Significant Genetic Diversity Research Articles

Ultramicrobacteria and filterable bacteria in the plankton of Lake Baikal

In Lake Baikal, the number, diversity, and structure of femtoplankton – bacteria passing through filters with a 0.2 μm pore size – were studied for the first time using a complex of methods. The bacterial abundance in the femtoplankton fraction was 7×104 cells/mL in the 0-50 m water layer, as measured by epifluorescence microscopy, and their contribution to the total bacterial number reached an average of 4.4%. High-throughput sequencing of 16S rRNA gene fragments revealed a significant genetic and taxonomic diversity of femtobacterioplankton in the pelagic and littoral zones of the lake. Dominant and minor phyla, orders, families, genera, and phylotypes of bacteria were identified in two fractions of Lake Baikal bacterioplankton: larger and smaller than 0.2 µm. We determined the contribution of ultra-small bacteria to the taxonomic composition of microbial communities in different parts of the lake. The microbiomes of bacterioplankton and femtobacterioplankton fractions differed significantly, and we described the peculiarities of ultramicrobacteria composition. The results demonstrated an important role of ultra-small bacteria in Lake Baikal’s ecosystem.

Species and genetic diversity of nontuberculous mycobacteria in suspected tuberculosis cases in East Azerbaijan, Iran: a cross-sectional analysis.

The incidence of nontuberculous mycobacterial (NTM) infections has increased worldwide, attracting attention in routine diagnostic settings, particularly among patients with suspected tuberculosis. This study aimed to acquire knowledge of NTM infections in patients with suspected tuberculosis and to evaluate the genetic diversity of the strains. In this study, 230 clinical specimens were collected from suspected tuberculosis patients. Following decontamination with N-Acetyl-L-cysteine-sodium hydroxide (NALC-NaOH), the sediments of specimens were inoculated onto Löwenstein-Jensen medium and then incubated at 37°C for 8 weeks. The samples that yielded positive cultures were evaluated through the sequencing of conserved fragments of IS6110 and hsp65. For those samples that were not identified as part of the M. tuberculosis complex (MTC) by IS6110 PCR, further analysis was conducted via PCR to detect fragments of the hsp65 gene. Twenty-one NTM species were isolated from 230 clinical specimens (14 NTM from pulmonary specimens and 7 from extrapulmonary specimens). Among these, 12 (57.14%) were rapid-growing mycobacteria (RGM), and 9 (42.85%) were slow-growing mycobacteria (SGM). No M. avium complex (MAC) was identified in any of the specimens. Notably, the M. kansasii, M. gordonae, and M. abscessus strains presented significant genetic diversity. The prevalence of infections attributed to nontuberculous species surpasses that attributed to tuberculosis. These findings underscore the importance of exploring NTM species in individuals suspected of having TB.

Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae.

Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.

CRISPR Technology in Infectious Disease Management: Principles, Applications, and Future Challenges with Emphasis on SARS-CoV-2, HIV, and HBV

Retroviruses and double-stranded DNA (dsDNA) viruses enter cells by integrating their genetic materials into host DNA. During this period, the virus stays dormant and can escape host immune surveillance, which is difficult to detect and kill clinically. Thus, viral diseases, especially those caused by RNA viruses, pose a huge threat to public health. Currently, more research shows that clearing the genome of the virus has become a direct and effective way to treat viral diseases. However, viral diseases such as SARS-CoV-2 exhibit significant genetic diversity, with over 300000 mutants discovered, covering the entire genome of the virus, which greatly limits the traditional gene editing techniques for diagnosing and clearing the virus sequence. CRISPR-Cas can target multiple regions, exhibiting stronger catalytic activity compared to other gene editing methods. At present, it has been widely used in the diagnosis and treatment of viral diseases. Therefore, understanding the principles of CRISPR-Cas technologies and identifying their potential applications in viral diseases is of great significance. This paper reviews the principles of this technology and its current applications in three aspects, COVID-19, HIV, and HBV. Additionally, this paper summarizes the difficulty in applying CRISPR-Cas technology and future expectations.

