Haplotype Diversity Research Articles

Molecular characterization of head and neck infection causing bacterial communities using 16S rRNA in eastern Indian population

Head and neck infections (HNI) are dangerous illnesses caused by a variety of bacterial species. The absence of enough surveillance as well as information regarding the bacteria prevalence in the infected area and the use of excessive antibiotics leads to multidrug-resistant (MDR) pathogens that cause serious health hazards. Thus, in the present study, a surveillance program was carried out in an eastern state of India, known as Odisha to decipher the pool of bacterial genus prevalence and their relationship with related species. The positive clinical specimens obtained through preliminary screening by Vitek 2 were further characterized by utilizing the 16S rRNA gene followed by population genetic and phylogenetic analysis. The investigation resulted four bacterial species, such as Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa. According to population genetic factors, the haplotype (Hd) and nucleotide diversity (π) ranged from 0.558 to 0.828 and 0.03236 to 0.28428. The phylogeny analysis revealed that the present isolates were closely related to Chinese isolates. The prevalence of these pathogens within the eastern part of India and its transboundary potential revealed through phylogenetic analysis need further in-depth research to obtain a better therapeutic approach.

Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.

Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.

Phylogeography, Genetic Diversity and Population Structure of Echinococcus granulosus Sensu Stricto Inferred by Mitochondrial DNA Markers between Southeast of Iran and Pakistan.

Current study was designed to provide a better insight into the circulating genotypes, genetic diversity, and population structure of Echinococcus spp. between southeast of Iran and Pakistan. From Jun 2020 to Dec 2020, 46 hydatid cysts were taken from human (n: 6), camel (n: 10), goat (n: 10), cattle (n: 10) and sheep (n: 10) in various cities of Sistan and Baluchestan Province of Iran, located at the neighborhood of Pakistan. DNA samples were extracted, amplified, and subjected to sequence analysis of cox1 and nad1 genes. The phylogeny inferred by the Maximum Likelihood algorithm indicated that G1 genotype (n: 19), G3 genotype (n: 14) and G6 genotype (n: 13) assigned into their specific clades. The diversity indices showed a moderate (nad1: Hd: 0.485) to high haplotype diversity (cox1: Hd: 0.867) of E. granulosus s.s. (G1/G3) and low nucleotide diversity. The negative value of Tajima's D and Fu's Fs test displayed deviation from neutrality indicating a recent population expansion. A parsimonious network of the haplotypes of cox1 displayed star-like features in the overall population containing IR9/PAK1/G1, IR2/PAK2/G3 and IR18/G6 as the most common haplotypes. A pairwise fixation index (Fst) indicated that E. granulosus s.s. populations are genetically moderate differentiated between southeast of Iran and Pakistan. The extension of haplotypes PAK18/G1 (sheep) and PAK26/G1 (cattle) toward Iranian haplogroup revealed that there is dawn of Echinococcus flow due to a transfer of alleles between mentioned populations through transport of livestock or their domestication. The current findings strengthen our knowledge concerning the evolutionary paradigms of E. granulosus in southeastern borders of Iran and is effective in controlling of hydatidosis.

Genetic diversity of Flaviviridae and Rhabdoviridae EVEs in Aedes aegypti and Aedes albopictus on Hainan Island and the Leizhou Peninsula, China

