Nucleotide Diversity Research Articles

Genetic diversity and intraspecific mitochondrial DNA variations in the Georgian Mountain breed of Bos taurus reveal admixture, introgression and potential parallel vs. convergent evolution patterns

This study elucidates the haplotype diversity and mechanisms of evolutionary divergence for a broad population of the Georgian Mountain breed (GMB) of Bos taurus, using the sequencing and analysis of its mitochondrial DNA (mtDNA). In the evolutionary analyses, sequences of the targeted mtDNA region, involving the D-loop, CYTB, tRNA-Thr, and tRNA-Pro encoding genetic loci were analyzed using MEGA11, DnaSP, and SplitsTree software packages. A total of 25 haplotypes were determined among 82 individuals of GMB, belonging predominantly to the haplogroups T (T3, T1, T2, T4) or Q (Q1). Ten singleton haplotypes could also be determined in the GMB population. In the maximum likelihood evolutionary analysis, the singleton haplotype SNGT-9 appeared to be most closely related to the Bos indicus sub-haplogroup I1a. The haplotype diversity (0.997), nucleotide diversity (0.00636) and the overall mean distance within a population (0.01) calculated for GMB were greater as compared to the respective estimates (0.930, 0.00482 and 0.00) determined for its closest cattle relatives globally, suggesting stronger selection. It is suggested that the GMB diversity has been shaped by both parallel and convergent evolution, as well as by possible introgression, while pinpointing this breed’s ancient origin collectively.

Genome resequencing reveals genetic status of Macrobrachium rosenbergii populations in China

The giant freshwater prawn (Macrobrachium rosenbergii) has been widely cultured in China since 1990s. In this study, 189 individuals were sampled from 10 distinct populations, including original populations introduced from abroad and domesticated strains in China, namely Florida (FD), "Nantaihu No.2" (NT), Vietnam (YN), Sri Lanka (SK), Bangladesh (ML), Thailand (TG), Taiwan (TW), "Shufeng No.1" (SF), Zhengda (ZD) and New Myanmar (NMD). The genetic diversity and population structure of these populations were analyzed based on a dataset of 300,828 genome-wide SNP loci. The population structure analysis showed that the 10 populations shared 4 ancestors, and the domestic populations (i.e., SF, ZD, TW and NT) shared a common ancestor. The phylogenetic analysis showed that the 10 populations were grouped into 4 branches, with all the domestic populations clustering together. Estimation of fixation index (Fst) values revealed relatively lower Fst values among the domestic populations, in contrast to the more significant differences observed between domestic and foreign-origin populations. Gene flow analysis revealed three significant events of genetic exchange among the 10 populations: (1) from YN to the common ancestor of FD, TG and the domestic populations, (2) from NMD to the common ancestor of TG and FD, and (3) from the common ancestor of NMD, YN, ML and SK to ZD population. In addition, selective sweep analysis, utilizing Fst and nucleotide diversity (Pi) estimations, was conducted on representative populations (i.e., ML and SF), and 7 positively selected genes were identified, including Prospero Homeobox 1 (Prox1), Forkhead Box L1 (Foxl1), Tousled Like Kinase 2 (TLK2), G Protein Subunit Alpha 14 (Gna14), Uronyl 2-sulfotransferase (Ust), MAX Network Transcriptional Repressor (Mnt) and Importin-9 (Ipo9). These findings contribute to elucidating the breeding potential of the introduced populations and provide insights into the genetic status of the domestic breeding strains of M. rosenbergii in China.