Molecular Characteristics and the Effect of Mutations in Different Sites of the rplD Gene Among Clinical Isolates of Azithromycin Resistance Neisseria gonorrhoeae in Eastern China

Background: The emergence of resistance to azithromycin complicates the treatment of Neisseria gonorrhoeae, the causative agent of gonorrhea. Objectives: The main objective of this study was to investigate the impact of mutations in different sites of the rplD gene on azithromycin resistance (AZM-R) and the molecular characteristics of N. gonorrhoeae. This study aimed to provide evidence for drug resistance and transmission. Methods: A total of 37 isolates of N. gonorrhoeae were collected within January 2018 to December 2020. These isolates were obtained from urine, semen, or vaginal secretions of different patients. Azithromycin resistance was assessed, and genes associated with AZM-R, namely rplD, and rplV, were analyzed using polymerase chain reaction (PCR) and deoxyribonucleic acid (DNA) sequencing. All clinical isolates were characterized through multi-locus sequence typing (MLST). Results: The study comprised 21 azithromycin-resistant N. gonorrhoeae isolates, with two of them demonstrating high resistance, indicated by a minimum inhibitory concentration (MIC) greater than 256 µg/mL. Additionally, 16 sensitive isolates were included in the study. Ten isolates were observed to have rplD point mutations, including mutations such as G70D, G70S, G68D, and A43T. No mutations were detected in rplV. The rate of point mutations in rplD was significantly different between the azithromycin-sensitive (AZM-S) group and the AZM-R group (P < 0.05). Among the 37 isolates studied, 12 distinct MLST types were identified and further grouped into four different MLST goeBURST groups. The two isolates with high-level AZM-R were ST1901 and ST1588, respectively. Conclusions: The clinical isolates of N. gonorrhoeae from Wenzhou, Eastern China, exhibit significant genetic diversity and a relatively high prevalence of AZM-R. Mutations in the rplD gene were identified, which reduced susceptibility to macrolides and were significantly associated with increased AZM-R.

Molecular evidence for multiple origins and high genetic differentiation of non-native winter crane fly, Trichocera maculipennis (Diptera: Trichoceridae), in the maritime Antarctic

Native biodiversity and ecosystems of Antarctica safeguarded from biological invasion face recent threats from non-native species, accelerated by increasing human activities and climate changes. Over two decades ago, the winter crane fly, Trichocera maculipennis, was first detected on King George Island. It has now successfully colonized several research stations across King George Island. To understand the origin, genetic diversity, and population structure of this Holarctic species, we conducted mitochondrial DNA cytochrome c oxidase subunit I (COI) sequence analysis across both its native and invasive ranges. In parallel, we performed microsatellite loci analysis within the invasive ranges, utilizing 12 polymorphic microsatellite markers. Furthermore, we compared body sizes among adult males and females collected from three different locations of King George Island. Our COI sequence analysis exhibited two different lineages present on King George Island. Lineage I was linked to Arctic Svalbard and Polish cave populations and Lineage II was related to Canadian Terra Nova National Park populations, implying multiple origins. Microsatellite analysis further exhibited high levels of genetic diversity and significant levels of genetic differentiation among invasive populations. Body sizes of adult T. maculipennis were significantly different among invasive populations but were not attributed to genetics. This significant genetic diversity likely facilitated the rapid colonization and establishment of T. maculipennis on King George Island, contributing to their successful invasion. Molecular analysis results revealed a substantial amount of genetic variation within invasive populations, which can serve as management units for invasive species control. Furthermore, the genetic markers we developed in the study will be invaluable tools for tracking impending invasion events and the travel routes of new individuals. Taken together, these findings illustrate the highly invasive and adaptable characteristics of T. maculipennis. Therefore, immediate action is necessary to mitigate their ongoing invasion and facilitate their eradication.

Molecular typing of a collection of Iranian clinical Trichophyton tonsurans isolates based on the non-transcribed spacer region of rDNA and antifungal susceptibility testing of the species.