BackgroundHainan Island and the Leizhou Peninsula, the southernmost part of mainland China, are areas where Aedes aegypti and Ae. albopictus are sympatric and are also high-incidence areas of dengue outbreaks in China. Many studies have suggested that Aedes endogenous viral components (EVEs) are enriched in piRNA clusters which can silence incoming viral genomes. Investigation the EVEs present in the piRNA clusters associated with viral infection of Aedes mosquitoes in these regions may provide a theoretical basis for novel transmission-blocking vector control strategies. MethodsIn this study, specific primers for endogenous Flaviviridae elements (EFVEs) and endogenous Rhabdoviridae elements (ERVEs) were used to detect the distribution of Zika virus infection associated EVEs in the genomes of individuals of the two Aedes mosquitoes. Genetic diversity of EVEs with a high detection rate was also analyzed. ResultsThe results showed that many EVEs associated with Zika virus infection were detected in both Aedes species, with the detection rates were 47.68% to 100% in Ae. aegypti and 36.15% to 92.31% in sympatric Ae. albopictus populations. EVEs detection rates in another 17 Ae. albopictus populations ranged from 29.39% to 89.85%. Genetic diversity analyses of the four EVEs (AaFlavi53, AaRha61, AaRha91 and AaRha100) of Ae. aegypti showed that each had high haplotype diversity and low nucleotide diversity. The number of haplotypes in AaFlavi53 was 8, with the dominant haplotype being Hap_1 and the other 7 haplotypes being further mutated from Hap_1 in a lineage direction. In contrast, the haplotype diversity of the other three ERVEs (AaRha61, AaRha91 and AaRha100) was more diverse and richer, with the haplotype numbers were 9, 15 and 19 respectively. In addition, these EVEs all showed inconsistent patterns of both population differentiation and dispersal compared to neutral evolutionary genes such as the Mitochondrial COI gene. ConclusionThe EFVEs and ERVEs tested were present at high frequencies in the field Aedes mosquito populations. The haplotype diversity of the EFVE AaFlavi53 was relatively lower and the three ERVEs (AaRha61, AaRha91, AaRha100) were higher. None of the four EVEs could be indicative of the genetic diversity of the Ae. aegypti population. This study provided theoretical support for the use of EVEs to block arbovirus transmission, but further research is needed into the mechanisms by which these EVEs are antiviral to Aedes mosquitoes.

Population genetic structure and demographic history of short mackerel, Rastrelliger brachysoma, in the Gulf of Thailand

The short mackerel Rastrelliger brachysoma (Bleeker 1851) is an important fish in the Gulf of Thailand (GoT). The biology of this species has been intensively studied, but its genetic diversity is little known. The genetic diversity, population genetic structure, and demographic history of this species in the GoT were studied using complete mt control region sequences. The CR sequences of 455 mackerel samples collected from 23 localities at four fishing grounds revealed 333 haplotypes with haplotype diversity (h) per population, ranging between 0.8933 and 1.000, with an average of 0.9781. In turn, the nucleotide diversity (µ) ranged between 0.0119 ± 0.0060 and 0.0333 ± 0.0174, with an average of 0.0220 ± 0.00059.A haplotype network analysis showed that all sequences segregated into two subgroups named, clade I and clade II. Two clades were separated by 26 mutational steps. Each clade formed star-like clusters with many haplotypes derived from a common haplotype. Moreover, an analysis of molecular variance (AMOVA) revealed no significant differences among the studied localities, suggesting the presence of a single population in the GoT. Pairwise differences between samples from different fishing regions also indicated no population structure. Both Tajima’s D and Fu’s F S statistics were highly significant for the two clades but nonsignificant for the entire population according to a mismatch distribution analysis. These results confirmed that both clades experienced demographic expansion. The estimated expansion times for clade I and clade II were 1,542.307 years (1.5423 ka BP) and 7,602.541 (7.6025 ka BP) years, respectively.

Unveiling interconnectedness between marine protected and non‐protected areas in Tanzania: Insights from barred mudskipper (Periophthalmus argentilineatus) population genetic structure

