Distinct Genetic Patterns Research Articles

Genetic diversity of closely related Calligounum species collected from Saudi habitats by analyzing the matK and rpoC1 genes, and SCoT and IRAP markers

Abstract The genus Calligonum L. Her (Polygonaceae) comprises 158 species with widespread distribution in regions such as India, China, North Africa, Pakistan, Afghanistan, Saudi Arabia, and South Europe. Calligonum L. is a prominent shrubby psammophyte found in deserts, known for its traditional medicinal uses. The aim of this study is to use Start Codon Target (SCoT) and Inter-Retrotransposon Amplified Polymorphism (IRAP) markers to evaluate the genetic diversity of Calligonum comosum and Calligonum tetrapterum in Saudi Arabia. In addition, it uses the raxmlHPC algorithm and DNA barcoding techniques (matK and rpoC1) to examine phylogenetic relationships. SCoT and IRAP markers revealed distinct genetic patterns, clustering Calligonum species based on their genetic similarities. DNA barcoding of matK and rpoC1 genes provided valuable insights into the evolutionary relationships within Calligonum species. Phylogenetic analyses highlighted well-supported structures with outgroup sequences showing early divergence. Conserved motifs analysis confirmed the presence of shared motifs in both isolated and identified genes, validating the potential use of isolated genes as biomarkers. This comprehensive genetic analysis enhances our understanding of Calligonum species’ genetic relationships, contributing valuable information for taxonomic classification and molecular marker validation. We are the first to add sequence of rpoC1 gene to Calligonum comosum and Calligonum tetrapterum in Gen-Bank. The identified conserved motifs and phylogenetic insights underscore the potential applications of Calligonum genes in various fields, including medicine and biodiversity conservation.

Precision medicine in gynecological cancer (Review).

The advent of personalized and precision medicine has revolutionized oncology and treatment of gynecological cancer. These innovative approaches tailor treatments to individual patient profiles beyond genetic markers considering environmental and lifestyle factors, thereby optimizing therapeutic efficacy and minimizing adverse effects. Precision medicine uses advanced genomic technologies such as next-generation sequencing to perform comprehensive tumor profiling. This allows identification of distinct genetic mutations, expression patterns and signaling pathway alterations, revealing the complex molecular landscape of gynecological cancer such as ovarian, cervical and uterine cancer. A major challenge in treating these cancers is their inherent molecular heterogeneity, which can influence tumor behavior, therapy response and prognosis. Precision medicine aims to overcome this by identifying biomarkers and molecular drivers for targeted therapy selection. For example, the identification of breast cancer (BRCA) gene mutations in ovarian cancer has guided the use of poly (ADP-ribose) polymerase inhibitors, leading to more effective treatments with fewer side effects. Similar targeted therapies and immunotherapies have also been developed for cervical and uterine cancer, marking progress toward personalized care. Future directions in gynecological oncology emphasize the importance of molecular profiling and development of targeted therapies. By understanding the unique molecular features of each patient, clinicians can select the most effective personalized treatment strategies to improve patient outcomes and quality of life.

Identification of beta-lactamase genes and molecular genotyping of multidrug-resistant clinical isolates of Klebsiella pneumoniae

BackgroundKlebsiella pneumoniae is a clinically relevant pathogen that has raised considerable public health concerns. This study aims to determine the presence of beta-lactamase genes and perform molecular genotyping of multidrug-resistant (MDR) K. pneumoniae clinical isolates.MethodsClinical isolates of MDR K. pneumoniae were collected from educational hospitals affiliated with Babol University of Medical Sciences. The isolates of K. pneumoniae were identified through standard microbial and biochemical tests. Antibiotic resistance was assessed using disk diffusion, modified Hodge test (MHT), combined disk, and polymerase chain reaction (PCR) methods. Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR was performed for molecular typing.ResultsA total of 42 MDR K. pneumoniae isolates were obtained from various clinical specimens. The highest antibiotic resistance was observed for ampicillin (100%), while the lowest resistance was noted for amikacin (19.04%). The MHT indicated that 38.09% of K. pneumoniae isolates produced carbapenemase enzymes. Metallo-beta-lactamase (MBL) production was found in 54.76% of isolates. Molecular detection of beta-lactamase genes revealed the presence of blaNDM (21.42%), blaKPC (42.85%), blaTEM (76.19%), blaSHV (47.16%), and blaCTX−M (80.95%) genes. ERIC-PCR molecular typing identified seven distinct genetic patterns among the isolates.ConclusionsThis investigation demonstrates the high resistance levels of K. pneumoniae strains. The beta-lactamase genes with the highest and lowest frequencies correspond to blaCTX−M and blaNDM genes, respectively. ERIC-PCR dendrograms suggest a common origin for K. pneumoniae clinical isolates and the propagation of similar clones within hospital wards. These findings indicate that K. pneumoniae isolates are highly virulent, necessitating the development of more effective resistance-fighting techniques and gene transfer research.Clinical trial numberNot applicable.