Wrestling, considered the national sport of Iran, has gained immense popularity among Iranians. Wrestlers frequently encounter skin conditions, with dermatophyte fungal infections, particularly tinea gladiatorum (TG), being a common issue. TG, caused by the Trichophyton genus, has emerged as a major health concern for wrestlers and other contact sport athletes worldwide. This study aimed to assess the genotypic diversity and antifungal susceptibility of Trichophyton tonsurans isolates responsible for TG in Iranian wrestlers from Mazandaran province, northern Iran. A total of 60 clinical T. tonsurans isolates collected from various cities in Mazandaran, were included in the study. The isolates were identified through PCR-restriction fragment length polymorphism and sequencing methods. Genomic DNA was extracted from these isolates, and the non-transcribed spacer (NTS) region of ribosomal RNA (rRNA) was targeted for genotyping using newly designed primers. Haplotype analysis was performed to explore genetic diversity, and antifungal susceptibility to terbinafine (TRB) and itraconazole (ITC) was assessed. The results revealed five distinct NTS types: NTS-I, NTS-II, NTS-III, NTS-IV and NTS-V, with NTS-IV being the most prevalent. The distribution of NTS types varied across different cities, suggesting potential transmission patterns among wrestlers. Antifungal susceptibility testing showed that all isolates were susceptible to TRB, while one isolate demonstrated resistance to ITC. Genotypic diversity was not correlated with antifungal susceptibility, emphasising the importance of monitoring susceptibility to ensure effective treatment. Haplotype analysis highlighted significant genetic diversity among the T. tonsurans isolates. This diversity may be attributed to factors such as human-to-human transmission, geographic location and lifestyle changes. The study's findings underscore the need for comprehensive genotypic analysis to understand the epidemiology and evolution of T. tonsurans infections in athletes. In conclusion, this study provides valuable insights into the genotypic diversity and antifungal susceptibility of T. tonsurans isolates causing TG in Iranian wrestlers. The presence of multiple NTS types and varying susceptibility patterns highlights the complexity of T. tonsurans infections in this population. Further research is warranted to track the transmission routes and genetic evolution of T. tonsurans strains among wrestlers and develop effective control measures.

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.

Genetic polymorphism of merozoite surface protein 1 and antifolate-resistant genes in Plasmodium falciparum from Mali and Niger.

Since 2015, countries in the Sahel region have implemented large-scale seasonal malaria chemoprevention (SMC). However, the mass use of sulfadoxine-pyrimethamine (SP) plus amodiaquine impacts the genetic diversity of malaria parasites and their sensitivity to antimalarials. This study aimed to describe and compare the genetic diversity and SP resistance of Plasmodium falciparum strains in Mali and Niger. We collected 400 blood samples in Mali and Niger from children aged 3-59 months suspected of malaria. Of them, 201 tested positive (Niger, 111, 55.2%; Mali, 90, 44.8%). Polymorphism of merozoite surface protein 1 (msp1) genetic marker showed 201 allotypes. The frequency of the RO33 allotype was significantly higher in Niger (63.6%) than in Mali (39.3%). There was no significant difference in the frequency of the K1 and MAD20 allotypes between the 2 countries. The multiplicity of infection was 2 allotypes per patient in Mali and one allotype per patient in Niger. The prevalence of strains with the triple mutants Pfdhfr51I/Pfdhfr59R/Pfdhps436A/F/H and Pfdhfr51I/Pfdhfr59R/Pfdhps437G was 18.1% and 30.2%, respectively, and 7.7% carried the quadruple mutant Pfdhfr51I/Pfdhfr59R/Pfdhps436A/F/H/Pfdhps437G. Despite the significant genetic diversity of parasite populations, the level of SP resistance was comparable between Mali and Niger. The frequency of mutations conferring resistance to SP still allows its effective use in intermittent preventive treatment in pregnant women and in SMC.

Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada.

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD) sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains, it ranged between 1.35 and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift was observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9 to 26 individuals whereas the wild population was estimated at 25,048-56,291 individuals. Further, a depletion of low-frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.

Molecular genetics, seed morphology and fatty acids diversity in castor (Ricinus communis L., Euphorbiaceae) Iranian populations.

Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs.

Identifikasi Struktur Protein Spike Varian Baru SARS-CoV-2 secara Bioinformatika dalam Pengembangan Kandidat Terapi COVID-19

Despite the relatively slow evolutionary rate of SARS-CoV-2 in comparison to other RNA viruses, the extensive and rapid transmission during the COVID-19 pandemic has led to the emergence of significant genetic diversity since the virus first infected the human population. This has resulted in various variants, such as Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), among others. Of particular concern are the Delta Variant and newly recognized Variants of Concern (VOCs), including lineages of B.1.617.2, as well as other VOCs discovered through local transmission, such as Epsilon (B.1.427/29-US) and B1.1.7/E484K-UK. The interactions between these variants and the spike protein of SARS-CoV-2, as well as the Angiotensin-converting enzyme 2 (ACE2), have become a primary focus in understanding the infection and spread of the SARS-CoV-2 virus. This research aims to comprehensively identify, evaluate, and explore the structural characteristics of the macromolecular spike protein of SARS-CoV-2 in the Beta, Gamma, and Delta variants using bioinformatics approaches. The methods employed in this study include homology modeling, molecular docking simulations, and molecular dynamics simulations. The research findings indicate that the spike protein of SARS-CoV-2 in the Gamma variant exhibits a strong affinity for ACE2. Therefore, this study is expected to serve as a reference for designing effective vaccine or antiviral candidates targeting various SARS-CoV-2 variants in the treatment of COVID-19 infections.

Prevalence of the virulence genes and their correlation with carbapenem resistance amongst the Pseudomonas aeruginosa strains isolated from a tertiary hospital in China.

Pseudomonas aeruginosa is one of the top-listed pathogens in nosocomial infection. It is notorious for its complicated virulence system and rapid adaptability to drugs or antimicrobials. In this study, we aimed to evaluate the prevalence of sixteen virulence genes in four groups including type III secretion system, biofilm formation, extracellular toxin biosynthesis and enzymes amongst 209 clinical Pseudomonas aeruginosa strains. We investigated the different distribution patterns of virulence genotypes based on carbapenem-resistant phenotype or the carriage of carbapenemase genes. The detection rate of each virulence gene varied greatly. phzM and plcN were detected in all collected strains, while pilB and exoU were only carried by a small portion of isolates (6.7% and 16.3%). Additionally, the number of genotypes observed in each group of examined virulence genes ranged from 4 to 8. Only the distribution of genotypes of type III secretion system showed statistical difference between carbapenem-mediated or carbapenem-resistant and carbapenem-sensitive strains. The virulence genotype of Pseudomonas aeruginosa was possibly interrelated to its resistance mechanism. Further research suggested that one particular TTSS genotype exhibited higher ratio in carbapenemase-producing strains and exoS was less frequently detected in CRPA strains carrying carbapenemase gene. Generally, the significant genetic diversity of virulence genes amongst Pseudomonas aeruginosa strains was highlighted in this study. Specific TTSS genotypes were associated with carbapenem-resistance. In particular, certain incompatibility might exist between exoS and carbapenemase genes, which provided valuable information for further understanding the relationship between carbapenem resistance and virulence.

Evolution, genetic recombination, and phylogeography of goose parvovirus

Goose parvovirus (GPV) has garnered global attention due to its association with severe symptoms in waterfowl. However, the process underlying the global emergence and spread of GPV remains largely elusive. In this study, we illustrated the evolutionary characteristics of GPVs from a global perspective using phylogenetic analysis, recombination analysis, selection pressure analysis, and phylogeographic analysis. Our findings indicate that GPV and muscovy duck parvovirus (MDPV) diverge into two distinct branches. Within GPV, there are two classifications: classical GPV (C-GPV) and novel GPV (N-GPV), each containing three subgroups, underscoring the significant genetic diversity of GPV. Recombination analysis revealed 11 recombination events, suggesting C-GPV, N-GPV, and MDPV co-infections. Further, phylogeographic analysis revealed that China is an important exporter of GPV and that trade might serve as a potential transmission conduit. Nonetheless, a detailed understanding of its geographic transmission dynamics warrants further investigation due to the limited scope of current genomic data in our study. This study offers novel insights into the evolutionary state and spread of GPV, holding promise for informing preventive and containment strategies against GPV infection.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame (Sesamum indicum L.) plays a crucial role in Ethiopian agriculture, serving both subsistence and commercial purposes. However, our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited. To address this knowledge gap, we genotyped 368 Ethiopian sesame germplasms, categorizing into four distinct breeding groups: Accessions, landraces, improved varieties, and wild types, using a comprehensive set of 28 polymorphic markers, including 23 simple sequence repeat (SSR) and five Insertion-Deletion (InDel) markers. These markers ensured robust genomic representation, with at least two markers per linkage group. Our results unveiled substantial genetic diversity, identifying a total of 535 alleles across all accessions. On average, each locus displayed 8.83 alleles, with observed and expected heterozygosity values of 0.30 and 0.36, respectively. Gene Diversity and Polymorphic Information Content (PIC) were recorded at 0.37 and 0.35. The percentage of polymorphic loci varied significantly among breeding groups, ranging from 8.00% to 82.40%, indicating high diversity in accessions (82.4%), moderate diversity in improved varieties (31.20%) and landraces (29.60%), and limited diversity in wild types (8.00). Analysis of Molecular Variance (AMOVA) results emphasized significant genetic differentiation among populations, with substantial diversity (P ​< ​0.001) within each population. Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations, while the larger proportion of genetic diversity (92%) resided within each individual sesame population, showcasing heightened diversity within each group. Our study's findings received support from both Bayesian clustering and Neighbor-joining (NJ) analysis, reaffirming the credibility of our genetic structure insights. Notably, Population structure analysis at its highest Δk value (k ​= ​2) revealed the existence of two primary genetic clusters, further subdivided into four sub-populations at k ​= ​4. Similarly, NJ analysis identified two prominent clusters, each displaying additional sub-clustering. In conclusion, our research provides a comprehensive understanding of genetic groups, subpopulations, and overall diversity within Ethiopian sesame populations. These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections. This genetic richness holds promise for breeding and conservation efforts, highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genetic Diversity Analysis and Molecular Diversity in Greengram (Vigna radiata (L.) Wilczek) Genotypes Using SSR Markers

A study on the genetic and molecular diversity of 40 genotypes of Greengram was conducted using SSR markers. The experimental material contained significant genetic diversity; nevertheless, for all yield-related and yield-attributing features, phenotypic coefficient of variation exceeded genotypic coefficient of variation. The genotypes LGG 574 (8.80), PDM 139 (8.34), and Pant Mung 6 had the highest seed yields (7.78). The highest observed cluster distances between clusters 5 and 6 (472.88) and clusters 4 and 5 (432.89). Among all the factors PC 1 to PC 10, the PC 1 (19.99) accounted maximum proportion of variability in the set of all variables and remaining components accounted for progressively lesser and lesser amount of variation. The first six principal components (PC-1 to PC-6) with eigen values of 2.94, 2.62, 2.18, 1.40, 1.28, and 0.86, respectively, accounted for 86.95% of the total variance for all the qualities, according to principal component analysis. The genotypes 23, 32, 33, and 21 were spread out relatively far from other genotypes in the scatter plot, suggesting that they might be different from other genotypes. PIC values of 10 SSR loci, where the VR 86 marker produced the greatest PIC Value percentage and highest heterozygosity percent. Fixation index is ranged from 1.000 to -0.076. In comparison to Cluster II, III, IV, and V, Cluster I has the most genotypes (25), and the use of SSR markers in this work to differentiate between genotypes was made possible by the high polymorphism information richness of this cluster.

Genetic diversity and molecular diagnosis of Giardia.

Giardia is a genus of flagellated protozoan parasites that infect the small intestine of humans and animals, causing the diarrheal illness known as giardiasis. Giardia exhibits significant genetic diversity among its isolates, which can have important implications for disease transmission and clinical presentation. This diversity is influenced by the coevolution of Giardia with its host, resulting in the development of unique genetic assemblages with distinct phenotypic characteristics. Although panmixia has not been observed, some assemblages appear to have a broader host range and exhibit higher transmission rates. Molecular diagnostic methods enable researchers to examine the genetic diversity of Giardia populations, enhancing our understanding of the genetic diversity, population structure, and transmission patterns of this pathogen and providing insights into clinical presentations of giardiasis.

Genetic diversity and population structure of selected tef core germplasm lines based on microsatellite markers.