AbstractMarine protected areas (MPAs) are globally recognised for their role in safeguarding marine fisheries from the detrimental impacts of human activities and climate change. Tanzania, in alignment with global conservation efforts, has designated 18 MPAs and plans to establish four more in the Southwestern Indian Ocean. However, a critical challenge arises from the lack of a thorough understanding of genetic connectivity between populations in MPAs and non‐protected areas (NPAs). To address this, 151 mitochondrial D‐loop sequences (357 base pairs) of Barred mudskipper (Periophthalmus argentilineatus) were analysed to assess genetic connectivity between MPAs and NPAs in Tanzania. The findings revealed a low and insignificant index of genetic differentiation (FST = −0.0046, p > 0.05) between populations in MPAs and NPAs. Furthermore, haplotypes from both MPAs and NPAs did not cluster based on their geographical origins, with over 9 haplotypes shared between these areas. Additionally, the measured haplotype and nucleotide diversities did not differ significantly between MPAs and NPAs (p > 0.05). However, MPAs showed a significantly higher number of private haplotypes compared to NPAs (p < 0.05). These findings suggest high genetic interconnectedness between populations in MPAs and NPAs, underlining the importance of existing MPAs in preserving local genetic diversity and their potential to replenish depleted NPAs. However, realising the full potential of this interconnectedness necessitates stringent enforcement of sustainable fishing practices to alleviate pressure on fish stocks. It also requires the protection of critical habitats that serve as corridors for fish dispersal, facilitating interconnectedness between MPAs and NPAs.

Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci

The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a complex genomic rearrangement (CGR). Although it has been identified as an important pathogenic DNA mutation signature in genomic disorders and cancer genomes, its architecture remains unresolved. Here, we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping, and single-cell DNA template strand sequencing (strand-seq), the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ∼2.2-5.5 kb of 100% nucleotide similarity within inverted repeat pairs. These data provide experimental evidence that inverted low-copy repeats act as recombinant substrates. This type of CGR can result in multiple conformers generating diverse SV haplotypes in susceptible dosage-sensitive loci.

Epidemiological Characterization and Genetic Variation of the SARS-CoV-2 Delta Variant in Palestine.

The emergence of new SARS-CoV-2 variants in Palestine highlights the need for continuous genetic surveillance and accurate screening strategies. This case series study aimed to investigate the geographic distribution and genetic variation of the SARS-CoV-2 Delta Variant in Palestine in August 2021. Samples were collected at random in August 2021 (n = 571) from eight districts in the West Bank, Palestine. All samples were confirmed as positive for COVID-19 by RT-PCR. The samples passed the quality control test and were successfully sequenced using the ARTIC protocol. The Delta Variant was revealed to have four dominant lineages: B.1.617 (19%), AY.122 (18%), AY.106 (17%), and AY.121 (13%). The study revealed eight significant purely spatial clusters (p < 0.005) distributed in the northern and southern parts of Palestine. Phylogenetic analysis of SARS-CoV-2 genomes (n = 552) showed no geographically specific clades. The haplotype network revealed three haplogroups without any geographic distribution. Chronologically, the Delta Variant peak in Palestine was shortly preceded by the one in the neighboring Israeli community and shortly followed by the peak in Jordan. In addition, the study revealed an extremely intense transmission network of the Delta Variant circulating between the Palestinian districts as hubs (SHR ≈ 0.5), with Al-Khalil, the district with the highest prevalence of COVID-19, witnessing the highest frequency of transitions. Genetic diversity analysis indicated closely related haplogroups, as haplotype diversity (Hd) is high but has low nucleotide diversity (π). However, nucleotide diversity (π) in Palestine is still higher than the global figures. Neutrality tests were significantly (p < 0.05) low, including Tajima's D, Fu-Li's F, and Fu-Li's D, suggesting one or more of the following: population expansion, selective sweep, and natural negative selection. Wright's F-statistic (Fst) showed genetic differentiation (Fst > 0.25) with low to medium gene flow (Nm). Recombination events were minimal between clusters (Rm) and between adjacent sites (Rs). The study confirms the utility of the whole genome sequence as a surveillance system to track the emergence of new SARS-CoV-2 variants for any possible geographical association and the use of genetic variation analysis and haplotype networking to delineate any minimal change or slight deviation in the viral genome from a reference strain.

Comparative Study of Two Himalayan Snow Trouts, Schizothorax esocinus and Schizothorax curvifrons Within the Schizothoracinae and Other Nearest Relatives of Cyprinidae, Inferred from Mitochondrial Sequences of Cytochrome b (Cyt-b) and Cytochrome Oxidase I (Co-I) Gene.