Genome-wide association studies unveil major genetic loci driving insecticide resistance in Anopheles funestus in four eco-geographical settings across Cameroon

BackgroundInsecticide resistance is jeopardising malaria control efforts in Africa. Deciphering the evolutionary dynamics of mosquito populations country-wide is essential for designing effective and sustainable national and subnational tailored strategies to accelerate malaria elimination efforts. Here, we employed genome-wide association studies through pooled template sequencing to compare four eco-geographically different populations of the major vector, Anopheles funestus, across a South North transect in Cameroon, aiming to identify genomic signatures of adaptive responses to insecticides.ResultsOur analysis revealed limited population structure within Northern and Central regions (FST<0.02), suggesting extensive gene flow, while populations from the Littoral/Coastal region exhibited more distinct genetic patterns (FST>0.049). Greater genetic differentiation was observed at known resistance-associated loci, resistance-to-pyrethroids 1 (rp1) (2R chromosome) and CYP9 (X chromosome), with varying signatures of positive selection across populations. Allelic variation between variants underscores the pervasive impact of selection pressures, with rp1 variants more prevalent in Central and Northern populations (FST>0.3), and the CYP9 associated variants more pronounced in the Littoral/Coastal region (FST =0.29). Evidence of selective sweeps was supported by negative Tajima’s D and reduced genetic diversity in all populations, particularly in Central (Elende) and Northern (Tibati) regions. Genomic variant analysis identified novel missense mutations and signatures of complex genomic alterations such as duplications, deletions, transposable element (TE) insertions, and chromosomal inversions, all associated with selective sweeps. A 4.3 kb TE insertion was fixed in all populations with Njombe Littoral/Coastal population, showing higher frequency of CYP9K1 (G454A), a known resistance allele and TE upstream compared to elsewhere.ConclusionOur study uncovered regional variations in insecticide resistance candidate variants, emphasizing the need for a streamlined DNA-based diagnostic assay for genomic surveillance across Africa. These findings will contribute to the development of tailored resistance management strategies crucial for addressing the dynamic challenges of malaria control in Cameroon.

Targeting liposarcoma: unveiling molecular pathways and therapeutic opportunities.

In recent years, an increasing number of studies have utilized molecular biology techniques to reveal important molecular heterogeneity among different subtypes of liposarcoma. Each subtype exhibits distinct genetic patterns and molecular pathways, which may serve as important targets for molecular therapy. In the present review, we focus on the molecular characteristics, molecular diagnostics, driver genes, and molecular mechanisms of liposarcoma. We also discuss the clinical research progress of related targeted therapies, with an aim to provide a reference and crucial insights for colleagues in the field.

Analysis of CNS autoimmunity in genetically diverse mice reveals unique phenotypes and mechanisms.

Multiple sclerosis (MS) is a complex disease with significant heterogeneity in disease course and progression. Genetic studies have identified numerous loci associated with MS risk, but the genetic basis of disease progression remains elusive. To address this, we leveraged the Collaborative Cross (CC), a genetically diverse mouse strain panel, and experimental autoimmune encephalomyelitis (EAE). The 32 CC strains studied captured a wide spectrum of EAE severity, trajectory, and presentation, including severe-progressive, monophasic, relapsing remitting, and axial rotary-EAE (AR-EAE), accompanied by distinct immunopathology. Sex differences in EAE severity were observed in 6 strains. Quantitative trait locus analysis revealed distinct genetic linkage patterns for different EAE phenotypes, including EAE severity and incidence of AR-EAE. Machine learning-based approaches prioritized candidate genes for loci underlying EAE severity (Abcc4 and Gpc6) and AR-EAE (Yap1 and Dync2h1). This work expands the EAE phenotypic repertoire and identifies potentially novel loci controlling unique EAE phenotypes, supporting the hypothesis that heterogeneity in MS disease course is driven by genetic variation.

Codon Usage Analysis Reveals Distinct Evolutionary Patterns and Host Adaptation Strategies in Duck Hepatitis Virus 1 (DHV-1) Phylogroups.

Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.

Distinct phylogeographic and population genetic patterns of decapod species across Mediterranean biogeographic barriers

Abstract The Mediterranean Sea is a semi-enclosed oceanic basin that communicates with the Atlantic Ocean and can be subdivided into seven geographical regions. It is considered a hotspot of biodiversity and is characterised by high rates of endemism. Over the past decades, many studies showed the presence of potential geographical breaks both across the Atlanto-Mediterranean transition and within the Mediterranean Sea. These investigations led to the identification of three distinct types of population genetic structures: (1) populations characterized by panmixia; (2) Atlanto-Mediterranean geographical partitioning; and (3) possible further subdivision between East and West Mediterranean basins. In this review, mainly focused on Christoph Schubart’s works and interests, we summarize the different patterns of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean Sea, recorded for decapod species living in littoral zones. Although some species share similar biological traits, larval dispersal mechanisms and habitat preferences, differences in their phylogeographic and population genetic structures do emerge. These findings confirm the complex nature of gene flows across the Atlanto-Mediterranean transition and within the Mediterranean basin and how difficult it is to achieve a generalised picture of the phylogeographical patterns of Atlantic-Mediterranean species.

Single-cell Profiling Uncovers Evolutionary Divergence of Hypocretin/Orexin Neuronal Subpopulations.

Brain nuclei are traditionally defined by their anatomy, activity, and expression of specific markers. The hypothalamus contains discrete neuronal populations that coordinate fundamental behavioral functions, including sleep and wakefulness, in all vertebrates. Particularly, the diverse roles of hypocretin/orexin (Hcrt)-releasing neurons suggest functional heterogeneity among Hcrt neurons. Using single-cell RNA sequencing (scRNA-seq) and high-resolution imaging of the adult male and female zebrafish hypothalamic periventricular zone (PVZ), we identified 21 glutamatergic and 28 GABAergic cell types. Integration of zebrafish and mouse scRNA-seq revealed evolutionary conserved and divergent hypothalamic cell types. The expression of specific genes, including npvf, which encodes a sleep-regulating neuropeptide, was enriched in subsets of glutamatergic Hcrt neurons in both larval and adult zebrafish. The genetic profile, activity, and neurite processing of the neuronal subpopulation that co-expresses both Hcrt and Npvf (Hcrt+Npvf+) differ from other Hcrt neurons. These inter-species findings provide a unified annotation of hypothalamic cell types, and suggest that the heterogeneity of Hcrt neurons enables multi-functionality, such as consolidation of both wake and sleep by the Hcrt- and Npvf-releasing neuronal subpopulation.Significance Statement The study reveals the intricate heterogeneity within the hypothalamic periventricular zone (PVZ) of zebrafish, identifying 21 glutamatergic and 28 GABAergic cell types through single-cell RNA sequencing (scRNA-seq) and high-resolution imaging. Comparative analysis with mouse scRNA-seq data revealed conserved and divergent cell types, transcriptional regulatory mechanisms, and neuropeptide localization. Notably, we identified a unique neuronal subpopulation co-expressing both hypocretin/orexin (Hcrt) and neuropeptide VF (Npvf) neuropeptides in zebrafish. The distinct genetic profiles, activity patterns, and neurite processing of this subpopulation suggest a role in regulating both sleep and wakefulness.

Genetic diversity and population dynamics of wild Mozambique tilapia (Oreochromis mossambicus) in South Africa

Urbanisation and water developments in South Africa have created numerous challenges in managing water resources. Consequently, the native fish species Oreochromis mossambicus, prominent to freshwater ecosystems in South Africa now faces the threat of extinction amidst introductions of alien Oreochromis species. The species has recently been classified as Vulnerable on the IUCN Red List. Despite the economic importance of O. mossambicus within the South African region, little is known about the genetic and population dynamics of the species. In this study, we aimed to establish baseline genetic and population data, and determine the impact of water management practices on population structure. This data is crucial for the conservation and monitoring of this species across South Africa. The study revealed relatively low genetic diversity within sample localities but significant differentiation among populations. The analyses identified 16 geographically correlated genetic clusters, indicating substantial differentiation across catchments. Anthropogenic activities, changes in catchment use, and water management strategies significantly influenced the genetic population structure in the studied regions. Given the distinct genetic patterns, conservation-oriented management should prioritise maintaining existing genetic diversity to ensure the long-term survival of this vulnerable species.

Abstract 1766: CREBBP, NOTCH2 and GNASmutational profile in uterine sarcomas

Abstract Background: Uterine sarcomas (US) present clinical challenges due to their dynamic behavior and limited treatment options. Representing 1-3% of uterine cancer cases, these tumors exhibit rapid growth, high recurrence rates, and resistance to the standard treatments. The present study aimed to validate several Loss-of-function mutations (LOF), obtained by NGS analysis in the CREBBP, NOTCH2, and GNAS sequences, in US through Sanger sequencing. Methods: Twenty-five samples of US were collected between 2000 and 2015 for genomic DNA extraction. An initial genetic screening of the samples by NGS method was followed by Sanger sequencing validation. Bioinformatics analysis through SnapGene confirmed the results. Results: A c.4063G&amp;gt;A mutation was confirmed in uterine leiomyosarcomas (ULMS), in the both strands. Notable variations in the forward strand, such as a C&amp;gt;G substitution at position 38 of the alignment and a degenerate base S at position 113, differentiated ULMS from uterine sarcomas (US). Two ULMSs exhibited the highest substitution rates: one with 18 and another with 6 substitutions. Despite the absence of the c.5527T&amp;gt;C CREBBP mutation, ULMS displayed increased insertions and deletions. Assessing the NOTCH2 gene in US revealed a complex genetic landscape, with a unique SU-specific duplication in the forward strand. The reverse strand maintained high genetic stability. Mutation c.6094C&amp;gt;A was exclusive to one US sample. Notably, the c.7223T&amp;gt;A mutation in NOTCH2 was not identified. Shared mutations between ULMS and US suggest genomic similarities in these regions. In the GNAS analysis, the c.2381A&amp;gt;C mutation was not found. However, in the forward sequence of one US sample, a deletion at the expected substitution site was detected, suggesting a specific genetic alteration. The c.706G&amp;gt;A mutation was consistently present in sample ULMS, indicating genetic stability in this sample. US exhibited a G&amp;gt;C substitution in the reverse sequence, hinting at a unique pattern of genetic variation. These findings underscore the complexity of genetic alterations in these critical gene regions. Conclusion: Our analysis identified specific alterations in ULMS and US. ULMS showed the c.4063G&amp;gt;A CREBBP mutation and unique variations, while US had a specific c.6094C&amp;gt;A NOTCH2 mutation. The absence of the c.2381A&amp;gt;C GNAS mutation in both ULMS and US, along with distinct genetic patterns (c.706G&amp;gt;A in ULMS and G&amp;gt;C substitution in US), underscores significant mutational differences in these critical gene regions. These findings enhance our understanding of uterine sarcoma genetics, prompting further exploration for potential diagnosis, prognosis and therapeutic advancements. Citation Format: Laura Gonzalez dos Anjos, Giovanna Quevedo, Edmund Baracat, Katia C. Carvalho. CREBBP, NOTCH2 and GNASmutational profile in uterine sarcomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1766.

Genetic diversity of lion populations in Kenya: Evaluating past management practices and recommendations for future conservation actions.

The decline of lions (Panthera leo) in Kenya has raised conservation concerns about their overall population health and long-term survival. This study aimed to assess the genetic structure, differentiation and diversity of lion populations in the country, while considering the influence of past management practices. Using a lion-specific Single Nucleotide Polymorphism (SNP) panel, we genotyped 171 individuals from 12 populations representative of areas with permanent lion presence. Our results revealed a distinct genetic pattern with pronounced population structure, confirmed a north-south split and found no indication of inbreeding in any of the tested populations. Differentiation seems to be primarily driven by geographical barriers, human presence and climatic factors, but management practices may have also affected the observed patterns. Notably, the Tsavo population displayed evidence of admixture, perhaps attributable to its geographic location as a suture zone, vast size or past translocations, while the fenced populations of Lake Nakuru National Park and Solio Ranch exhibited reduced genetic diversity due to restricted natural dispersal. The Amboseli population had a high number of monomorphic loci likely reflecting a historical population decline. This illustrates that patterns of genetic diversity should be seen in the context of population histories and that future management decisions should take these insights into account. To address the conservation implications of our findings, we recommend prioritizing the maintenance of suitable habitats to facilitate population connectivity. Initiation of genetic restoration efforts and separately managing populations with unique evolutionary histories is crucial for preserving genetic diversity and promoting long-term population viability.

Transmission restriction and genomic evolution co-shape the genetic diversity patterns of influenza A virus

Influenza A virus (IAV) shows an extensive host range and rapid genomic variations, leading to continuous emergence of novel viruses with significant antigenic variations and the potential for cross-species transmission. This causes global pandemics and seasonal flu outbreaks, posing sustained threats worldwide. Thus, studying all IAVs' evolutionary patterns and underlying mechanisms is crucial for effective prevention and control. We developed FluTyping to identify IAV genotypes, to explore overall genetic diversity patterns and their restriction factors. FluTyping groups isolates based on genetic distance and phylogenetic relationships using whole genomes, enabling identification of each isolate's genotype. Three distinct genetic diversity patterns were observed: one genotype domination pattern comprising only H1N1 and H3N2 seasonal influenza subtypes, multi-genotypes co-circulation pattern including majority avian influenza subtypes and swine influenza H1N2, and hybrid-circulation pattern involving H7N9 and three H5 subtypes of influenza viruses. Furthermore, the IAVs in multi-genotypes co-circulation pattern showed region-specific dominant genotypes, implying the restriction of virus transmission is a key factor contributing to distinct genetic diversity patterns, and the genomic evolution underlying different patterns was more influenced by host-specific factors. In summary, a comprehensive picture of the evolutionary patterns of overall IAVs is provided by the FluTyping's identified genotypes, offering important theoretical foundations for future prevention and control of these viruses.

Novel data-driven subtypes and stages of brain atrophy in the ALS–FTD spectrum

BackgroundTDP-43 proteinopathies represent a spectrum of neurological disorders, anchored clinically on either end by amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). The ALS–FTD spectrum exhibits a diverse range of clinical presentations with overlapping phenotypes, highlighting its heterogeneity. This study was aimed to use disease progression modeling to identify novel data-driven spatial and temporal subtypes of brain atrophy and its progression in the ALS–FTD spectrum.MethodsWe used a data-driven procedure to identify 13 anatomic clusters of brain volume for 57 behavioral variant FTD (bvFTD; with either autopsy-confirmed TDP-43 or TDP-43 proteinopathy-associated genetic variants), 103 ALS, and 47 ALS–FTD patients with likely TDP-43. A Subtype and Stage Inference (SuStaIn) model was trained to identify subtypes of individuals along the ALS–FTD spectrum with distinct brain atrophy patterns, and we related subtypes and stages to clinical, genetic, and neuropathological features of disease.ResultsSuStaIn identified three novel subtypes: two disease subtypes with predominant brain atrophy in either prefrontal/somatomotor regions or limbic-related regions, and a normal-appearing group without obvious brain atrophy. The limbic-predominant subtype tended to present with more impaired cognition, higher frequencies of pathogenic variants in TBK1 and TARDBP genes, and a higher proportion of TDP-43 types B, E and C. In contrast, the prefrontal/somatomotor-predominant subtype had higher frequencies of pathogenic variants in C9orf72 and GRN genes and higher proportion of TDP-43 type A. The normal-appearing brain group showed higher frequency of ALS relative to ALS–FTD and bvFTD patients, higher cognitive capacity, higher proportion of lower motor neuron onset, milder motor symptoms, and lower frequencies of genetic pathogenic variants. The overall SuStaIn stages also correlated with evidence for clinical progression including longer disease duration, higher King’s stage, and cognitive decline. Additionally, SuStaIn stages differed across clinical phenotypes, genotypes and types of TDP-43 pathology.ConclusionsOur findings suggest distinct neurodegenerative subtypes of disease along the ALS–FTD spectrum that can be identified in vivo, each with distinct brain atrophy, clinical, genetic and pathological patterns.

Genetic Diversity and Population Dynamics of Invasive Ascidiella aspersa: Insights from Cytochrome Oxidase Subunit I and 18S rDNA Analyses in Korean and Global Populations

Ascidiella aspersa, originally native to the northeastern Atlantic, has emerged as a prolific invasive species in coastal waters worldwide. In 2010, it was identified as an alien species in Republic of Korea, rapidly colonizing artificial harbor structures and outcompeting native species. This study employs morphological analyses and genetic sequencing, focusing on mitochondrial DNA (cytochrome oxidase subunit I; mt-COI) and nuclear markers (18S rRNA), to unravel the genetic structure and haplotype diversity (Hd) of A. aspersa populations in Republic of Korea and globally. The analysis of 154 mt-COI and 127 18S rDNA global population sequences, as well as 80 mt-COI and 79 18S-rDNA Korean population sequences, revealed distinct genetic patterns. Among global populations, the mt-COI gene displayed significant genetic diversity, with 21 distinct haplotypes distributed across 41 polymorphic sites, which is indicative of extensive genetic variability. In contrast, the 18S rDNA marker exhibited limited diversity, with only four haplotypes identified at three polymorphic sites. In Korean populations, the mt-COI gene also exhibited substantial genetic diversity, with 14 distinct haplotypes displaying genetic variations at 29 polymorphic sites. Conversely, the 18S rDNA marker in Korean populations revealed a unique genetic pattern, with only one shared haplotype. These findings emphasize the complex genetic diversity within A. aspersa populations, both globally and in Republic of Korea. This genetic analysis provides valuable insights into the species’ colonization history and adaptation mechanisms, shedding light on the factors shaping its genetic structure. Further research is warranted to elucidate the ecological implications of these genetic patterns in the context of invasion biology.

Assessment of Genetic Diversity and Fingerprinting of Sugarcane Varieties Using Simple Sequence Repeat (SSR) Markers

Simple sequence repeat (SSR) fingerprinting was chosen because of its high polymorphism, which enables precise analysis of genetic diversity, for the assessment of genetic variety among several sugarcane varieties. This method focuses on certain areas of the sugarcane genome and offers important insights into the distinctive genetic patterns and relationships between the many sugarcane types under study. To increase sugarcane production and resilience, crop development plans, breeding programmes, and conservation activities must be guided by the data obtained by SSR fingerprinting. This study aimed to assess the genetic diversity and fingerprinting of eight sugarcane varieties (Isd 16, Isd 20, Isd 21, Isd 24, Isd 28, Isd 29, Isd 30, and Isd 31) using four SSR primers. A simple and efficient method for DNA isolation was employed, and the primers successfully amplified a total of 59 bands from the eight varieties. The results showed that the marker SMC687CS exhibited the highest number of alleles and genotypes per locus, followed by SMC336BS and SMC334BS, while SMC119CG showed the lowest. The highest PIC value was obtained from the marker SMC687CS, indicating its high level of polymorphism. The four SSR markers were able to distinguish 56.25% of all the cultivars evaluated, with the highest linkage distance recorded between the varieties Isd 24 and Isd 28. This study identified and classified the eight sugarcane varieties, indicating genetic differences among them that coincide with their field performances.

Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics.

Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever and, in some cases, chronic carriage after resolution of acute disease. This study examined sequential isolates of S. Typhi from a single host with persistent asymptomatic infection. These isolates, along with another S. Typhi isolate recovered from a household contact with typhoid fever, were subjected to whole genome sequencing and analysis. In addition, direct sequencing of the bile fluid from the host with persistent infection was also performed. Comparative analysis of isolates revealed three sub-populations of S. Typhi with distinct genetic patterns. Metagenomic sequencing recognised only two of the three sub-populations within the bile fluid. The detection and investigation of insertion sequences IS10R and associated deletions complemented analysis of single nucleotide polymorphisms. These findings improve our understanding of within-host dynamics of S. Typhi in cases of persistent infection and inform epidemiological investigations of transmission events associated with chronic carriers.

Thai Local Chicken Breeds, Chee Fah and Fah Luang, Originated from Chinese Black-Boned Chicken with Introgression of Red Junglefowl and Domestic Chicken Breeds

Knowledge of the genetic characteristics, origin, and local adaptation of chickens is essential to identify the traits required for chicken breeding programs. Chee Fah and Fah Luang are black-boned chicken breeds reared in Chiang Rai, Thailand. Chickens are an important part of the local economy and socio-culture; however, the genetic diversity, characteristics, and origins of these two breeds have been poorly studied. Here, we investigated the genetic diversity, gene pool, and origin of the Chee Fah and Fah Luang chickens using mitochondrial DNA D-loop (mtDNA D-loop) sequencing and microsatellite genotyping, as well as habitat suitability analysis using maximum entropy modeling. The MtDNA D-loop sequencing and microsatellite genotype analyses indicated that the Chee Fah and Fah Luang chickens shared haplogroups A, B, and CD with Chinese black-boned chickens. Gene pool analysis revealed that the Chee Fah and Fah Luang chickens have distinct genetic patterns compared to Thai domestic chickens and red junglefowl. Some gene pools of red junglefowl and other Thai domestic chickens were observed within the Chee Fah and Fah Luang chicken gene pool structures, suggesting genetic exchange. The data indicate that the Chee Fah and Fah Luang chickens originated from Chinese indigenous black-boned chicken breeds and experienced crossbreeding/hybridization and introgression with red junglefowl and other domestic breeds during domestication. Interestingly, the Chee Fah and Fah Luang chickens from Chiang Rai shared the same allelic gene pool, which was not shared with the Chee Fah and Fah Luang chickens from Mae Hong Son, suggesting at least two gene pool origins in the Chee Fah and Fah Luang chicken populations. Alternatively, different gene pools in the Chee Fah and Fah Luang chickens from different localities might be caused by differences in environmental factors, especially elevation.

The role of niche breadth in oak phylogeography: Quercus glaucoides as a study case

AbstractAimThe extent of genetic diversity and its distribution among populations have been associated with species attributes such as mating system, dispersal ability and geographic range size. Another attribute that could contribute to intraspecific phylogeographic patterns is niche breadth, but this has rarely been tested. Here, we ask whether a Mexican oak with a comparatively narrow climatic niche breadth has distinct genetic diversity patterns compared to other codistributed oaks with a broader climatic niche.LocationMexico.TaxonQuercus glaucoides M. Martens &amp; Galeotti (Fagaceae).MethodsDescriptors of genetic diversity and structure were calculated for 21 Q. glaucoides populations using chloroplast DNA (cpDNA) and nuclear microsatellites (nSSRs). Historical demographic dynamics were inferred with approximate Bayesian computation (ABC) and past potential distribution models. To test for an association between niche breadth and phylogeographic patterns, we used genetic diversity and differentiation values of Q. glaucoides plus those previously published for 10 other Mexican oak taxa. Niche breadth was estimated for all taxa and linear regressions were performed.ResultsGenetic diversity calculated from nSSRs (HO = 0.539; HE = 0.714) was among the lowest and cpDNA differentiation (NST = 0.88) was the highest so far obtained for comparable Mexican oaks. Moderate changes in demographic size and distribution shifts throughout the last glacial cycle were inferred, explaining some of the observed genetic patterns. A positive correlation of HO and a negative correlation of NST with niche breadth were detected across taxa.Main ConclusionsDistinct phylogeographic patterns in Q. glaucoides could be explained because a narrower niche may cause lower historical effective population sizes and more fragmented distributions in comparison to species with a wider niche breadth, even with similar range sizes. Our results indicate that niche breadth would be an interesting ecological attribute to be included in future comparative phylogeographic studies.

Additive and non-additive epigenetic signatures of natural hybridization between fish species with different mating systems

ABSTRACT Hybridization is a major source of evolutionary innovation. In plants, epigenetic mechanisms can help to stabilize hybrid genomes and contribute to reproductive isolation, but the relationship between genetic and epigenetic changes in animal hybrids is unclear. We analysed the relationship between genetic background and methylation patterns in natural hybrids of two genetically divergent fish species with different mating systems, Kryptolebias hermaphroditus (self-fertilizing) and K. ocellatus (outcrossing). Co-existing parental species displayed highly distinct genetic (SNPs) and methylation patterns (37,000 differentially methylated cytosines). Hybrids had predominantly intermediate methylation patterns (88.5% of the sites) suggesting additive effects, as expected from hybridization between genetically distant species. The large number of differentially methylated cytosines between hybrids and parental species (n = 5,800) suggests that hybridization may play a role in increasing genetic and epigenetic variation. Although most of the observed epigenetic variation was additive and had a strong genetic component, we also found a small percentage of non-additive, potentially stochastic, methylation differences that might act as an evolutionary bet-hedging strategy and increase fitness under environmental instability.