Genetic Distance Research Articles

Molecular systematics of the subgenus Gephyromantis (Phylacomantis) with description of a new subspecies

The mantellid subgenus Phylacomantis (genus Gephyromantis) currently contains four species of frogs distributed in the South (G. corvus, G. kintana), West (G. atsingy), North East, North, and Sambirano regions (G. pseudoasper) in Madagascar. We assess the molecular systematics of these amphibians based on extended sampling and analysis of multiple nuclear-encoded and mitochondrial genes. We confirm the delimitation of the four known species, which form monophyletic groups in a mitochondrial tree and separate phylogroups without haplotype sharing in haplotype networks of four nuclear markers. Newly included samples of G. pseudoasper from the North and North East regions confirm a comparatively low genetic variation of this species across its range, with pairwise genetic distance in the 16S gene not exceeding 1.4%. On the contrary, newly collected specimens from three sites in the North East and North West of the island strongly differed from all other Phylacomantis, with genetic distances exceeding 4.8% for the16S gene. Mitochondrial and nuclear markers strongly suggest them to be sister to G. corvus from the South. Due to haplotype sharing in two nuclear genes, absence of detectable morphological differences, and lack of data on bioacoustic differentiation, we describe these populations as a new subspecies, G. corvus bakilana ssp. nov., emphasizing that this taxon may be elevated to species status in the future pending new data. This biogeographic pattern, with apparently disjunct sister lineages in the South vs. North West of Madagascar, is rare among Malagasy anurans and calls for increased exploration of the remaining humid forest fragments in the North West and West of the island.

Mengelola Perbedaan, Membangun Kembali Nilai Persaudaraan: Kajian Studi Perdamaian terhadap Memori Kolektif dalam Film Cahaya dari Timur Beta Maluku

This concept of diversity is one of the parts that can be found in social life. This concept is also often found in various regions of Indonesia and one of them is in Maluku. With the existence of various diversity in Maluku, it is not used as a difference but it becomes a very strong kinship system. The system that was built was based on genealogical relationships as well as based on traditional and cultural values which later became a philosophy for the Moluccans. The life of the basudara people became very close. But when conflicts occur, the relationship begins to erode and form various differences based on religious identity. Thus the purpose of this paper will discuss the collective memory built on the customs and cultural values of the basudara people using the analysis of the film "light from the east beta Maluku". The research method used is descriptive qualitative with a research question, namely how the influence of collective memory can be built into a reconciliation in the light film from the east beta Maluku. In this paper, the author will also explain that the existence of a collective memory built on traditional and cultural values in Maluku will make a great contribution in building a reconciliation as brothers and establishing a wall of difference

Epidemiological and molecular study of Providencia rettgeri outbreak at a university hospital during the COVID-19 reference center.

In 2014, Brazil detected New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales from a Providencia rettgeri isolate obtained through surveillance swabs in the Southern region. Subsequently, various species have reported several NDM enzymes. However, comprehensive data on the current epidemiology of NDM-producing P. rettgeri in Brazil remains limited. This study, aimed to provide a detailed characterization of the phenotypic, genotypic, and epidemiological profile of clinical isolates of P. rettgeri NDM. From April 2020 to December 2022, 18 carbapenem-resistant P. rettgeri strains, previously identified using Vitek2®, were isolated at the University Hospital of Londrina. Resistance and virulence genes were assessed through genetic analysis using ERIC PCR and NextSeq (Illumina) sequencing. Statistical analysis was conducted using SPSS version 2.0. Genomic analysis confirmed the presence of β-lactamase blaNDM-1 and blaOXA-1. All isolates showed the presence of the NDM encoding gene and genetic similarity above 90% between isolates. Clinical parameters of patients infected with P. rettgeri exhibited significant association with mechanical ventilation, prior use of carbapenems, and polymyxins. We also report a significant association between P. rettgeri infection and death outcome. This study characterizes NDM-1 metallo-β-lactmases isolates, among P. rettgeri isolates from patients at the University Hospital (HU), during the COVID-19 pandemic. The emergence of this novel resistance mechanism among P. rettgeri poses a significant challenge, limiting the therapeutic options for infections in our hospital.