The Himalayan region encompasses varied aquatic ecosystems, characterized by the presence of diverse ichthyofauna, particularly represented by members of the Schizothorax genus, commonly referred to as snow trout. The primary objective of this work was to examine the molecular phylogeny of Schizothoracinae, specifically focusing on the two species, Schizothorax esocinus and Schizothorax curvifrons, which are known to inhabit the northern and north-eastern regions of the Himalayas. This investigation was conducted by analyzing the entire mitochondrial Cyt-b and Co-I gene sequences. The aligned Cyt-b and Co-I sequences for S. esocinus, S. curvifrons, and related members within the subfamily Schizothoracinae, spanned 1130 to 1141 and 1536 to 1551 base pairs, respectively. Using these gene, phylogenetic trees were created to compare Schizothoracinae species to other subfamilies of the family Cyprinidae (Barbinae, Alburninae, Leuciscinae, Xenocyprinae, Cyprininae, and Cultrinae). Genetic distances for Cyt-b and Co-I sequence at three hierarchical levels shows significant disparities in their average score. For Cyt-b, average p-distances for intraspecies, intragenus, and intrafamily were 2.13%, 4.1%, and 15.23%, respectively. Similarly, for Co-I, average p-distances were 1.19%, 3.6%, and 13.8% for intraspecies, intragenus, and intrafamily, respectively. Total number of haplotypes (h) based on Cyt-b and Co-I gene were 6 and 12 within the target Schizothorax spp. In the present study, the observed range of haplotype diversity (hd) for the Cyt-b gene varied from 0.00 to 0.847, with an average haplotype diversity of 0.847 ± 0.034. Similarly, for the Co-I gene, the observed haplotype diversity ranged from 0.00 to 0.931, with an average value of haplotype diversity estimated to be 0.931 ± 0.024. The results of the present study clearly shows that the representative species exhibited close affinities with members of Barbinae and Cyprininae, while other subfamilies formed distinct groups. The findings of the study also indicated that the Cyt-b and Co-I gene exhibits polymorphism and has the potential to serve as a marker for identifying genetic differentiation among populations based on ecological habitats. Mitochondrial Cyt-b and Co-I have been established as a universally accepted and validated genetic marker within a comprehensive bio-identification system at the species level.

High mitochondrial gene diversity of Pediculus humanus capitis among children in northern Iran.

The head louse, Pediculus humanus capitis, is an obligate ectoparasite and its infestation remains a major public health issue worldwide. Determining the genetic characteristics of the existing clades is essential to identify the population structure and to develop head lice-control programs. Hence, we aimed to investigate the genetic diversity of head lice among infested individuals in northern Iran. Adult head lice were collected from 100 infested individuals referring to the health centers throughout five geographical regions in Mazandaran Province, Iran. Partial fragments of the mitochondrial cytb gene were amplified by PCR, then consequently sequenced. The results of the phylogenetic tree of collected head lice confirmed the existence of two clades, A and B, in the studied areas. Thirteen haplotypes were detected in the studied populations, of which 11 were novel haplotypes. Clade A was the dominant form and accounted for 75% of samples, while clade B included the rest. Haplotype and nucleotide diversity were 0.999 and 0.0411, respectively. Clade A and B of Pediculus humanus capitis exist among the human populations of northern Iran. We observed high genotypic diversity of this head lice.

Maternal genetic diversity and phylogenetic analysis of Indian riverine and swamp buffaloes: insights from complete mitochondrial genomes.

