FROM AUTHOR]

Purpose: The CYP2D6 gene exhibits significant polymorphism, contributing to variability in responses to drugs metabolized by CYP2D6. While CYP2D6*2 and CYP2D6*35 are presently designated as alleles encoding normal metabolism, this classification is based on moderate level evidence. Additionally, the role of the formerly called "enhancer" single nucleotide polymorphism (SNP) rs5758550 is unclear. In this study, the impacts of CYP2D6*2, CYP2D6*35 and rs5758550 on CYP2D6 activity were investigated using risperidone clearance as CYP2D6 activity marker. Methods: A joint parent-metabolite population pharmacokinetic model was used to describe 1,565 serum concentration measurements of risperidone and 9-hydroxyrisperidone in 512 subjects. Risperidone population clearance was modeled as the sum of a CYP2D6-independent clearance term and the partial clearances contributed from each individually expressed CYP2D6 allele or haplotype. In addition to the well-characterized CYP2D6 alleles (*3-*6, *9, *10 and *41), *2, *35 and two haplotypes assigned as CYP2D6*2-rs5758550G and CYP2D6*2-rs5758550A were evaluated. Results: Each evaluated CYP2D6 allele was associated with significantly lower risperidone clearance than the reference normal function allele CYP2D6*1 (p < 0.001). Further, rs5758550 differentiated the effect of CYP2D6*2 (p = 0.005). The haplotype-specific clearances for CYP2D6*2-rs5758550A, CYP2D6*2-rs5758550G and CYP2D6*35 were estimated to 30%, 66% and 57%, respectively, relative to the clearance for CYP2D6*1. Notably, rs5758550 is in high linkage disequilibrium (R2 > 0.85) with at least 24 other SNPs and cannot be assigned as a functional SNP. Conclusion: CYP2D6*2 and CYP2D6*35 encode reduced risperidone clearance, and the extent of reduction for CYP2D6*2 is differentiated by rs5758550. Genotyping of these haplotypes might improve the precision of genotype-guided prediction of CYP2D6-mediated clearance. [ABSTRACT FROM AUTHOR]

The singular BRCA1/2 mutational landscape of Asturias is updated 10 years after the first study. We analyzed BRCA1 and BRCA2 pathogenic variants in 1653 index cases. In total, 238 families were identified to carry a pathogenic variant, 163 families in BRCA1 and 75 families in BRCA2. This yielded a prevalence rate of 14.4%. Seven recurrent variants were found accounting for 55% of the cases. Among them, three are widely distributed (BRCA1 c.211A>G, c.470_471del and c.3331_3334del) and four had been reported as novel in Asturias: two in BRCA1 (c.1674del and c.2901_2902dup) and two in BRCA2 (c.2095C>T and c.4040_4035delinsC). A common haplotype was established for all recurrent variants indicating a shared ancestral origin. Three splicing analyses are shown: BRCA1:c.5152+3A>C and BRCA1:c.5333‐3T>G that lead to skipping of exon 18, and 22 respectively, and BRCA1:c.5278‐1G>T giving rise to two transcripts, one lacking exon 21 (p.Ille1760Glyfs*60) and one lacking the first 8 nucleotides of exon 21 (p.Phe1761Asnfs*14), supporting pathogenicity for these variants. [ABSTRACT FROM AUTHOR]