Ability of Genomic Prediction to Bi-Parent-Derived Breeding Population Using Public Data for Soybean Oil and Protein Content.

Genomic selection (GS) is a marker-based selection method used to improve the genetic gain of quantitative traits in plant breeding. A large number of breeding datasets are available in the soybean database, and the application of these public datasets in GS will improve breeding efficiency and reduce time and cost. However, the most important problem to be solved is how to improve the ability of across-population prediction. The objectives of this study were to perform genomic prediction (GP) and estimate the prediction ability (PA) for seed oil and protein contents in soybean using available public datasets to predict breeding populations in current, ongoing breeding programs. In this study, six public datasets of USDA GRIN soybean germplasm accessions with available phenotypic data of seed oil and protein contents from different experimental populations and their genotypic data of single-nucleotide polymorphisms (SNPs) were used to perform GP and to predict a bi-parent-derived breeding population in our experiment. The average PA was 0.55 and 0.50 for seed oil and protein contents within the bi-parents population according to the within-population prediction; and 0.45 for oil and 0.39 for protein content when the six USDA populations were combined and employed as training sets to predict the bi-parent-derived population. The results showed that four USDA-cultivated populations can be used as a training set individually or combined to predict oil and protein contents in GS when using 800 or more USDA germplasm accessions as a training set. The smaller the genetic distance between training population and testing population, the higher the PA. The PA increased as the population size increased. In across-population prediction, no significant difference was observed in PA for oil and protein content among different models. The PA increased as the SNP number increased until a marker set consisted of 10,000 SNPs. This study provides reasonable suggestions and methods for breeders to utilize public datasets for GS. It will aid breeders in developing GS-assisted breeding strategies to develop elite soybean cultivars with high oil and protein contents.

Angiopterisnodosipetiolata (Marattiaceae), a new fern species from Yunnan, China.

Angiopterisnodosipetiolata Ting Wang tris, H.F.Chen & Y.H.Yan, a new fern of Marattiaceae, is described and illustrated. Morphologically, A.nodosipetiolata is similar to A.chingii with more than one naked pulvinus on the stipe and numerous jointed hairs on the undersides of the mature pinnae. However, the pinnae of A.nodosipetiolata are lanceolate and can reach up to 4-6 pairs, whereas they are elliptic and occur in 2-3 pairs in A.chingii. Phylogenetic and genetic distance analysis, based on the plastid genomes, also indicates that A.nodosipetiolata is not closely related to A.chingii. Currently, there are ca. 500 mature individuals in Gulinqing Nature Reserve and we suggest A.nodosipetiolata should be categorised as an Endangered (EN) species according to the criteria of IUCN.

Insights into chloroplast genome evolution in Rutaceae through population genomics

Chloroplast genomes, pivotal for understanding plant evolution, remain unexplored in Rutaceae, a family with key perennial crops like citrus. Leveraging next-generation sequencing data from 509 Rutaceae accessions across 15 species, we conducted a de novo assembly of 343 chloroplast genomes, unveiling a chloroplast variation map highlighting the heterogeneous evolution rates across genome regions. Notably, differences in chloroplast genome size primarily originate from large single-copy and small single-copy regions. Structural variants predominantly occurred in the single-copy region, with two insertions located at the single-copy and inverted repeat region boundary. Phylogenetic analysis, principal component analysis, and population genetic statistics confirmed the cohesive clustering of different Citrus species, reflecting evolutionary dynamics in Citrus diversification. Furthermore, a close chloroplast genetic affinity was revealed among Atalantia (previously regarded as primitive citrus), Clausena, and Murraya. Zanthoxylum formed a distinct group with heightened genetic diversity. Through expanding our analysis to include 34 published chloroplast genomes, we explored chloroplast gene selection, revealing divergent evolutionary trends in photosynthetic pathways. While Photosystem I and Photosystem II exhibited robust negative selection, indicating stability, the Nicotinamide adenine dinucleotide (NADH) dehydrogenase pathway demonstrated rapid evolution, which was indicative of environmental adaptation. Finally, we discussed the effects of gene length and GC content on chloroplast gene evolution. In conclusion, our study reveals the genetic characterization of chloroplast genomes during Rutaceae diversification, providing insights into the evolutionary history of this family.

A new species of marine algae from the Mexican Atlantic based on morphology and molecular data: Gelidium rodrigueziae sp. nov. (Gelidiaceae, Rhodophyta)

Abstract The algae of the genus Gelidium can be found as frequent and abundant inhabitants in the rocky intertidal zone of the Mexican Atlantic. Six species of this genus have been reported in this region, but only Gelidium americanum has been confirmed with morphological and molecular tools, despite how important both tools have proven to be for the group. This research aimed to evaluate the Mexican specimens previously identified as Gelidium through morphological and molecular approaches, using rbcL and COI-5P markers. This study examined 20 specimens found living attached to the shell of a gastropod Stramonita rustica in the mid-high intertidal zone of the Mexican Atlantic and ten specimens found living on rocks. Phylogenetic analyses resolved these specimens to be an independent species closely related to G. gonzalezii, G. yangmeikengense, and G. indonesianum. Genetic distances and morphological information confirmed this. Gelidium rodrigueziae sp. nov. is described as a new species. It is distinguished from its related species by having a simpler branching pattern, a smaller number and size of medullary cells, and the smaller quantity and distribution of restricted internal rhizoid filaments around the medulla.

Morphological and molecular description of a new species of sandfly, Sergentomyia (Neophlebotomus) ashwanii sp. nov. (Diptera: Psychodidae) from Western Ghats, India

Objective: To report a new species of sandfly, Sergentomyia (Neophlebotomus) ashwanii sp. nov. (Diptera: Psychodidae) from Western Ghats, India. Methods: A systematic sandfly survey was conducted in the Thrissur and Kollam districts of Kerala, India using mechanical aspirators, light and sticky traps, both indoor and outdoor habitats, for a period of one year. Deoxyribonucleic acid barcoding of samples was performed targeting mitochondrial cytochrome oxidase I (COI) gene and sequence generated was subjected to phylogenetic analysis. Results: Sergentomyia (Neophlebotomus) ashwanii, a new sandfly species is recorded and described in this communication. A single row of 10-12 pointed teeth in the cibarium with 4-6 small denticles or fore-teeth are the key characteristics that is distinctive from other members of the subgenus Neophlebotomus. Mitochondrial COI barcode followed by phylogenetic analysis of the nucleotide sequence confirms that specimens of the species belong to the same taxonomic group while the genetic distance (14.2%) with the congeners established it to be a different species. Conclusions: The Western Ghats' being an important biodiversity hotspot and has dearth of systematic entomological surveys on sandflies. The current study tried to fill the void and also report a new sandfly species.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Synthesizing environmental, epidemiological and vector and parasite genetic data to assist decision making for disease elimination.

We present a framework for identifying when conditions are favourable for transmission of vector-borne diseases between communities by incorporating predicted disease prevalence mapping with landscape analysis of sociological, environmental and host/parasite genetic data. We explored the relationship between environmental features and gene flow of a filarial parasite of humans, Onchocerca volvulus, and its vector, blackflies in the genus Simulium. We generated a baseline microfilarial prevalence map from point estimates from 47 locations in the ecological transition separating the savannah and forest in Ghana, where transmission of O. volvulus persists despite onchocerciasis control efforts. We generated movement suitability maps based on environmental correlates with mitochondrial population structure of 164 parasites from 15 communities and 93 vectors from only four sampling sites, and compared these to the baseline prevalence map. Parasite genetic distance between sampling locations was significantly associated with elevation (r = .793, p = .005) and soil moisture (r = .507, p = .002), while vector genetic distance was associated with soil moisture (r = .788, p = .0417) and precipitation (r = .835, p = .0417). The correlation between baseline prevalence and parasite resistance surface maps was stronger than that between prevalence and vector resistance surface maps. The centre of the study area had high prevalence and suitability for parasite and vector gene flow, potentially contributing to persistent transmission and suggesting the importance of re-evaluating transmission zone boundaries. With suitably dense sampling, this framework can help delineate transmission zones for onchocerciasis and would be translatable to other vector-borne diseases.

Validation of deep amplicon sequencing of Dicrocoelium in small ruminants from Northern regions of Pakistan.

Dicrocoelium lancet flukes cause significant production loss in ruminant livestock. Although co-infection with multiple Dicrocoelium species within a host is common, techniques for studying the composition of these complex parasite communities are lacking. The pathogenicity, epidemiology, and therapeutic susceptibility of different helminth species vary, and little is known about the interactions that take place between co-infecting species and their hosts. Here, we describe the first applicationof metabarcoding deep amplicon sequencing method to studythe Dicrocoelium species in sheep and goats. First, rDNA ITS-2 sequences of four Dicrocoelium species (Dicrocoelium dendriticum, Dicrocoelium hospes, Dicrocoelium orientalis, and Dicrocoelium chinensis) were extracted from the NCBI public database. Phylogenetic analysis revealed separate clades of Dicrocoelium species; hence, molecular differentiation between each species is possible in co-infections. Second, 202 flukes belonging to seventeen host populations (morphologically verified as belonging to the Dicrocoelium genus) were evaluated to determine the deep amplicon sequencing read threshold of an individual fluke for each of the four species. The accuracy of the method in proportional quantification of samples collected from single hosts was further assessed. Overall, 198 (98.01%) flukes were confirmed as D. dendriticum and 1.98% produced no reads. The comparison of genetic distances between rDNA ITS-2 revealed 86% to 98% identity between the Dicrocoelium species. Phylogenetic analysis demonstrated a distinct clustering of species, apart from D. orientalis and D. chinensis, which sit very close to each other in a single large clade whereas D. hospes and D. dendriticum are separated into their own clade. In conclusion each sample was identified as D. dendriticum based on the proportion of MiSeq reads and validated the presence of this group of parasites in the Gilgit Baltistan and Khyber Pakhtunkhwa provinces of Pakistan. The metabarcoding deep amplicon sequencing technology and bioinformatics pathway have several potential applications, including species interactions during co-infections, identifying the host and geographical distribution of Dicrocoelium in livestock, drug therapy response evaluation and understanding of the emergence and spread of drug resistance.

Ethnobotanical studies on rice landraces under on-farm conservation in Xishuangbanna of Yunnan Province, China

BackgroundA complex interaction and mutual influence exists among landscapes, cultures, and landraces, with rice culture being a typical embodiment of this relationship. The conservation of landraces operates alongside preserving traditional practices. The Xishuangbanna region stands out as a hub for the genetic diversity of landraces, boasting rich genetic resources. Despite the diverse rice resources in this region, a comprehensive and systematic study has not been undertaken.MethodsFrom October to November 2023, we collected rice landraces under the on-farm conservation in 18 townships including Menghai, Mengla and Jinghong in Xishuangbanna. Employing semi-structured interviews and various methods, we investigated factors influencing the preservation and loss of rice landraces in the region. Statistical analysis was applied to the agronomic traits of collected local rice, encompassing indica or japonica, glutinous or non-glutinous, grain shape, and hull color as second category traits. The second category included quantitative traits like thousand grain weight and grain length. Rice diversity among different regions, traits, and ethnic groups was assessed using the Shannon–Wiener index. Additionally, clustering analysis via the UPGMA method depicted the distribution characteristics of the resources.ResultsA total of 70 rice landraces were collected in the Xishuangbanna region, each exhibiting distinct characteristics. Differences were observed across regions, trait, naming, and ethnic groups. Diversity analysis revealed that Mengla had the highest diversity, followed by Menghai, while Jinghong exhibited the lowest diversity. The second category of traits displayed broader diversity than the first, with the Dai people’s glutinous rice showcasing greater diversity than other ethnic groups. Cluster analysis categorized the 70 samples into seven groups at a genetic distance of 1.15. Ethnobotanical interviews emphasized the rapid loss of rice landraces resources in Xishuangbanna, with indigenous ethnic cultures playing a vital role in the conservation of rice landraces. Dai traditions, in particular, played a crucial role in protecting glutinous rice resources, showcasing a mutual dependence between Dai culture and glutinous rice.ConclusionsThe rich natural environment and diverse ethnic cultures in Xishuangbanna have given rise to various rice landraces. The Dai, primary cultivators of glutinous rice with higher diversity, intertwine their traditional ethnic culture with the conservation of glutinous rice resources. At the same time, the preserving glutinous rice resources promotes the inheritance of Dai ethnic culture. However, rice landraces are facing the risk of loss. Hence, collecting and documenting rice landraces is crucial. Encourage local communities to sustain and expand their cultivation, promoting on-farm conservation. These measures contribute valuable germplasm and genes for rice breeding and serve as a means of cultural preservation.

Genome-based surveillance reveals cross-transmission of MRSA ST59 between humans and retail livestock products in Hanzhong, China.

Methicillin-resistant Staphylococcus aureus (MRSA) has been recognized in hospitals, community and livestock animals and the epidemiology of MRSA is undergoing a major evolution among humans and animals in the last decade. This study investigated the prevalence of MRSA isolates from ground pork, retail whole chicken, and patient samples in Hanzhong, China. The further characterization was performed by antimicrobial susceptibility testing and in-depth genome-based analysis to identify the resistant determinants and their phylogenetic relationship. A total of 93 MRSA isolates were recovered from patients (n = 67) and retail livestock products (n = 26) in Hanzhong, China. 83.9% (78/93) MRSA isolates showed multiple drug resistant phenotype. Three dominant livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) sequence types were identified: ST59-t437 (n = 47), ST9-t899 (n = 10) and ST398 (n = 7). There was a wide variation among sequence types in the distribution of tetracycline-resistance, scn-negative livestock markers and virulence genes. A previous major human MRSA ST59 became the predominant interspecies MRSA sequence type among humans and retail livestock products. A few LA-MRSA isolates from patients and livestock products showed close genetic similarity. The spreading of MRSA ST59 among livestock products deserving special attention and active surveillance should be enacted for the further epidemic spread of MRSA ST59 in China. Data generated from this study will contribute to formulation of new strategies for combating spread of MRSA.

Whole genome sequence of Lactiplantibacillus plantarum strain HA9 isolated from conventional Iraqi cheese: First report

Background: Lactiplantibacillus plantarum is a renowned probiotic known for its ability to enhance health when ingested in sufficient quantities. While L. plantarum typically exhibits unique characteristics, variations in strains and environments can occur. Therefore, it is crucial to conduct genetic identification of the strain before incorporating it into products or administering it for health benefits.Methods: After being isolated from classic artisanal milk cheeses, the bacterial DNA extraction kit from GENEAID, Korea, was used, and strain HA9's genomic DNA was isolated. Then, the highly conserved section of ribosomal RNA was amplified with universal primers. The results were confirmed by a blast analysis of the NCBI database. The genome of HA9 was sequenced using the Illumina and PacBio Sequel II technologies (HN00194138; Psomagen/USA). The Prokaryotic Dynamic Programming Gene-Finding Algorithm software was applied to forecast coding genes. The Pathosystems Resource Integration Center constructed the L. plantarum genome.Result: According to the findings, the genome of the L. plantarum HA9 strain has a length of 3,321,986 bp and a GC percentage of 44.40. This assembled genome contained a total of 1,420 coding proteins and 82 contigs, as discovered by the Comprehensive Genome Analysis. The isolate had been submitted to the NCBI and received the HA9 genome sequence (accession ID: JAUTDL000000000.1).Conclusion Microbes' whole-genome sequencing plays a crucial role in clarifying their probiotic properties and enables accurate identification down to the strain level. The authors argue that further research should be done on probiotics' whole genomes, with a special emphasis on second-generation strains.Keywords: Lactiplantibacillus plantarum; Probiotics; Whole genome sequencing

Phenotypic Characteristics, Pathogenicity, and Molecular Identification of Hypomyces perniciosus Causing Wet Bubble Disease of Edible Mushrooms

Abstract The research aimed to determine the phenotypic characteristic, pathogenicity and molecular characterization of Hypomyces perniciosus isolates responsible for wet bubble disease of the white button mushroom Agaricus bisporus. Phenotypic characteristics such as colony appearance, mycelium texture, and pigmentation were studied on four different agar media, i.e., potato dextrose agar (PDA), malt extract agar (MEA), Czapek-Dox yeast agar (CYA), and Sabouraud dextrose agar (SDA), after eight days of incubation. Additionally, the growth rate of the tested isolates was studied depending on the pH of the medium. Fungal isolates showed the highest mycelial growth on MEA and SDA at pH 6.0. However, on CYA at pH 7.0, the mycelium exhibited the worst growth. Isolate identification and genetic relationship analysis were carried out using internal transcribed spacer region sequencing and the random amplified polymorphic DNA method. The research confirmed that all Polish isolates belong to the species H. perniciosus, and the genetic diversity is relatively low. Phylogenetic analyses revealed three subgroups of H. perniciosus isolates. The first group included three genetically distinct isolates with a similarity coefficient in the range of 0.76–0.85 to isolates CBS 815.73 and CBS 322.52. The second group was divided into two subgroups and included 16 isolates with a genetic similarity range of 0.91 to 1.0 to CBS 815.73 and CBS 322.52 isolates. Furthermore, the eight genetically similar isolates exhibited the greatest pathogenicity towards A. bisporus.

Forensic Examination of Fingerprint Patterns among Different Generations in South Indian Families

Fingerprint patterns are unique and reliable for identification. This research paper focuses on a comparative analysis to determine the inheritance of fingerprint patterns within Indian families. The sample collection process for this comparative analysis involved working with 10 families. The study aims to gain insights into the hereditary aspects of fingerprint characteristics among the Indian population. The research methodology involves the collection of fingerprints and the analysis of patterns using microscopes, magnifying lenses, and software. The results reveal both class and individual characteristics within fingerprints, contributing to our understanding of dermatoglyphics. The average class characteristics percentage totals around 71.5%, with an average individual characteristic percentage of approximately 13.6%. The research has implications for forensic investigations, genetics, and personal identification systems. Further studies with larger sample sizes and genetic analysis integration are recommended for future research.

Genetic diversity analysis and molecular characterization of tropical rose (Rosa spp.) varieties

Characterization of rose varieties becomes essential for understanding, utilizing, and preserving the diversity among them, for their genetic improvement, cultivation, and conservation. With this purpose, 19 tropical rose varieties were evaluated via quantitative morphological and molecular markers. A significant degree of variation was observed across nearly all descriptors, suggesting a notable level of genetic diversity among the released rose varieties. Traits like flower diameter, flower yield/plot, and shelf life, considered to be of vital importance given the aesthetic value of rose, exhibited remarkable differences that would further aid in the selection of desirable varieties. The maximum flower diameter, flower yield/plot, and shelf life were recorded in Yellow Page, Lambada, and Delhi Princess, respectively. The varieties were evaluated by correlation matrix, hierarchical agglomerative clustering method-based dendrogram, network plot on phenotypic correlation, colour intensity graph including Red-Green-Blue (RGB) scattered plot. In the correlation matrix, it was found that more number of primary shoot contributes to higher flower yield, while increase in leaf area degraded the shelf life of the flower. Realizing the importance of molecular characterization, 10 selected polymorphic inter simple sequence repeats (ISSR) and start codon targeted (SCoT) polymorphism primers were tested that amplified total 187 polymorphic loci with 94.4 % polymorphism. Cent percent polymorphism were found with SCoT-2, SCoT-18, SCoT-19, HB-12 and ISSCR3 primers. A principal component analysis based on molecular diversity highlighted that First Red, Local Selection 2, and Himroz exhibited distinct characteristics compared to the other varieties. The 19 varieties were grouped into 8 clusters viaunweighted pair group method with arithmetic mean-based dendrogram at 0.4 similarity co-efficient. The analysis revealed a significant genetic distance between Himroz, First Red, and Grand Gala, suggesting their potential to be utilized in hybridization programs for crop improvement. The distinguishable genetic background and high degree of variation revealed by molecular markers, specifically ISSR and SCoT, offer valuable insights that can contribute to the strategic improvement of roses. These findings provide a foundation for expediting rose breeding programs and comprehensive crop improvement strategies.

Phenotypic variation seems not to be associated with the genetic profile in Zygopetalum (Orchidaceae): a case study of a high-elevation rocky complex.

Hybridization associated with polyploidy studies is rare in the tropics. The genus Zygopetalum (Orchidaceae) was investigated here as a case study of Neotropical plants. In the rocky highlands of the Ibitipoca State Park (ISP), southeast Brazil, individuals with intermediate colors and forms between the species Z. maculatum and Z. triste were commonly identified. Chromosomal analysis and DNA quantity showed a uniform population. Regardless of the aspects related to the color and shape of floral structures, all individuals showed 2n = 96 chromosomes and an average of 14.05pg of DNA. Irregularities in meiosis associated with chromosome number and C value suggest the occurrence of polyploidy. The genetic distance estimated using ISSR molecular markers revealed the existence of genetic variability not related to morphological clusters. Morphometric measurements of the flower pieces revealed that Z. maculatum shows higher variation than Z. triste although lacking a defined circumscription. The observed variation can be explained by the polyploid and phenotypic plasticity resulting from the interaction of the genotypes with the heterogeneous environments observed in this habitat.

An esculentin-1 homolog from a dark-spotted frog (Pelophylax nigromaculatus) possesses antibacterial and immunoregulatory properties

BackgroundEsculentin-1, initially discovered in the skin secretions of pool frogs (Pelophylax lessonae), has demonstrated broad-spectrum antimicrobial activity; however, its immunomodulatory properties have received little attention.ResultsIn the present study, esculentin-1 cDNA was identified by analysing the skin transcriptome of the dark-spotted frog (Pelophylax nigromaculatus). Esculentin-1 from this species (esculentin-1PN) encompasses a signal peptide, an acidic spacer peptide, and a mature peptide. Sequence alignments with other amphibian esculentins-1 demonstrated conservation of the peptide, and phylogenetic tree analysis revealed its closest genetic affinity to esculentin-1P, derived from the Fukien gold-striped pond frog (Pelophylax fukienensis). Esculentin-1PN transcripts were observed in various tissues, with the skin exhibiting the highest mRNA levels. Synthetic esculentin-1PN demonstrated antibacterial activity against various pathogens, and esculentin-1PN exhibited bactericidal activity by disrupting cell membrane integrity and hydrolyzing genomic DNA. Esculentin-1PN did not stimulate chemotaxis in RAW264.7, a murine leukemic monocyte/macrophage cell line. However, it amplified the respiratory burst and augmented the pro-inflammatory cytokine gene (TNF-α and IL-1β) expression in RAW264.7 cells.ConclusionsThis novel finding highlights the immunomodulatory activity of esculentin-1PN on immune cells.

Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.

Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.