This study explored the genetic diversity and evolutionary history of riverine and swamp buffaloes in India, utilizing complete mitochondrial genome sequences. Through comprehensive sampling across varied agro-climatic zones, including 91 riverine buffaloes from 12 breeds and 6 non-descript populations, along with 16 swamp buffaloes of the Luit breed, this study employed next-generation sequencing techniques to map the mitogenomic landscape of these subspecies. Sequence alignments were performed with the buffalo mitochondrial reference genome to identify mitochondrial DNA (mtDNA) variations and distinct maternal haplogroups among Indian buffaloes. The results uncovered the existence of 212 variable sites in riverine buffaloes, yielding 67 haplotypes with high haplotype diversity (0.991), and in swamp buffaloes, 194 variable sites resulting in 12 haplotypes, displaying haplotype diversity of 0.950. Phylogenetic analyses elucidated the genetic relationships between Indian buffaloes and the recognized global haplogroups, categorizing Indian swamp buffaloes predominantly into the SA haplogroup. Intriguingly, the haplogroup SB2b was observed for the first time in swamp buffaloes. Conversely, riverine buffaloes conformed to established sub-haplogroups RB1, RB2, and RB3, underscoring the notion of Northwestern India as a pivotal domestication site for riverine buffaloes. The study supports the hypothesis of independent domestication events for riverine and swamp buffaloes, highlighting the critical role of genetic analysis in unraveling the complex evolutionary pathways of domestic animals. This investigation contributes to the global understanding of buffalo mitogenome diversity, offering insights into this important livestock species' domestication and dispersal patterns.

Genetic Diversity Based on the Analysis of 27 Y- Short Tandem Repetition (STR) Loci in Two Populations in the Apuseni Mountains, Romania.

Y chromosome analysis is used in various fields of forensic genetics, genetic genealogy, and evolutionary research, due to its unique characteristics. Short tandem repetitions (STR) are particularly relevant in population genetic studies. The aimof this study is to analyze the genetic profile of two populations in the Apuseni Mountains area, Băița and Roșia Montană, Romania. 27 STR loci of the Y chromosome were analyzed to investigate the genetic profile of two populations from the Apuseni Mountains area. Investigating genetic diversity by analyzing allele frequency, haplotype frequency, calculating forensic parameters, and presenting the main haplogroups identified based on Y-STR markers. Gene diversity in the batch from Băița varies from 0.515 for the DYS393 locus to 0.947 for the DYS385 locus. In the Roșia Montană population, gene diversity ranges from 0.432 for DYS393 to 0.931 for DYS385. The haplotype diversity in Roșia Montană was 0.991, and the haplotype diversity was 1.000 in the population from Băița. A total of nine haplogroups was identified in the batch from Băița, while only seven haplogroups were observed in the batch from Roșia Montană. Both groups are based on the same five major haplogroups (E, G, I, J, and R) and the most common haplogroup is R1b in both populations. In this study, the genetic diversity of two distinct populations was assessed using genetic analyses based on different markers. Analysis of Y-STR profiles revealed significant genetic diversity in both studied groups. All haplogroups identified were similar to those present in other Romanian populations.

Molecular phylodiagnosis of Echinococcus multilocularis and Echinococcus granulosus among canids in Guilan province, northern Iran

Canine-transmitted worms and an uncontrolled deworming program of stray dogs have caused that accurate diagnosis of zoonotic parasites received notable attention in endemic regions. This study aimed to assess the presence of E. multilocularis and E. granulosus infections in canids from Guilan province, northern Iran. A total of 272 fecal samples from carnivores were collected across 24 different regions in Guilan province between 2023 and 2024. All fecal specimens were observed following concentration and flotation techniques. DNAs of taeniid eggs were extracted, amplified, and sequenced targeting of specific mitochondrial Cox1 gene for E. granulosus and NAD 1 gene for E. multilocularis. On the base of molecular and phylogenetic analysis 1.47 % (in jackal) and 25 % (in dogs and jackal) of samples were positive for E. multilocularis and E. granulosus sensu strico G1 genotype, respectively. Molecular technique was found to be more sensitive in detecting infection in comparison with conventional techniques. Sequence analysis of Cox1 indicated a high genetic diversity (Haplotype diversity; 0.933; Number of haplotypes, h: 7) in E. granulosus G1. Current findings show that canids particularly jackals play potential role of definitive host in maintenance and transmission dynamic of E. multilocularis and E. granulosus in northern Iran. The presence of these infections is of particular concern in Guilan province due to the high influx of tourists, increasing the risk of transmission to humans. Therefore, the implementation of preventive programs is warranted to apply hygienic practices and adjusting deworming programs for the canids and at-risk individuals in the region.