Many herbivorous insect species exhibit phenotypic plasticity when using multiple hosts, which facilitates survival in heterogeneous host environments. Physiological host acclimation is an important part of it, yet the effects of host acclimation on insect feeding behaviour are not well studied, particularly for insect vectors of plant pathogens.We studied the combined effects of host acclimation and infection with a plant pathogenic symbiont on feeding behaviour of Bactericera cockerelli, an oligophagous psyllid widespread in both crop and natural habitats that feed primarily on Solanaceae and transmit an economically important plant pathogen, Candidatus Liberibacter solanacearum (CLso).We used a factorial design and the electrical penetration graphing technique to disentangle the effects of host acclimation, CLso infection and psyllid haplotype on the within‐plant feeding behaviour of B. cockerelli during conspecific and heterospecific host switches. This approach allows to connect phenotypic plasticity with the role of B. cockerelli as a vector by quantifying the frequency and duration of behaviours involved in CLso transmission.We found significant reductions in multiple metrics of B. cockerelli feeding efficiency, exacerbated by infection with CLso, which could lead to reduced transmission of this pathogen. Psyllid genotype was also important; the Central haplotype exhibited less dramatic changes in feeding efficiency than the Western haplotype during heterospecific host switches.Our study shows that host acclimation and heterospecific host switching directly alter feeding behaviours underlying pathogen transmission, and that the magnitude of feeding efficiency reductions depends on both host genotype and infection status. [ABSTRACT FROM AUTHOR]

Abstract A ~ 1 Mb inversion polymorphism exists within the 17q21.31 locus of the human genome as direct (H1) and inverted (H2) haplotype clades. This inversion region demonstrates high linkage disequilibrium, but the frequency of each haplotype differs across ancestries. While the H1 haplotype exists in all populations and shows a normal pattern of genetic variability and recombination, the H2 haplotype is enriched in European ancestry populations, is less frequent in African ancestry populations, and nearly absent in East Asian ancestry populations. H1 is a known risk factor for several neurodegenerative diseases, and has been associated with many other traits, suggesting its importance in cellular phenotypes of the brain and entire body. Conversely, H2 is protective for these diseases, but is associated with predisposition to recurrent microdeletion syndromes and neurodevelopmental disorders such as autism. Many single nucleotide variants and copy number variants define H1/H2 haplotypes and sub-haplotypes, but identifying the causal variant(s) for specific diseases and phenotypes is complex due to the extended linkage equilibrium. In this review, we assess the current knowledge of this inversion region regarding genomic structure, gene expression, cellular phenotypes, and disease association. We discuss recent discoveries and challenges, evaluate gaps in knowledge, and highlight the importance of understanding the effect of the 17q21.31 haplotypes to promote advances in precision medicine and drug discovery for several diseases. Graphical Abstract

Abstract Background This study examined population genetics of Aedes aegypti in El Salvador and Honduras, two adjacent countries in Central America. Aedes aegypti is associated with yellow fever, dengue, chikungunya, and Zika. Each year, thousands of cases of dengue are typically reported in El Salvador and Honduras. Methods In El Salvador, collections were obtained from five Departments. In Honduras, samples were obtained from six municipalities in four Departments. Mitochondrial DNA cytochrome oxidase I (COI) was sequenced, and consensus sequences were combined with available sequences from El Salvador to determine haplotype number, haplotype diversity, nucleotide diversity, and Tajima’s D. A haplotype network was produced to examine the relationship between genotypes. Results In El Salvador, there were 17 haplotypes, while in Honduras there were 4 haplotypes. In both El Salvador and Honduras, Haplotype 1 is most abundant and widespread. In El Salvador, haplotype H2 was also widespread in 10 of 11 sampled municipalities, but it was not present in Honduras. The capital of El Salvador (San Salvador) and the eastern region of ES had the highest haplotype diversity of regions sampled. Conclusions Haplotype 1 and H2 each belong to different phylogenetic lineages of Ae. aegypti. The most geographically widespread haplotype (H1) may have been present the longest and could be a remnant from previous eradication programs. These data may contribute to future control programs for Ae. aegypti in the two countries. Graphical Abstract

Objective The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck. Methods These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program. Results A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes. Conclusion The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.

Petroleuciscus borysthenicus is a species with a wide distribution from the eastern, western, and northern Black Sea and Azov Sea basins, the Aegean Sea basin, and Northwestern Türkiye. However, there has been relatively little attention on the genetic variability of this species in their native distribution range, and nearly no study has been conducted in Türkiye despite its importance in biodiversity. The aim of this study was to elucidate the genetic variability and population structure of P. borysthenicus from Northwestern Türkiye using an integrated molecular method. A total of 72 specimens were collected from 13 localities in the Northwestern part of Türkiye. A total of six haplotypes were identified in all specimens. A relatively low level of genetic variability was found for P. borysthenicus throughout the study region based on the indices of genetic diversity including haplotype diversity and nucleotide diversity for the cytochrome oxidase subunit I (h = 0.507, π = 0.0027). The pairwise FST values between the samples ranged from −0.123 to 1.000. Furthermore, our results revealed no provable recent demographic expansion for P. borysthenicus from Northwestern Türkiye. However, more studies using additional geographic sampling and molecular analysis are needed to enhance our knowledge of the diversity and distribution of this species. [ABSTRACT FROM AUTHOR]

Background: High blood pressure, also known as hypertension (HTN), is a complicated disorder that is controlled by a complex network of physiological processes. Untreated hypertension is associated with increased death incidence, rise the need for understanding the genetic basis affecting hypertension susceptibility and development. The current study sought to identify the genetic association between twelve single nucleotide polymorphisms (SNPs) within seven candidate genes (NOS3, NOS1AP, REN, PLA2G4A, TCF7L, ADRB1, and PTPRD) Methods: The current study included 200 Jordanian individuals diagnosed with hypertension, compared to 224 healthy controls. Whole blood samples were drawn from each individual for DNA isolation and genotyping. The SNPStats tool was used to assess haplotype, genotype, and allele frequencies by the mean of chi-square (χ2). Results: Except for rs10739150 of PTPRD (P = 0.0003), the genotypic and allelic distribution of the SNP was identical between patients and controls. The prevalence of the G/G genotype in healthy controls (45.5%) was lower than in hypertension patients (64.3%), suggesting that it might be a risk factor for the disease. PTPRD TTC genetic haplotypes were strongly linked with hypertension (P = 0.003, OR = 4.03). Conclusion: This study provides a comprehensive understanding of the involvement of rs10739150 within the PTPRD gene in hypertension. This new knowledge could potentially transform the way we approach hypertension diagnosis, providing an accurate diagnostic tool for classifying individuals who are at a higher risk of developing this condition. [ABSTRACT FROM AUTHOR]

Faba bean is an important legume crop. The genetic diversity among faba bean genotypes is very important for the genetic improvement of target traits. A set of 128 fab bean genotypes that are originally from Egypt were used in this study to investigate the genetic diversity and population structure. The 128 genotypes were genotyped using the Single Primer Enrichment Technology (SPET) by which a set of 6759 SNP markers were generated after filtration. The SNP markers were distributed on all chromosomes with a range extending from 822 (Chr. 6) to 1872 (Chr.1). The SNP markers had wide ranges of polymorphic information content (PIC), gene diversity (GD), and minor allele frequency. The analysis of population structure divided the Egyptian faba bean population into five subpopulations. Considerable genetic distance was found among all genotypes, ranging from 0.1 to 0.4. The highly divergent genotype was highlighted in this study and the genetic distance among genotypes ranged from 0.1 and 0.6. Moreover, the structure of linkage disequilibrium was studied, and the analysis revealed a low level of LD in the Egyptian faba bean population. A slow LD decay at the genomic and chromosomal levels was observed. Interestingly, the distribution of haplotype blocks was presented in each chromosome and the number of haplotype block ranged from 65 (Chr. 4) to 156 (Chr. 1). Migration and genetic drift are the main reasons for the low LD in the Egyptian faba bean population. The results of this study shed light on the possibility of the genetic improvement of faba bean crop in Egypt and conducting genetic association analyses to identify candidate genes associated with target traits (e.g. protein content, grain yield, etc.) in this panel. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently. A phylogenetic analysis of Salmonella Typhi isolated from returning travelers to the United Kingdom between 1980 and 1995 suggests that H58 emerged from a chronic carrier in India in 1987 before spreading globally and was already multidrug resistant. [ABSTRACT FROM AUTHOR]

Introduction: Autotetraploid rice holds high resistance to abiotic stress and substantial promise for yield increase, but it could not be commercially used because of low fertility. Thus, our team developed neo-tetraploid rice with high fertility and hybrid vigor when crossed with indica autotetraploid rice. Despite these advances, the molecular mechanisms underlying this heterosis remain poorly understood. Methods: An elite indica autotetraploid rice line (HD11) was used to cross with neo-tetraploid rice, and 34 hybrids were obtained to evaluate agronomic traits related to yield. WE-CLSM, RNA-seq, and CRISPR/Cas9 were employed to observe endosperm structure and identify candidate genes from two represent hybrids. Results and discussion: These hybrids showed high seed setting and an approximately 55% increase in 1000-grain weight, some of which achieved grain yields comparable to those of the diploid rice variety. The endosperm observations indicated that the starch grains in the hybrids were more compact than those in paternal lines. A total of 119 seed heterosis related genes (SHRGs) with different expressions were identified, which might contribute to high 1000-grain weight heterosis in neo-tetraploid hybrids. Among them, 12 genes had been found to regulate grain weight formation, including OsFl3, ONAC023, OsNAC024, ONAC025, ONAC026, RAG2, FLO4, FLO11, OsISA1, OsNF-YB1, NF-YC12, and OsYUC9. Haplotype analyses of these 12 genes revealed the various effects on grain weight among different haplotypes. The hybrids could polymerize more dominant haplotypes of above grain weight regulators than any homozygous cultivar. Moreover, two SHRGs (OsFl3 and SHRG2) mutants displayed a significant reduction in 1000-grain weight and an increase in grain chalkiness, indicating that OsFl3 and SHRG2 positively regulate grain weight. Our research has identified a valuable indica autotetraploid germplasm for generating strong yield heterosis in combination with neo-tetraploid lines and gaining molecular insights into the regulatory processes of heterosis in tetraploid rice. [ABSTRACT FROM AUTHOR]

The assignment of variants across haplotypes, phasing, is crucial for predicting the consequences, interaction, and inheritance of mutations and is a key step in improving our understanding of phenotype and disease. However, phasing is limited by read length and stretches of homozygosity along the genome. To overcome this limitation, we designed MethPhaser, a method that utilizes methylation signals from Oxford Nanopore Technologies to extend Single Nucleotide Variation (SNV)-based phasing. We demonstrate that haplotype-specific methylations extensively exist in Human genomes and the advent of long-read technologies enabled direct report of methylation signals. For ONT R9 and R10 cell line data, we increase the phase length N50 by 78%-151% at a phasing accuracy of 83.4-98.7% To assess the impact of tissue purity and random methylation signals due to inactivation, we also applied MethPhaser on blood samples from 4 patients, still showing improvements over SNV-only phasing. MethPhaser further improves phasing across HLA and multiple other medically relevant genes, improving our understanding of how mutations interact across multiple phenotypes. The concept of MethPhaser can also be extended to non-human diploid genomes. MethPhaser is available at https://github.com/treangenlab/methphaser. The assignment of genetic variants to the two copies of the genome present in cells (phasing) is crucial for predicting the consequences, interaction and inheritance of variants, but is limited by the length of sequencing reads and stretches of homozygosity in the genome. Here the authors develop a method that utilizes DNA methylation signals from Oxford Nanopore Technologies sequencing data to improve phasing. [ABSTRACT FROM AUTHOR]

Neandertais and Denisovans, having inhabited distinct regions in Eurasia and possibly Oceania for over 200,000 y, experienced ample time to adapt to diverse environmental challenges these regions presented. Among present-day human populations, Papua New Guineans (PNG) stand out as one of the few carrying substantial amounts of both Neandertal and Denisovan DNA, a result of past admixture events with these archaic human groups. This study investigates the distribution of introgressed Denisovan and Neandertal DNA within two distinct PNG populations, residing in the highlands of Mt Wilhelm and the lowlands of Daru Island. These locations exhibit unique environmental features, some of which may parallel the challenges that archaic humans once confronted and adapted to. Our results show that PNG highlanders carry higher levels of Denisovan DNA compared to PNG lowlanders. Among the Denisovan-like haplotypes with higher frequencies in highlander populations, those exhibiting the greatest frequency difference compared to lowlander populations also demonstrate more pronounced differences in population frequencies than frequency-matched nonarchaic variants. Two of the five most highly differentiated of those haplotypes reside in genomic areas linked to brain development genes. Conversely, Denisovan-like haplotypes more frequent in lowlanders overlap with genes associated with immune response processes. Our findings suggest that Denisovan DNA has provided genetic variation associated with brain biology and immune response to PNG genomes, some of which might have facilitated adaptive processes to environmental challenges. [ABSTRACT FROM AUTHOR]

The COVID-19 pandemic has profoundly affected all aspects of our lives. Through real-time monitoring and rapid vaccine implementation, we succeeded in suppressing the spread of the disease and mitigating its consequences. Finally, conclusions can be summarized and drawn. Here, we use the example of Poland, which was seriously affected by the pandemic. Compared to other countries, Poland has not achieved impressive results in either testing or vaccination, which may explain its high mortality (case fatality rate, CFR 1.94%). Through retrospective analysis of data collected by the COVID-19 Data Portal Poland, we found significant regional differences in the number of tests performed, number of cases detected, number of COVID-19-related deaths, and vaccination rates. The Masovian, Greater Poland, and Pomeranian voivodeships, the country's leaders in vaccination, reported high case numbers but low death rates. In contrast, the voivodeships in the eastern and southern parts of Poland (Subcarpathian, Podlaskie, Lublin, Opole), which documented low vaccination levels and low case numbers, had higher COVID-19-related mortality rates. The strong negative correlation between the CFR and the percentage of the population that was vaccinated in Poland supports the validity of vaccination. To gain insight into virus evolution, we sequenced more than 500 genomes and analyzed nearly 80 thousand SARS-CoV-2 genome sequences deposited in GISAID by Polish diagnostic centers. We showed that the SARS-CoV-2 variant distribution over time in Poland reflected that in Europe. Haplotype network analysis allowed us to follow the virus transmission routes and identify potential superspreaders in each pandemic wave. [ABSTRACT FROM AUTHOR]

Objectives: The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. Data description: The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement. [ABSTRACT FROM AUTHOR]

Obg-like ATPase 1 (OLA1) protein has GTP and ATP hydrolyzing activities and is important for cellular growth and survival. The human OLA1 gene maps to chromosome 2 (locus 2q31.1), near Titin (TTN), which is associated with familial dilated cardiomyopathy (DCM). In this study, we found that expression of OLA1 was significantly downregulated in failing human heart tissue (HF) compared to non-failing hearts (NF). Using the Sanger sequencing method, we characterized the human OLA1 gene and screened for mutations in the OLA1 gene in patients with failing and non-failing hearts. Among failing and non-failing heart patients, we found 15 different mutations in the OLA1 gene, including two transversions, one substitution, one deletion, and eleven transitions. All mutations were intronic except for a non-synonymous 5144A>G, resulting in 254Tyr>Cys in exon 8 of the OLA1 gene. Furthermore, haplotype analysis of these mutations revealed that these single nucleotide polymorphisms (SNPs) are linked to each other, resulting in disease-specific haplotypes. Additionally, to screen the 254Tyr>Cys point mutation, we developed a cost-effective, rapid genetic screening PCR test that can differentiate between homozygous (AA and GG) and heterozygous (A/G) genotypes. Our results demonstrate that this PCR test can effectively screen for OLA1 mutation-associated cardiomyopathy in human patients using easily accessible cells or tissues, such as blood cells. These findings have important implications for the diagnosis and treatment of cardiomyopathy. [ABSTRACT FROM AUTHOR]