Global Burden of Fungal Infections and Antifungal Resistance from 1961 to 2024: Findings and Future Implications

Background: Antifungal resistance (AFR) is a global public health problem with devastating effects, especially among immunocompromised individuals. Addressing AFR requires a One Health approach including Antifungal Stewardship (AFS). This study aimed to comprehensively review global studies published on fungal infections and AFR and to recommend solutions to address this growing problem. Materials and Methods: This was a narrative review that was conducted using published papers on fungal infections, AFR, and AFS between January 1961 and March 2024. The literature was searched using PubMed, Google Scholar, Web of Science, and EMBASE. Results: This found that there has been an increase in fungal infections globally, especially among immunocompromised patients. Due to this increase in fungal infections, there has been a proportionate increase in the use of antifungal agents to prevent and treat fungal infections. This increased use of antifungal agents has worsened the problem of AFR contributing to increased morbidity and mortality. Globally, fungal infections have contributed to 150 million infections annually and 1.7 million deaths per year. By the year 2023, over 3.8 million people died from fungal infections. Addressing AFR remains a challenge because the treatment of antifungal-resistant infections is difficult. Finally, the treatment of fungal infections is a global challenge exacerbated by the limited number of antifungal agents to treat invasive fungal infections. Conclusion: The results of this study indicated that fungal infections and AFR are prevalent across humans, animals, agriculture, and the environment. Addressing this problem requires the provision of solutions such as improving the awareness of AFR, conducting further research on the discovery of new antifungal agents, and implementing AFS programs. If this global problem is not addressed, the morbidity and mortality associated with AFR will continue to rise in the future.

Candidemia chronicles:Retrospective analysis of candidemia epidemiology,species distribution,and antifungal susceptibility patterns in Bahrain

BACKGROUND Invasive fungal infections,particularly candidemia,pose significant clinical challenges globally.Understanding local epidemiology,species distribution,and antifungal susceptibility patterns is crucial for effective management despite regional variations.AIM To investigate the epidemiology,species distribution,antifungal susceptibility patterns,and associated risk factors of candidemia among patients in Bahrain from 2021 to 2023.METHODS This retrospective study analyzed demographic data,Candida species distribution,antifungal susceptibility profiles,and risk factors among candidemia patients treated at a tertiary care hospital in Bahrain over three years.Data was collected from medical records and analyzed using descriptive statistics.RESULTS A total of 430 candidemia cases were identified.The mean age of patients was 65.7 years,with a mortality rate of 85.5%.Candida albicans(C.albicans)was the most common species,followed by Candida parapsilosis,Candida tropicalis(C.tropicalis),and emerging multidrug-resistant Candida auris(C.auris).Antifungal susceptibility varied across species,with declining susceptibility to azoles observed,particularly among C.albicans and C.tropicalis.Major risk factors included central venous catheters,broad-spectrum antibiotics,and surgical procedures.CONCLUSION This study highlights the substantial burden of candidemia among older adults in Bahrain,characterized by diverse Candida species.It also concerns levels of antifungal resistance,notably in C.auris.The findings underscore the importance of local epidemiological surveillance and tailored treatment strategies to improve outcomes and mitigate the spread of multidrug-resistant Candida species.Future research should focus on molecular resistance mechanisms and optimizing therapeutic approaches to address this growing public health concern.

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties.This study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene structures.Subsequently,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)infestation.Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding.Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation.Metabolomic results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid contents.Omics association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH infestation.In summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

Comparative and Phylogenetic Analysis of the Complete Chloroplast Genomes of 19 Species in Rosaceae Family

Rosaceae represents a vast and complex group of species,with its classification being intricate and contentious.The taxonomic placement of many species within this family has been a subject of ongoing debate.The study utilized the Illumina platform to sequence 19 plant species from 10 genera in the Rosaceae.The cp genomes,vary-ing in size from 153,366 to 159,895 bp,followed the typical quadripartite organization consisting of a large single-copy(LSC)region(84,545 to 87,883 bp),a small single-copy(SSC)region(18,174 to 19,259 bp),and a pair of inverted repeat(IR)regions(25,310 to 26,396 bp).These genomes contained 132–138 annotated genes,including 87 to 93 protein-coding genes(PCGs),37 tRNA genes,and 8 rRNA genes using MISA software,52 to 121 simple sequence repeat(SSR)loci were identified.D.arbuscular contained the least of SSRs and did not have hexanotides,A.lineata contained the richest SSRs.Long terminal repeats(LTRs)were primarily composed of palindromic and forward repeat sequences,meanwhile,The richest LTRs were found in Argentina lineata.Except for Argentina lineata,Fragariastrum eriocarpum,and Prunus trichostoma,which varied in gene type and position on both sides of the boundary,the remaining species were found to be mostly conserved according to IR boundary analysis.The examination of the Ka/Ks ratio revealed that only the infA gene had a value greater than 1,indicating that this gene was primarily subjected to positive selection during evolution.Additionally,9 hotspots of variation were identified in the LSC and SSC regions.Phylogenetic analysis confirmed the scientific validity of the genus Prunus L.sensu lato(s.l.)within the Rosaceae family.The separation of the three genera Argentina Hill,Fragariastrum Heist.ex Fabr.and Dasiphora Raf.from Potentilla L.may be a more scientific classification.These results offer fresh perspectives on the taxonomy of the Rosaceae.

Pear genomes display significant genetic diversity and provide novel insights into the fruit quality traits differentiation

The pear(Pyrus spp.)is well known for diverse flavors,textures,and global horticultural importance.However,the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored.Here,we de novo assembled and annotated the genomes of the maternal(PsbM)and paternal(PsbF)lines of the hybrid‘Yuluxiang'pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm.Using the constructed pangenome,we identified 21224 gene PAVs(Presence-absence variation)and 1158812 SNPs(Single Nucleotide Polymorphism)in the non-reference genome that were absent in the PsbM reference genome.Compared with SNP markers,PAV-based analysis provides additional insights into the pear population structure.In addition,some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations.Moreover,our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in‘Xuehuali'which is vital for pear quality.PsbMGH3.1 may play a role in the IAA pathway,contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene.This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Impact of Vegetation Restoration on Soil Fungal Community Structure in Karst Rocky Desertification Areas

In this paper,managed forest(MF)and natural forest(NF)in the Huajiang Demonstration Zone of Guanling,Guizhou were selected as research objects,and cropland(CL)was taken as control.High-throughput sequencing technology was used to study the characteristics of fungal community composition and species diversity in the surface(0-10 cm)soil of each restoration measure,in order to reveal the dominant soil fungal groups and fungal community composition in karst rocky desertification areas,which was conducive to a more comprehensive understanding of the soil conditions of different vegetation restoration measures.Research has shown that vegetation restoration significantly affected the diversity of soil fungal community,with significant increases in Sob index,Ace index,and Chao index.The vegetation restoration has significantly changed the composition of fungal community.The dominant fungi in the CL topsoil are Sordariomycetes(62.28%),Dothideomycetes(12.34%),and Eurotiomycetes(9.12%);the dominant fungi in the MF soil are Sordariomycetes(45.05%),Dothideomycetes(14.74%),and Mortierellomycetes(10.40%);the dominant fungi in the NF soil are unclassified fungal community(26.38%),Sordariomycetes(19.78%),and Agaricomycetes(13.82%).Vegetation restoration has changed the key fungal groups in the soil.Sordariomycetes,Fusarium,and Setophoma are the key dominant fungal groups in CL soil;Dioszegia is key dominant fungal group in MF soil;c_unclassified_k_Fungi,p_unclassified_k_Fungi,o_unclassified_k_Fungi,f_unclassified_k_Fungi,g_unclassified_k_Fungi,Teichospora,and Diaporthe are key dominant fungal groups in NF soil.

Detection of Differentiation Among BB, CC and EE Genomes in the Genus Oryza by Two-probe Genomic in situ Hybridization (GISH)

The genus Oryza consists of two cultivated species (O. sativa L. and O. glaberrima Steud.) and approximately 20 wild relative species widely distributed in the pan-tropics. These species have been classified into four complexes following the Vaughan's taxonomic system([1]). The O. officinalis complex is the largest complex in the genus, which includes ten species, having BE, CC, on, and EE genomes in the diploids as well as BBCC and CCDD genomes in the tetraploids. The relationships among the BE, CC, and EE genomes still remain unclear, although previous studies have indicated certain affinities of these genomes([2-4]). Genomic in situ hybridization (GISH) is a powerful technique to detect the relationships among the related genomes at chromosome and DNA levels. The objective of the present study was to investigate the relationships among the BE, CC and EE genomes in the genus Oryza by the two-probe GISH.

A chromosome-level genome assembly for Chinese plum‘Wushancuili'reveals the molecular basis of its fruit color and susceptibility to rain-cracking

Chinese plum(Prunus salicina Lindl.)originates from China and makes a large contribution to the global production of plums.The P.salicina‘Wushancuili'has a green coloration and high fruit quality and is economically important in eliminating poverty and protecting ecology in the Yangtze River Three Gorges Reservoir.However,rain-induced cracking(rain-cracking,literally skin cracking caused by rain)is a limitation to‘Wushancuili'fruit production and causes severe losses.This study reported a high-quality‘Wushancuili'genome assembly consisting of a 302.17-Mb sequence with eight pseudo-chromosomes and a contig N50 of 23.59 Mb through the combination of Illumina sequencing,Pacific Biosciences HiFiⅢsequencing,and high-throughput chromosome conformation capture technology.A total of 25109 protein-coding genes are predicted and 54.17%of the genome is composed of repetitive sequences.‘Wushancuili'underwent a remarkable orthoselection during evolution.Gene identification revealed that loss-of-function in four core MYB10 genes results in the anthocyanin deficiency and absence of red color,revealing the green coloration due to the residual high chlorophyll in fruit skin.Besides,the occurrence of cracking is assumed to be closely associated with cell wall modification and frequently rain-induced pathogen enrichment through transcriptomic analysis.The loss of MYB10 genes might render fruit more susceptible to pathogen-mediated cracking by weakening the epidermal strength and reactive oxygen species(ROS)scavenging.Our findings provided fundamental knowledge regarding fruit coloration and rain-cracking and will facilitate genetic improvement and cultivation management in Chinese plums.

The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

Genome-edited rabbits:Unleashing the potential of a promising experimental animal model across diverse diseases

Animal models are extensively used in all aspects of biomedical research,with substantial contributions to our understanding of diseases,the development of pharmaceuticals,and the exploration of gene functions.The field of genome modification in rabbits has progressed slowly.However,recent advancements,particularly in CRISPR/Cas9-related technologies,have catalyzed the successful development of various genome-edited rabbit models to mimic diverse diseases,including cardiovascular disorders,immunodeficiencies,agingrelated ailments,neurological diseases,and ophthalmic pathologies.These models hold great promise in advancing biomedical research due to their closer physiological and biochemical resemblance to humans compared to mice.This review aims to summarize the novel gene-editing approaches currently available for rabbits and present the applications and prospects of such models in biomedicine,underscoring their impact and future potential in translational medicine.

Chromosome-level genome and population genomics of the intermediate horseshoe bat(Rhinolophus affinis)reveal the molecular basis of virus tolerance in Rhinolophus and echolocation call frequency variation

Horseshoe bats(genus Rhinolophus,family Rhinolophidae)represent an important group within chiropteran phylogeny due to their distinctive traits,including constant high-frequency echolocation,rapid karyotype evolution,and unique immune system.Advances in evolutionary biology,supported by high-quality reference genomes and comprehensive whole-genome data,have significantly enhanced our understanding of species origins,speciation mechanisms,adaptive evolutionary processes,and phenotypic diversity.However,genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data,with only a single published genome of R.ferrumequinum currently available.In this study,we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat(R.affinis).Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae.Notably,we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV-2 signaling pathway,DNA repair,and apoptosis,which displayed signs of rapid evolution.In addition,we observed an expansion of the major histocompatibility complex class II(MHC-II)region and a higher copy number of the HLA-DQB2 gene in horseshoe bats compared to other chiropteran species.Based on whole-genome resequencing and population genomic analyses,we identified multiple candidate loci(e.g.,GLI3)associated with variations in echolocation call frequency across R.affinis subspecies.This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research.

Diverse responses of fungal functional groups to desertification in forest soils of Pinus densata on the Chinese Tibetan plateau

Rapid increase in desertification is an environ-mental concern,especially for the health and sustainabil-ity of ecosystems in changing climates.How ecosystems respond to such changes may be partially understood by studying interactions and performance of critically impor-tant groups such as soil fungi functional groups.This study investigated variations in diversities of three soil fungi functional guilds(saprotrophic,symbiotic,pathogenic)and influencing abiotic factors in a Pinus densata forest on the southeast Tibetan Plateau where desertification is intense.The results indicate desertification significantly decreased the proportion of dominant fungal guild-symbiotic fungi(mean relative abundance decreasing from 97.0%to 68.3%),in contrast to saprotrophic fungi(increasing from 2.7%to 25.7%)and pathogenic(from 0.3%to 5.9%).Soil pH had the most significant impact on fungal community structure and negatively correlated with symbiotic fungal richness,which was significantly lower in arid soils,and positively correlated with saprotrophic and pathogenic fungal alpha-diversity,which were abundant.Different community struc-tures and regulators of the three fungi communities were observed,with pH,total phosphorus and ammonium(NH_(4)^(+))as the main determinants.This study links the biotic and abi-otic components during desertification and the interactions between them,and may be used as indicators of ecosystem health and for amendments to mitigate the effects of a chang-ing climate.

3D genome organization and its study in livestock breeding

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Phylogenetic study on Scenedesmacae with the description of a new genus Coccoidesmus gen.nov.(Chlorophyceae,Chlorophyta)and chloroplast genome analyses

Members of the family Scenedesmaceae are some of the most common algal taxa in inland ecosystems,and they are widely distributed in freshwaters,aerial,and sub-aerial habitats.With the continuous updating of methods,the classic morphological taxonomy of this family needs to be revised.In recent years,many genera of Scenedesmaceae have been established via the use of molecular methods.The phylogenetic relationships within Scenedesmaceae were analyzed using different molecular markers and morphological data,and the new freshwater genus Coccoidesmus Wang,Hou et Liu gen.nov.was described.Two new species in this genus were also described.Phylogenetic analysis based on tufA genes revealed that the new genus formed an independent clade closely related to Comasiella.However,these two genera are characterized by significant morphological differences in colony arrangement and cell shape.The chloroplast genome of the type species was assembled and annotated,and analyses of genome structure and sequences were conducted.More genome data could help clarify the phylogenetic relationships within this family.

Contribution to the Study of Fungal Strains Contaminating Peanut Pastes in Bangui (Central African Republic)

Introduction: Peanut pastes are food products resulting from artisanal or industrial processing, used in cooking in Africa in general and in Central African Republic in particular. These peanut pastes are often contaminated by molds and filamentous fungi involved in the degradation of hygienic and organoleptic or even toxicological quality. This study aims to determine the epidemiological profile of molds contaminating peanut pastes sold on the Central African market. Methodology: This was a cross-sectional study carried out from June to September 2023. Samples of peanut pastes sold on Central African market were taken and analyzed at the National Laboratory of Clinical Biology and Public Health using the conventional microbiology method according to ISO 7954 standards. The data obtained were collected in the ODK 2023.3.1 application and analyzed with the Epi Info 7 software. A multivariate analysis by logistic regression, Ficher’s exact test, and chi2 at the 5% threshold (p Penicillium sp.;11.25% of Mucor sp.;10.63% of Aspergillus terrei;3.13% of Aspergillus niger;1.25% of Aspergillus medullans;28.13% of Aspergillus flavus;2.50% of Aspergillus fumigatus. Peanut pastes stored beyond three days were more contaminated (94.19%). Conclusion: The results of this study made it possible to highlight strains of mold that impact the hygienic and organoleptic quality of peanut pastes sold at the Central African market. Most of the isolated strains were the Aspergillus flavus species which is recognized by its toxigenic effects. This species is much more incriminated in the contamination of foodstuffs with the production of the toxin which causes underlying pulmonary pathologies in humans.

Chromosome-level assembly of triploid genome of Sichuan pepper(Zanthoxylum armatum)

As an important spice species in Rutaceae, the Sichuan pepper (Zanthoxylum armatum) can provide pungent and numbing taste, as well as aroma in its mature fruit. Here we assembled a chromosome-level genome of green prickly ash which was widely cultivated in a major production area including Chongqing and Sichuan province, China. We generated 712 Gb (~112×) PacBio long reads and 511 Gb (~82×) Hi-C data, and yielded an assembly of 99 pseudochromosomes with total size of 5.32 Gb and contig N50 of 796 kb. The genomic analyses and cytogenetic experiments both indicated that the cultivarZhuye Huajiao’ was a triploid. We identified a Zanthoxylum-specific whole genome duplication event emerging about 24.8 million years ago (Mya). We also detected a transposition burst event (0.3-0.4 Mya) responsible for the large genome size of Z. armatum. Metabolomic analysis of the Zanthoxylum fruits during development stages revealed profiles of39 volatile aroma compounds and 528 secondary metabolites, from which six types of sanshools were identified. Based on metabolomic and transcriptomic network analysis, we screened candidate genes encoding long chain acyl-CoA synthetase, fatty acid desaturase,branched-chain amino acid aminotransferase involved in sanshool biosynthesis and three genes encoding terpene synthase during fruit development. The multi-omics data provide insights into the evolution of Zanthoxylum and molecular basis of numbing and aroma flavor of Sichuan pepper.

To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant

Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community.

Gene characterization and phylogenetic analysis of four mitochondrial genomes in Caenogastropoda

Caenogastropoda is a highly diverse group,containing~60%of all existing gastropods.Species in this subclass predominantly inhabit marine environments and have a high ecological and economic value.Owing to the increase in relevant phylogenetic studies,our understanding of between species relatedness in Caenogastropoda has improved.However,the biodiversity,taxonomic status,and phylogenetic relationships of this group remain unclear.In the present study,we performed next-generation sequencing of four complete mitochondrial genomes from three families(Buccinidae,Columbellidae,and Cypraeidae)and the four mitogenomes were classical circular structures,with a length of 16177 bp in Volutharpa ampullacea,16244 bp in Mitrella albuginosa,16926bp in Mauritia arabica asiatica and 15422 bp in Erronea errones.Base composition analysis indicated that whole sequences were biased toward A and T.Then compared them with 171 complete mitochondrial genomes of Caenogastropoda.The phylogenetic relationship of Caenogastropoda derived from Maximum Likelihood(ML)and Bayesian Inference(BI)trees constructed based on CDS sequences was consistent with the results of traditional morphological analysis,with all three families showing close relationships.This study supported Caenogastropoda at the molecular level as a separate clade of Mollusca.According to our divergence time estimations,Caenogastropoda was formed during the middle Triassic period(~247.2–237 Ma).Our novel mitochondrial genomes provide evidence for the speciation of Caenogastropoda in addition to elucidating the mitochondrial genomic evolution of this subclass.

Mitochondrial genomes of Tapes dorsatus and Cardita variegata:insights into Heteroconchia phylogeny

Heteroconchia,a widespread and abundant aquatic invertebrate,is an important clade of bivalve mollusks.The relationship between the three branches of Heteroconchia,Palaeoheterodonta,Archiheterodonta,and Euheterodonta has become a main controversy in molecular studies of the relationships between bivalves.In the present study,we assembled the complete mitochondrial genomes of Tapes dorsatus(Veneridae)and Cardita variegata(Carditidae)using high-throughput sequencing.C.variegata is the first mitochondrial genome belonging to the family Carditidae to be reported.We used 12 protein coding genes(excluding atp8)from the complete mitochondrial genomes of 146 species to recover the internal relationships of Heteroconchia.Our results support the traditional view of early branching of Palaeoheterodonta and the recovery of the monophyly of Palaeoheterodonta,Anomalodesmata,Imparidentia.Rearrangement analysis show that gene arrangement within Venerida was highly variable.Time-calibrated phylogenetic studies based on a relaxed molecular clock model suggested that Veneridae originated approximately 337.62 million years ago(Ma)and split into two major clades,whereas Carditidae originated approximately 510.09 Ma.Our results provide evidence of the internal relationships of Heteroconchia.