Genetic Diversity and Population Structure of the Endangered Salamander Hynobius yiwuensis Inferred from Mitochondrial DNA Sequences.

Understanding the genetic diversity patterns of endangered species is crucial for biodiversity conservation. The endangered salamander Hynobius yiwuensis, endemic to the mainland and Zhoushan Island in Zhejiang, China, has suffered from sharp population declines due to habitat loss. However, the levels and patterns of genetic diversity, differentiation, and population structure of H. yiwuensis remain poorly understood. Here, we explored the genetic diversity and phylogeography of H. yiwuensis based on partial mtDNA sequences (Cytb and CO1) through 111 individuals collected from seven localities. Relatively high overall haplotype diversity (h = 0.965) and low nucleotide diversity (π = 0.013) were detected. Our results, through phylogenetic trees and haplotype network analyses, revealed two divergent haplogroups, mainland and island, and the estimated divergence time indicated they diverged ~2.44 million years ago, which coincided with the period when Zhoushan Island became separated from the mainland.

The longevity-associated BPIFB4 gene guarantees vascular homeostasis and immune protection through platelets.

Beyond their activity in hemostasis and thrombosis, recent advances attribute platelets a pro-youthful role capable to attenuate immune senescence and age-related neuroinflammation. Previous studies from our group associated a polymorphic haplotype variant in the BPIFB4 gene (LAV-BPIFB4) with exceptional longevity. Transfer of the LAV-BPIFB4 in preclinical models has proved strategic to cope with frailty conditions, aging-related events, e.g., cardiovascular ones, and immune dysfunction mainly through a favorable conditioning of the immune system. However, whether platelets participate in LAV-BPIFB4 therapeutic action is currently unknown.Herein, we discovered that platelets were instrumental in boosting the favorable health outcomes of the systemic AAV-LAV-BPIFB4 gene transfer in vivo, as the α-CD42b platelet depletion completely abolished the vascular protective action of LAV-BPIFB4 and suppressed its pro-resolutive CD206 + anti-/CD86 + pro-inflammatory Ly6C + monocyte skewing to LPS stimulation. Of note, this is associated with a huge drop in the protective levels of BPIFB4 in the plasma of AAV-LAV-BPIFB4-injected C57BL/6 mice, indicating that plasma circulating platelets may be a reservoir of the BPIFB4 protein. Indeed, we noticed that BPIFB4 was released by human platelets, a process that is amplified in LAV-allele carrier donors. Accordingly, lentivirus-mediated overexpression of human LAV-BPIFB4 isoform, but not WT-BPIFB4 isoform was able in leading differentiated megakaryocytes to release more platelet-like-particles enriched for BPIFB4. In addition, in vitro, the M2 macrophage polarization increased when releasate from platelets, and even more from LAV pre-stimulated once, was added in monocyte cell culture. Our data suggest that platelet release of BPIFB4 and of yet-to-be-determined unidentified factors mediates the therapeutic efficacy of LAV-BPIFB4 treatment.

Mitochondrial DNA (mtDNA) genetic variability of cytochrome B gene (CYTB) in three populations of native rabbits in Egypt