Tef is an indigenous and important food, feed, and cash crop for smallholder Ethiopian farmers. Knowledge of the natural genetic composition of the crop provides the option to further exploit its genetic potential through breeding. However, there are insufficient reports on the genetic variability of Ethiopian tef using a medium-throughput marker system. Hence, the current study was designed to evaluate the genetic variability of released and core germplasm that was collected earlier. Eighty-one tef genotypes collected from eight Ethiopian ecological zones and released varieties were targeted using 14 SSR markers. The study yielded a total of 122 alleles across the entire locus and population. The molecular variance analysis indicated the existence of large genetic differentiation (FIS and FIT = 0.87), with 86% and 13% of the total variation accounted for among genotypes within the population and across all genotypes used for this study, respectively. However, low genetic differentiation among the populations (FST = 0.014, which accounts for 1%) was observed. Multivariate analyses such as clustering and PCoA did not cluster genotypes into distinct groups according to their geographical areas of population. This is presumably due to gene flow among populations. In conclusion, our findings show that there is significant genetic diversity within populations, particularly in the Jimma, Tigray, and released varieties, as well as the presence of private alleles and heterozygosity. The study also indicates the existence of genotypic admixture in the studied materials. The identification of private alleles and their differentiation will be helpful in selecting breeding materials and creating breeding plans.

Molecular epidemiological study on rubella virus circulating in Yunnan Province during 2011-2021

Objective: To understand the genotype distribution and transmission pattern of rubella virus (RuV) circulating in Yunnan Province. Methods: Throat swab samples were collected from rubella outbreaks and sporadic cases in nine prefectures/cities of Yunnan Province from 2011 to 2021. Virus isolation, amplification of target genes and sequence determination were performed on the RuV-positive samples. The genotypes and lineages of Yunnan strains were determined by comparing them with the reference strains, and further phylogenetic analysis was performed with Yunnan strains and strains circulating in other provinces of China during the same period. Results: RuV circulating in Yunnan province during 2011-2021 showed significant genetic diversity, and three lineages, 1E-L1, 2B-L1 and 1E-L2, were detected. Two lineage-switches were also identified, including the conversion of 1E-L1 to 2B-L1 between 2012 and 2013, and the replacement of 2B-L1 to 1E-L2 after 2018. The time of the switches was basically consistent with the outbreak in Yunnan province in 2012 and the time of the rubella reemergence and epidemic between 2018 and 2019. The amino acid sequence of RuV virus strains in Yunnan province was highly conserved, and no important functional regions were changed. Conclusions: The transmission pattern of RuV in Yunnan province is generally consistent with the epidemic trend of RuV in other provinces of China.

The genomic analysis unveils reduced genetic variability but an increased proportion of heterozygote genotypes of the intensively managed mezcal agave, Agave angustifolia Haw.

The central Oaxaca Basin has a century-long history of agave cultivation, and it is hypothesized to be the region of origin of other cultivated crops. Widely cultivated for mezcal production, the perennial crop known as "espadín" is putatively derived from wild Agave angustifolia. Nevertheless, little is known about its genetic relationship to the wild A. angustifolia or how the decades-long clonal propagation has affected its genetics. Using RADseq and over 8,000 SNPs, we studied aspects of the population genomics of wild and cultivated A. angustifolia in Puebla and Oaxaca, Mexico. We assessed patterns of genetic diversity, inbreeding, distribution of genetic variation, and differentiation among and within wild populations and plantations. Genetic differentiation between wild and cultivated plants was strong, and both gene pools harbored multiple unique alleles. Nevertheless, we found several cultivated individuals with high genetic affinity with wild samples. Higher heterozygosity was observed in the cultivated individuals, while in total, they harbored considerably fewer alleles and presented higher linkage disequilibrium compared to the wild plants. Independently of geographic distance among sampled plantations, the genetic relatedness of the cultivated plants was high, suggesting a common origin and prevalent role of clonal propagation. The considerable heterozygosity found in "espadín" is contained within a network of highly related individuals, displaying high linkage disequilibrium generated by decades of clonal propagation and possibly by the accumulation of somatic mutations. Wild A. angustifolia, on the other hand, represents a significant genetic diversity reservoir that should be carefully studied and conserved. This article is protected by copyright. All rights reserved.