Comprehensive diagnosis and genetic analysis of two children with ring chromosome 18

To clarify the genetic diagnosis of two children with ring chromosome 18 and explore their mechanisms and clinical phenotypes. Two patients treated at the Children's Hospital of Henan Province respectively in June 2022 and March 2023 were selected as the study subjects. Genetic testing and diagnosis were carried out through copy number variation sequencing (CNV-seq), G-banded chromosomal karyotyping, and whole exome sequencing (WES). Child 1 had mainly manifested developmental delay, white matter hypoplasia, type 1 diabetes mellitus, and micropenis. He was found to have a chromosomal karyotype of 46,XY,r(18)(p11.21q22.1)[40]/46,XY[7], and CNV-seq results showed that he has a 14.86 Mb deletion at 18p11.21p11.32 and a 14.02 Mb deletion at 18q22.1q23. Child 2 had peculiar facial features, delayed white matter myelination, developmental delay, atrial septal defect, severe sensorineural deafness, and congenital laryngeal stridor. He was found to have a chromosomal karyotype of 46,XY,r(18)(p11.2q23). CNV-seq result proved that he had a 14.86 Mb deletion at 18p11-21p11.32 and a 20.74 Mb deletion at 18q21.32q23. WES has failed to detect single nucleotide variants (SNVs) in either child, but revealed a large segmental deletion at chromosome 18 in both of them. Both children were diagnosed with ring chromosome 18 syndrome. The different size of the deletional fragments in the 18q region and mosaicism of ring chromosome 18 in child 1 may underlay the variation in their clinical phenotypes. The type 1 diabetes mellitus and micropenis noted in both children are novel features for ring chromosome 18 syndrome.

Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China.

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed.

Population Genomics of Plasmodium malariae from Four African Countries.

Plasmodium malariae is geographically widespread but neglected and may become more prevalent as P. falciparum declines. We completed the largest genomic study of African P. malariae to-date by performing hybrid capture and sequencing of 77 isolates from Cameroon (n=7), the Democratic Republic of the Congo (n=16), Nigeria (n=4), and Tanzania (n=50) collected between 2015 and 2021. There is no evidence of geographic population structure. Nucleotide diversity was significantly lower than in co-localized P. falciparum isolates, while linkage disequilibrium was significantly higher. Genome-wide selection scans identified no erythrocyte invasion ligands or antimalarial resistance orthologs as top hits; however, targeted analyses of these loci revealed evidence of selective sweeps around four erythrocyte invasion ligands and six antimalarial resistance orthologs. Demographic inference modeling suggests that African P. malariae is recovering from a bottleneck. Altogether, these results suggest that P. malariae is genomically atypical among human Plasmodium spp. and panmictic in Africa.

Exploring genetic diversity, population structure, and subgenome differences in the allopolyploid Camelina sativa: implications for future breeding and research studies

Abstract Camelina (Camelina sativa), an allohexaploid species, is an emerging aviation biofuel crop that has been the focus of resurgent interest in recent decades. To guide future breeding and crop improvement efforts, the community requires a deeper comprehension of subgenome dominance, often noted in allopolyploid species, alongside and understanding of the genetic diversity and population structure of material present within breeding programs. We conducted population genetic analyses of a C. sativa diversity panel, leveraging a new genome, to estimate nucleotide diversity and population structure, and analyzed for patterns of subgenome expression dominance among different organs. Our analyses confirm that C. sativa has relatively low genetic diversity, and show that the SG3 subgenome has substantially lower genetic diversity compared to the other two subgenomes. Despite the low genetic diversity, our analyses identified thirteen distinct subpopulations including two distinct wild populations and others putatively representing founders in existing breeding populations. When analyzing for subgenome composition of long non-coding RNAs, which are known to play important roles in (a)biotic stress tolerance, we found that the SG3 subgenome contained significantly more lincRNAs compared to other subgenomes. Similarly, transcriptome analyses revealed that expression dominance of SG3 is not as strong as previously reported, and may not be universal across all organ-types. From a global analysis, SG3 was only significant higher expressed in flower, flower bud, and fruit organs, which is an important discovery given that the crop yield is associated with these organs. Collectively, these results will be valuable for guiding future breeding efforts in camelina.

Previously unmeasured genetic diversity explains part of Lewontin's paradox in a -mer-based meta-analysis of 112 plant species.

At the molecular level, most evolution is expected to be neutral. A key prediction of this expectation is that the level of genetic diversity in a population should scale with population size. However, as was noted by Richard Lewontin in 1974 and reaffirmed by later studies, the slope of the population size-diversity relationship in nature is much weaker than expected under neutral theory. We hypothesize that one contributor to this paradox is that current methods relying on single nucleotide polymorphisms (SNPs) called from aligning short reads to a reference genome underestimate levels of genetic diversity in many species. To test this idea, we calculated nucleotide diversity ( ) and -mer-based metrics of genetic diversity across 112 plant species, amounting to over 205 terabases of DNA sequencing data from 27,488 individual plants. We then compared how these different metrics correlated with proxies of population size that account for both range size and population density variation across species. We found that our population size proxies scaled anywhere from about 3 to over 20 times faster with -mer diversity than nucleotide diversity after adjusting for evolutionary history, mating system, life cycle habit, cultivation status, and invasiveness. The relationship between -mer diversity and population size proxies also remains significant after correcting for genome size, whereas the analogous relationship for nucleotide diversity does not. These results suggest that variation not captured by common SNP-based analyses explains part of Lewontin's paradox in plants.

Genetic variability of Myxobolus nagaraensis (Bivalvulida: Myxobolidae) infecting freshwater gobies Rhinogobius Gill 1859 (Gobiiformes: Oxudercidae) from rivers in Japan

Myxobolus nagaraensis is a myxozoan parasite first reported in freshwater gobies (Rhinogobius spp.) from the Nagara River, Gifu Prefecture, Japan. Myxospores of M. nagaraensis form plasmodia in the visceral cavities of gobies, commonly presenting as distended abdomens. Although Rhinogobius is a common fish genus in Japan, details of M. nagaraensis, including genetic information, remain unknown. We compared the nucleotide sequences of the ribosomal RNA gene (rDNA) of M. nagaraensis from three different host species (R. fluviatilis, R. nagoyae, and R. similis) caught in three different rivers in Japan (Sakai, Sagami, and Kaname). The ITS region (ITS-1, 5.8S rDNA, and ITS-2) and large subunit (LSU) rDNA exhibited 49 and 55 variable sites, respectively. The highest nucleotide diversity was observed in the ITS region (0.00962), whereas that of the LSU rDNA was 0.00187. Differences in host species, rather than rivers, were a significant factor for genetic variation in both the ITS region (62.58%; P < 0.001) and LSU rDNA (55.22%; P < 0.01). Significant genetic variation was observed in M. nagaraensis from R. similis compared to R. fluviatilis (P < 0.001) or R. nagoyae (P < 0.001) from the same river. Such details are valuable for understanding parasite dispersal and its ecological impact on Rhinogobius hosts.

INTRA- AND INTER-HOST EVOLUTION OF HUMAN NOROVIRUS IN HEALTHY ADULTS.

Human noroviruses are a leading cause of acute and sporadic gastroenteritis worldwide. The evolution of human noroviruses in immunocompromised persons has been evaluated in many studies. Much less is known about the evolutionary dynamics of human norovirus in healthy adults. We used sequential samples collected from a controlled human infection study with GI.1/Norwalk/US/68 virus to evaluate intra- and inter-host evolution of a human norovirus in healthy adults. Up to 12 samples from day 1 to day 56 post-challenge were sequenced using a norovirus-specific capture probe method. Complete genomes were assembled, even in samples that were below the limit of detection of standard RT-qPCR assays, up to 28 days post-challenge. Analysis of 123 complete genomes showed changes in the GI.1 genome in all persons, but there were no conserved changes across all persons. Single nucleotide variants resulting in non-synonymous amino acid changes were observed in all proteins, with the capsid VP1 and nonstructural protein NS3 having the largest numbers of changes. These data highlight the potential of a new capture-based sequencing approach to assemble human norovirus genomes with high sensitivity and demonstrate limited conserved immune pressure-driven evolution of GI.1 virus in healthy adults.

PLASTID GENOME SEQUENCING OF TULIPA SPECIES FROM KAZAKHSTAN: INSIGHTS INTO GENOMIC STRUCTURE, REPEATS, NUCLEOTIDE DIVERSITY, AND PHYLOGENETIC RELATIONSHIPS

We sequenced and analyzed the plastid genomes of Tulipa species using the Illumina NovaSeq 6000 platform. The plastomes exhibited a typical quadripartite structure with LSC, SSC, and IR regions, displaying a GC content ranging from 36.63% to 36.69%. Gene annotation revealed 136 genes across all species, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Repeat sequence analysis identified simple sequence repeats, predominantly mononucleotide repeats, and long repeat types, with palindromic repeats being the most abundant. Nucleotide diversity analysis indicated protein-coding genes with high variability. Phylogenetic analysis based on nucleotide sequences of complete plastid genomes grouped the species into three main clades corresponding to Tulipa subgenera. This study provides insights into the plastid genome structure, repeat sequences, and phylogenetic relationships in Tulipa, highlighting the potential of the ycf1 gene as a DNA barcode for Tulipa species. This research was funded by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan (Grant No. AP14870612).

Invisible dynamics: exploring the genetic diversity of peacock bass in Brazil

In Brazil, the introduction of non-native species into freshwater environments, such as peacock bass (Cichla spp.), was driven by aquaculture and sport fishing. These Amazonian fish possess phenotypic plasticity and resilience that facilitate their invasion and establishment in new habitats. Due to the taxonomic complexity of cichlids, studies on intraspecific variation are essential to mitigate the impacts of biological invasions. This study aimed to analyze the genetic diversity of peacock bass, assessing how invasive populations have diversified over time and across different regions in Brazil. Samples were collected from different invasive populations in Maranhão, São Paulo, Paraná, and Goiás. DNA was extracted and the 16S and COX1 genes were amplified. Ninety-seven specimens of the genus Cichla Schneider, 1801 were identified as Cichla monoculus Agassiz, 1831 (n=12); Cichla kelberi Kullander and Ferreira, 2006 (n=75); and Cichla piquiti (Kullander and Ferreira, 2006) (n=10). Sixteen 16S haplotypes (445bp) were identified, with haplotype diversity and nucleotide diversity values of Hd: 0.830 and Pi: 0.03777, respectively. The results showed proximity between the invasive populations from Maranhão and São Paulo, with haplotype sharing among Parque Nacional dos Lençóis Maranhenses, Baixada Maranhense, and Ilha Solteira. This highlights the fragility of species delimitation and definitions within the group, based solely on morphological data. By evaluating the set of morphological and genetic data, we found significant intraspecific variations, despite expecting population homogeneity due to the founder effect and bottleneck commonly observed in invasive populations. This underscores the adaptive potential of these cichlids.

DNA BARCODING ANALYSIS OF THE ASTERACEAE SPECIES FROM KAZAKHSTAN

Asteraceae is the largest family of flowering plants in the world, containing more than 1.900 genera and more than 32.000 individual species. Many members of the Asteraceae family are important for medicinal, ornamental, and economic purposes. In Kazakhstan, the family is represented by 146 genera and 883 species. Many species of Asteraceae are currently being used for medicinal purposes in Kazakhstan. The species of this family including Artemisia dracunculus, Pentanema caspicum, Achillea nobilis, Leuzea altaica, Klasea cardunculus, and their derivatives are effective in the treatment of diseases, possess anti-fatigue, and anti-inflammatory properties. They also have immunomodulatory properties that can to reduce inflammation, speed up wound healing, and boost the immune system in response to bacterial or viral infection. Commercially important plants of the Asteraceae family include food crops, aside from consumption, the seeds, roots, etc. can be used to produce cooking oil and spices. Other commercially important species of the Asteraceae family are members of the Tanacetum genera, which have insecticidal properties. Given the many valuable members of the Asteraceae described above, a method to authenticate an Asteraceae species is essential to ensure drug and food safety. DNA barcoding is a method that uses a short piece of DNA sequence from a standard locus as a tool for species identification. In our study DNA was extracted from plant material using the CTAB method, followed by the selection of universal barcode primers (ITS, matK, rbcL) based on established literature. The result of PCR products were purified and subjected to Sanger sequencing. The assembled sequences were compared with existing DNA sequences using BLAST function of the National Center for Biotechnology (NCBI), with outgroup sequences (Acicarpha tribuloides, Alseuosmia macrophylla) and were analyzed in MEGA 11. Maximum Likelihood analysis was conducted using 24 different nucleotide substitution models including ITS (K2+G), matK (GTR+G), rbcL (K2+G). Basic indicators of genetic diversity were evaluated, including nucleotide divergence (Pi), the proportion of conservative (C), polymorphic, and segregating (S) regions. The ITS regions showed the highest divergence (Pi = 0.127), with conservative regions accounting for 68.7% and polymorphic regions varying within 29.6%. The rbcL regions showed higher conservatism (Pi = 0.02), with 94.6% conservative regions and only 5.4% variable regions. The matK regions exhibited intermediate values (Pi = 0.052), with 87.5% conservative and 12.5% variable regions. The G+C content of the aligned sequences ranged from 34.9% to 55.0%. The effectiveness of the BLAST tool in identifying identical sequences in the NCBI database was limited at the species level for the chloroplast DNA markers rbcL and matK. However, using the ITS DNA marker, the search within the NCBI database successfully identified only the species Achillea millefolium and Achillea nobilis with 100% accuracy. Intra-specific discrepancies were observed for other species such as Psephellus sibiricus (99.37%), Scorzonera parviflora (99.37%), Klasea cardunculus (99.79%). All investigated DNA barcodes were tested successfully identified species at the genus level with 100% accuracy.

Exploring the Role of the TAS2R16 Protein and Its Single Nucleotide Variants in Pituitary Adenoma Development.

Pituitary adenoma (PA) is a common benign tumor that develops in the pituitary gland, causing hormonal imbalances and potential health issues. The TAS2R16 gene codes for a taste receptor and is involved in bitter taste perception, but there is currently no known direct link between this gene and pituitary adenoma. This study included 221 healthy controls and 131 patients with pituitary adenoma (PA) from the Lithuanian population. DNA was isolated from peripheral venous blood using the salt precipitation method. Genotyping was performed via RT-PCR. Statistical analysis was conducted with IBM SPSS Statistics 29.0 software, incorporating the Bonferroni correction for multiple comparisons. This study found that the TAS2R16 rs978739 C allele is less common in the non-invasive PA group compared to the control group (p = 0.045). The TAS2R16 rs860170 CT genotype reduces the likelihood of developing non-invasive PA by 1.9-fold under the codominant (p = 0.024) and overdominant (p = 0.030) models. The odds of developing non-invasive PA are reduced by 2-fold under the dominant (p = 0.021) model for TAS2R16 rs860170 CT + CC genotypes and by 2-fold under the additive (p = 0.018) model for each TAS2R16 rs860170 C allele. The PA group had higher serum levels of TAS2R16 than the control group (p < 0.001). The present study found that patients with the TAS2R16 rs978739 TT or CT genotype had higher serum TAS2R16 levels and protein concentrations than healthy individuals (p = 0.025 and p = 0.019, respectively), and those with the AA or AG genotype of TAS2R16 rs1357949 had higher protein concentrations (p = 0.005 and p = 0.007, respectively). The TAS2R16 rs978739 C allele was less common in the non-invasive PA group compared to the control group, while the TAS2R16 rs860170 CT genotype was linked to a reduced likelihood of developing non-invasive PA. Additionally, the PA group showed higher serum levels of TAS2R16, and increased serum protein concentrations were observed in PA patients with specific TAS2R16 variants.

Conservation genomic study of Hopea hainanensis (Dipterocarpaceae), an endangered tree with extremely small populations on Hainan Island, China.

Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs). This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 H. hainanensis populations on Hainan Island. The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise F st. In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

Repurposing tRNA isodecoders for non-canonical functions via tRNA cleavage.

The human genome encodes hundreds of transfer RNA (tRNA) genes to decode 61 codons. The basis for such genetic redundancy is unclear but the increase in the number of tRNA genes goes in concert with the complexity of an organism. While changes in the expression of isoacceptor tRNA pools can reflect adaptation to demanding protein synthesis needs and/or codon usage, the variations in the expression of the individual tRNA isodecoders are documented but poorly understood. Such expression variations are hypothesized to contribute to non-canonical tRNA functions, yet physiological relevance remains ambiguous. We report here that specific tRNA isodecoders can be functionally repurposed through cleavage that produces tRNA-derived RNAs (tDRs). The repurposing employs nucleotide variations in isodecoders leading to the production of distinct sets of tDRs with variable bioactivities.

Nanopore sequencing provides snapshots of the genetic variation within salmonid alphavirus-3 (SAV3) during an ongoing infection in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta)

Frequent RNA virus mutations raise concerns about evolving virulent variants. The purpose of this study was to investigate genetic variation in salmonid alphavirus-3 (SAV3) over the course of an experimental infection in Atlantic salmon and brown trout. Atlantic salmon and brown trout parr were infected using a cohabitation challenge, and heart samples were collected for analysis of the SAV3 genome at 2-, 4- and 8-weeks post-challenge. PCR was used to amplify eight overlapping amplicons covering 98.8% of the SAV3 genome. The amplicons were subsequently sequenced using the Nanopore platform. Nanopore sequencing identified a multitude of single nucleotide variants (SNVs) and deletions. The variation was widespread across the SAV3 genome in samples from both species. Mostly, specific SNVs were observed in single fish at some sampling time points, but two relatively frequent (i.e., major) SNVs were observed in two out of four fish within the same experimental group. Two other, less frequent (i.e., minor) SNVs only showed an increase in frequency in brown trout. Nanopore reads were de novo clustered using a 99% sequence identity threshold. For each amplicon, a number of variant clusters were observed that were defined by relatively large deletions. Nonmetric multidimensional scaling analysis integrating the cluster data for eight amplicons indicated that late in infection, SAV3 genomes isolated from brown trout had greater variation than those from Atlantic salmon. The sequencing methods and bioinformatics pipeline presented in this study provide an approach to investigate the composition of genetic diversity during viral infections.

The evolutionary features and roles of single nucleotide variants and charged amino acid mutations in influenza outbreaks during NPI period

The epidemic and outbreaks of influenza B Victoria lineage (Bv) during 2019–2022 led to an analysis of genetic, epitopes, charged amino acids and Bv outbreaks. Based on the National Influenza Surveillance Network (NISN), the Bv 72 strains isolated during 2019–2022 were selected by spatio-temporal sampling, then were sequenced. Using the Compare Means, Correlate and Cluster, the outbreak data were analyzed, including the single nucleotide variant (SNV), amino acid (AA), epitope, evolutionary rate (ER), Shannon entropy value (SV), charged amino acid and outbreak. With the emergence of COVID-19, the non-pharmaceutical interventions (NPIs) made Less distant transmission and only Bv outbreak. The 2021–2022 strains in the HA genes were located in the same subset, but were distinct from the 2019–2020 strains (P < 0.001). The codon G → A transition in nucleotide was in the highest ratio but the transversion of C → A and T → A made the most significant contribution to the outbreaks, while the increase in amino acid mutations characterized by polar, acidic and basic signatures played a key role in the Bv epidemic in 2021–2022. Both ER and SV were positively correlated in HA genes (R = 0.690) and NA genes (R = 0.711), respectively, however, the number of mutations in the HA genes was 1.59 times higher than that of the NA gene (2.15/1.36) from the beginning of 2020 to 2022. The positively selective sites 174, 199, 214 and 563 in HA genes and the sites 73 and 384 in NA genes were evolutionarily selected in the 2021–2022 influenza outbreaks. Overall, the prevalent factors related to 2021–2022 influenza outbreaks included epidemic timing, Tv, Ts, Tv/Ts, P137 (B → P), P148 (B → P), P199 (P → A), P212 (P → A), P214 (H → P) and P563 (B → P). The preference of amino acid mutations for charge/pH could influence the epidemic/outbreak trends of infectious diseases. Here was a good model of the evolution of infectious disease pathogens. This study, on account of further exploration of virology, genetics, bioinformatics and outbreak information, might facilitate further understanding of their deep interaction mechanisms in the spread of infectious diseases.

Apelin (APLN) is a biomarker contributing to the diagnosis and prognosis of hepatocellular carcinoma

Liver cancer, classified as a malignant hepatic tumor, can be divided into two categories: primary, originating within the liver, and secondary, resulting from metastasis to the liver from other organs. Hepatocellular carcinoma (HCC) is the main form of primary liver cancer and the third leading cause of cancer-related deaths. The diagnosis and prognosis of HCC using current methods still face numerous challenges. This study aims to develop novel diagnostic and prognostic models while identifying new biomarkers for improved HCC treatment. Diagnostic and prognostic models for HCC were constructed using traditional binary classification methods and machine learning algorithms based on the TCGA database (Downloaded in August 2023). The mechanisms by which APLN (Apelin) affects HCC were investigated using single-cell sequencing data sourced from the GEO database (GSE149614). The diagnostic models yielded by various algorithms could effectively distinguished HCC samples from normal ones. The prognostic model, composed of four genes, was constructed using LASSO and Cox regression algorithms, demonstrating good performance in predicting the three-year survival rate of HCC patients. The HCC biomarker Apelin (APLN) was identified in this study. APLN in liver cancer tissues mainly comes from endothelial cells and is associated with the carcinogenesis of these cells. APLN expression is significantly upregulated in liver cancer tissues, marking it as a viable indicator of endothelial cell malignancy in HCC. Furthermore, APLN expression was determined to be an independent predictor of tumor endothelial cell carcinogenesis, unaffected by its modifications such as single nucleotide variation, copy number variation, and methylation. Additionally, liver cancers characterized by high APLN expression are likely to progress rapidly after T2 stage. Our study presents diagnostic and prognostic models for HCC with appreciably improved accuracy and reliability compared to previous reports. APLN is a reliable HCC biomarker and contributes to the establishment of our models.

Clinical-grade whole genome sequencing-based haplarithmisis enables all forms of preimplantation genetic testing

High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution.

Rampant intraspecific variation of plastid genomes in Gentiana section Chondrophyllae.

Exploring the level of intraspecific diversity in taxa experienced radiation is helpful to understanding speciation and biodiversity assembly. Gentiana section Chondrophyllae sensu lato encompasses more than 180 species and occupies more a half of species in the genus. In this study, we collected samples across the range of three species (Gentiana aristata, G. crassuloides and G. haynaldii) in section Chondrophyllae s.l., and recovered the intra-species variation by comparing with closely related taxon. Using 25 newly sequenced plastid genomes together with previously published data, we compared structural differences, quantified the variations in plastome size, and measured nucleotide diversity in various regions. Our results showed that the plastome size variation in the three Chondrophyllae species ranged from 285 to 628 bp, and the size variation in LSC, IR and SSC ranged from 236 to 898 bp, 52 to 393 bp and 135 to 356 bp, respectively. Nucleotide diversity of plastome or any of the four regions was much higher than the control species. The average nucleotide diversity in plastomes of the three species ranged from 0.0010 to 0.0023 in protein coding genes, and from 0.0023 to 0.0061 in intergenic regions. More repeat sequence variations were detected within the three Chondrophyllae species than the control species. Various plastid sequence matrixes resulted in different backbone topology in two target species, showed uncertainty in phylogenetic relationship based inference. In conclusion, our results recovered that species of G. section Chondrophyllae s.l. has high intraspecific plastome variation, and provided insights into the radiation in this speciose lineage.