The current study aimed to detect the genetic variability of mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in 80 native Egyptian rabbits (NER) belonging to three populations in three different agriculture regions (Delta, Middle, and Upper Egypt) and also investigate the origin of these breeds by phylogenetic relationship analysis. A total of 62 haplotypes were recorded among the three NER populations. The native Upper Egypt rabbits (NUER) expressed the highest number of haplotypes, mutations, polymorphic sites, and haplotype diversity (23, 55, 51, and 1.00, respectively). While it gave the lowest values of nucleotide diversity (0.0262) and Tajima's D (−0.01435), the percentage of mutual haplotypes was 4.8 % between the Middle and Delta Egypt populations. The phylogenetic analysis showed that there were more separated haplotypes of NUER compared to other populations. The same finding was also observed when supported by 31 sequences of different rabbit breeds retrieved from the GeneBank database. A mutual haplotype was observed between native Delta Egyptian rabbits (NDER) and New Zealand (NWZ) rabbits. The results of this study shed light on the importance of indigenous breeds in rural areas through mtDNA, which contributes to finding sustainable strategies to conserve and improve genetic resources in Egyptian rural areas.

Genetic diversity and population structure of threeline grunt Parapristipoma trilineatum (Perciformes: Haemulidae) in China and Japan based on mtDNA control region

Parapristipoma trilineatum is an edible and economically important marine fish with high farming potential; however, this fish has not been widely investigated. To understand the germplasm resources of this marine fish, we investigated the range of P. trilineatum from Maizuru, Japan, to Hainan, China. Using the mitochondrial control region as a molecular marker, we analyzed the population structure, genetic diversity, and population history dynamics of P. trilineatum. The control region exhibited high haplotype diversity and nucleotide diversity of 0.996 and 0.016, respectively. The genetic differentiation coefficients indicated low differentiation between Japanese and other populations. Additionally, based on the results of SAMOVA, AMOVA, and genetic differentiation coefficients, P. trilineatum can be divided into two management units in fishery resources management: China and Japan. Populations with high genetic diversity are useful as genetic breeding materials. This study provides a basis for the selection and breeding of P. trilineatum.

Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

Immunoglobulins (IGs), critical components of the human immune system, are composed of heavy and light protein chains encoded at three genomic loci. The IG Kappa (IGK) chain locus consists of two large, inverted segmental duplications. The complexity of the IG loci has hindered use of standard high-throughput methods for characterizing genetic variation within these regions. To overcome these limitations, we use long-read sequencing to create haplotype-resolved IGK assemblies in an ancestrally diverse cohort (n = 36), representing the first comprehensive description of IGK haplotype variation. We identify extensive locus polymorphism, including novel single nucleotide variants (SNVs) and novel structural variants harboring functional IGKV genes. Among 47 functional IGKV genes, we identify 145 alleles, 67 of which were not previously curated. We report inter-population differences in allele frequencies for 10 IGKV genes, including alleles unique to specific populations within this dataset. We identify haplotypes carrying signatures of gene conversion that associate with SNV enrichment in the IGK distal region, and a haplotype with an inversion spanning the proximal and distal regions. These data provide a critical resource of curated genomic reference information from diverse ancestries, laying a foundation for advancing our understanding of population-level genetic variation in the IGK locus.

Insights into haplotype distribution and population dynamics of Biscogniauxia mediterranea in cork oak forests in Tunisia

Biscogniauxia mediterranea is a pathogenic fungus associated with Quercus species causing charcoal canker disease in forests. Its phenotypic and genetic variability has been well studied in Tunisia but little is known about its demographic history. Population dynamic of B. mediterranea was evaluated among 30 isolates from different cork oak forests in Northwestern Tunisia. The genetic structure analyzed with two DNA markers (ITS and tef-1α) showed low genetic differentiation associated with high genetic flow among populations. The polymorphism analysis showed low nucleotide diversity but high haplotypic diversity among and within B. mediterranea populations which could be due to rapid growth from a small ancestral population. This hints at recent population growth after a period of decline likely due to a catastrophic event involving fires and human-induced tree cutting. The resulting genetic diversity within populations primarily arises from the emergence of new haplotypes. Overall, this study provides insights into the polymorphism of B. mediterranea and its potential adaptive strategy.

Afila, the origin and nature of a major innovation in the history of pea breeding.

The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea - Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown. Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes. Our results show that deletion of two tandemly arranged genes encoding Q-type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af-harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes. Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops.