Molecular Evolutionary Analysis Research Articles

Molecular prevalence and associated risk factors of Entamoeba spp. in donkeys in Shanxi Province, North China

Abstract Background The intestinal protozoa Entamoeba spp. can infect humans and various animals, including donkeys, causing diarrhea and malabsorption and presenting significant risks to animal husbandry and public health. Most Entamoeba species are not pathogenic except for Entamoeba histolytica. China has among the highest rates of donkey farming worldwide. Donkey (Equus asinus) farming is increasingly important in China because of their draft and medicinal value; however, epidemiological data on Entamoeba spp. in donkeys remains limited globally. This study aimed to investigate the prevalence of Entamoeba in donkeys in Shanxi Province, North China, and assess associated risk factors using a molecular approach. Methods Fecal samples of 815 donkeys from three representative geographical locations in Shanxi Province were collected to investigate the presence of Entamoeba spp. A portion of the small-subunit rRNA gene (SSU rRNA) was amplified and sequenced to determine the prevalence and species/genotypes of Entamoeba spp. Statistical analysis of possible risk factors was performed using Statistical Product and Service Solutions (SPSS) 26.0 software. The phylogenetic relationship of Entamoeba spp. was reconstructed using the neighbor-joining (NJ) method in Molecular Evolutionary Genetics Analysis (Mega) 7.0 software. Results The overall prevalence of Entamoeba spp. in donkeys in Shanxi Province was 7.12% (58/815). Two species (Entamoeba sp. RL9 and Entamoeba equi) were identified by sequence analysis; of these, Entamoeba sp. RL9 was the most prevalent species in donkeys in this study. Statistical analysis revealed that the donkeys' sex, region, age, and altitude are the risk factors associated with Entamoeba spp. prevalence (P < 0.05). Phylogenetic analysis indicated that the sequences of Entamoeba sp. RL9 and E. equi isolated from donkeys in this study were clustered with previously reported animal-derived Entamoeba sp. RL9 and E. equi sequences, respectively. Conclusions This study reports the occurrence and prevalence of Entamoeba spp. in donkeys worldwide for the first time to our knowledge. This not only expands the geographical distribution but also broadens the host range of Entamoeba spp., addressing the knowledge gap regarding the prevalence of Entamoeba spp. in donkeys, providing baseline data for carrying out prevention and control of Entamoeba spp. in donkeys in China. Graphical Abstract

Melocular Evolution on Cold Temperature Adaptation of Chinese Rhesus Macaques

Introduction: Currently, macaques are used as animal models for human disease in biomedical research. There are two macaques species widely used as animal models, i.e., cynomolgus macaques and rhesus macaques. These two primates distribute widely, and their natural habitats are different. Cynomolgus macaques distribute in tropical climates, while rhesus macaques mostly distribute in relatively cold environments, and cynomolgus macaques have a common frostbite problem during winter when they are transferred to cold environments. Methods: In order to explore the molecular mechanisms underlying the temperature adaptation in macaques, genetic analysis and natural selection tests were performed. Based on the analysis of heat shock protein genes, DNAJC22, DNAJC28, and HSF5 showed positive selection signals. To these 3 genes, the significantly differential expression had been confirmed between cynomolgus macaques and Chinese rhesus macaques. Results: Molecular evolution analysis showed that mutations of DNAJC22, DNAJC28, and HSF5 in Chinese rhesus macaques could enable them to gain the ability to rapidly regulate body temperature. The heat shock proteins provided an important function for Chinese rhesus macaques, allowing them to adapt to a wide range of temperatures and spread widely. The selection time that was estimated suggested that the cold adaptation of Chinese rhesus macaques coincided with the time that the modern human populations migrated northward from tropic regions to relatively cold regions, and the selection genes were similar. Conclusion: This study elucidated the evolutionary history of cynomolgus macaques and rhesus macaques from molecular adaptation. Furthermore, it provided an evolutionary perspective to reveal the different distribution and adaptation of macaques. Cynomolgus macaques is an ideal biomedical animal model to mimic human natural frostbite.

In-silico Analysis of Peroxidase from Raphanus Sativus

Background:: In-silico study plays an important role in bioinformatics. It is a fastexpanding field to modelling, predicting and explaining biological activity at the molecular level using computational methods. Peroxidases are heme or non-heme-containing key antioxidant enzyme belonging to the oxidoreductase family. They can bioremediate the different environmental pollutants such as dioxins, petroleum hydrocarbons, synthetic dyes, herbicides, pesticides, chlorinated hydrocarbons, different phenolic and nonphenolic compounds etc. The current work aims to extend knowledge among researchers in better understanding structure of peroxidase purified from Raphanus sativus by analysing it’s physicochemical properties, secondary structure prediction, and 3D modelling of protein sequences and its validation using a variety of conventional computational methods. Objective:: Using bioinformatics techniques, it is feasible to figure out the relationship between sequence, structure, and function using enzyme protein sequences. To improve catalytic efficacy, thermostability, structure prediction, and validation, in-silico studies of the protein sequences of several industrially important enzymes have been performed recently. Method:: The physical and chemical parameters of radish peroxidase was analysed by using protparam tool-Expasy. SOPMA, SWISS MODEL, PROCHECK, ERRAT and Verify3D tools were used for structural analysis and validation of peroxidase protein sequence of Raphanus Sativus. The Molecular Evolutionary Genetics Analysis (MEGA 11) tool was used to align the protein sequences automatically and manually using the query sequence and peroxidase from various plant sources. Interaction of Radish peroxidase with the different organic substrates like guaiacol, o-cresol, mcresol, p-cresol, hydroquinone, catechol, resorcinol, benzaldehyde and aniline were analysed by molecular docking technique. Result:: This research gave critical information regarding the properties and functioning of Raphanus sativus peroxidase. The computational molecular weight for the query protein sequence of radish peroxidase was found to be 37.503 KDa. The analysis of secondary structure prediction using SOPMA tool revealed that random coil (Cc) was present in the highest percentage as 39.18 %. From the instability index (II) value and the aliphatic index value it was confirmed that the protein was slightly unstable but thermally stable in a wide range of temperature. The phylogenetic tree constructed by Molecular Evolutionary Genetics Analysis (MEGA 11) server revealed that the peroxidase and other plant peroxidases had been evolved from a common ancestor. Molecular docking analysis revealed that all the ligand had binding energy > -4.0 Kcal/mol. The interaction involved in the docking of radish peroxidase with selected ligands were conventional hydrogen bond, pi-cation, alkyl, pi-alkyl, pi-pi stacked, pi-sigma, carbon hydrogen bond, pi-lone pair. Conclusion:: In summary, these in-silico investigations provide a strong basis for carrying out wetlab experiments to boost production, research for novel sources with a metagenomics strategy and attempt directed evolution to include desired functional features. From this study, we found the active site of the enzyme and the key amino acid residues that are used in the enzyme-ligand interaction. The novel information presented in this work will promote proteomics research and the development of novel bioinformatics techniques. The investigation of enzyme-ligand interactions will aid in the creation of a fresh approach to the synthesis of organic molecules.

Coronavirus Cryptic Landscape and Draft Genome of a Novel CoV Clade Related to MERS From Bats Circulating in Northeastern Brazil.

We identified seven distinct coronaviruses (CoVs) in bats from Brazil, classified into 229E-related (Alpha-CoV), Nobecovirus, Sarbecovirus, and Merbecovirus (Beta-CoV), including one closely related to MERS-like CoV with 82.8% genome coverage. To accomplish this, we screened 423 oral and rectal swabs from 16 different bat species using molecular assays, RNA sequencing, and evolutionary analysis. Notably, gaps in the spike-encoding gene led us to design new primers and perform Sanger sequencing, which revealed high similarities to MERS-related (MERSr) CoV strains found in humans and camels. Additionally, we identified key residues in the receptor-binding domain (RBD) of the spike protein, suggesting potential interactions with DPP4, the receptor for MERSr-CoV. Our analyses also revealed evidence of recombination involving our laboratory-produced sequences. These findings highlight the extensive genetic diversity of CoVs, the presence of novel viral lineages, and the occurrence of recombination events among bat CoVs circulating in Brazil, underscoring the critical role bats play as reservoirs for emerging viruses and emphasizing the necessity of ongoing surveillance to monitor the public health risks associated with CoV spillover events.

Evolutionary and functional divergence of Sfx, a plasmid-encoded H-NS homolog, underlies the regulation of IncX plasmid conjugation.

Conjugative plasmids are widespread among prokaryotes, highlighting their evolutionary success. Conjugation systems on most natural plasmids are repressed by default. The negative regulation of F-plasmid conjugation is partially mediated by the chromosomal nucleoid-structuring protein (H-NS). Recent bioinformatic analyses have revealed that plasmid-encoded H-NS homologs are widespread and exhibit high sequence diversity. However, the functional roles of most of these homologs and the selective forces driving their phylogenetic diversification remain unclear. In this study, we characterized the functionality and evolution of Sfx, a H-NS homolog encoded by the model IncX2 plasmid R6K. We demonstrate that Sfx, but not chromosomal H-NS, can repress R6K conjugation. Notably, we find evidence of positive selection acting on the ancestral Sfx lineage. Positively selected sites are located in the dimerization, oligomerization, and DNA-binding interfaces, many of which contribute to R6K repression activity-indicating that adaptive evolution drove the functional divergence of Sfx. We additionally show that Sfx can physically interact with various chromosomally encoded proteins, including H-NS, StpA, and Hha. Hha enhances the ability of Sfx to regulate R6K conjugation, suggesting that Sfx retained functionally important interactions with chromosomal silencing proteins. Surprisingly, the loss of Sfx does not negatively affect the stability or dissemination of R6K in laboratory conditions, reflecting the complexity of selective pressures favoring conjugation repression. Overall, our study sheds light on the functional and evolutionary divergence of a plasmid-borne H-NS-like protein, highlighting how these loosely specific DNA-binding proteins evolved to specifically regulate different plasmid functions.IMPORTANCEConjugative plasmids play a crucial role in spreading antimicrobial resistance and virulence genes. Most natural conjugative plasmids conjugate only under specific conditions. Therefore, studying the molecular mechanisms underlying conjugation regulation is essential for understanding antimicrobial resistance and pathogen evolution. In this study, we characterized the conjugation regulation of the model IncX plasmid R6K. We discovered that Sfx, a H-NS homolog carried by the plasmid, represses conjugation. Molecular evolutionary analyses combined with gain-of-function experiments indicate that positive selection underlies the conjugation repression activity of Sfx. Additionally, we demonstrate that the loss of Sfx does not adversely affect R6K maintenance under laboratory conditions, suggesting additional selective forces favoring Sfx carriage. Overall, this work underscores the impact of protein diversification on plasmid biology, enhancing our understanding of how molecular evolution affects broader plasmid ecology.

MEGA12: Molecular Evolutionary Genetic Analysis version 12 for adaptive and green computing.

We introduce the 12th version of the Molecular Evolutionary Genetics Analysis (MEGA) software. This latest version brings many significant improvements by reducing the computational time needed for selecting optimal substitution models and conducting bootstrap tests on phylogenies using maximum likelihood (ML) methods. These improvements are achieved by implementing heuristics that minimize likely unnecessary computations. Analyses of empirical and simulated datasets show substantial time savings by using these heuristics without compromising the accuracy of results. MEGA12 also implements an evolutionary sparse learning approach to identify fragile clades and associated sequences in evolutionary trees inferred through phylogenomic analyses. In addition, this version includes fine-grained parallelization for ML analyses, support for high-resolution monitors, and an enhanced Tree Explorer. MEGA12 can be downloaded from https://www.megasoftware.net.

Molecular detection and evolutionary analysis of porcine epidemic diarrhea virus in Henan and Shaanxi provinces in China.

Porcine epidemic diarrhea (PED) caused by porcine epidemic diarrhea virus (PEDV) is a highly contagious and devastating enteric disease of pigs characterized by diarrhea, dehydration and 80-100% mortality in piglets, leading to substantial economic losses in the global swine industry. To investigate the prevalence of PEDV in Henan and Shaanxi provinces of China from 2022 to 2023, a total of 87 clinical samples (including intestinal tissues and faeces) were collected from diseased piglets during outbreaks of diarrhea on pig farms. Of the 87 samples, 32 (36.7%) tested positive for PEDV by RT-PCR, and the complete S gene from nine positive samples and the ORF3 gene from 11 positive samples, all from different farms, were subsequently sequenced. Phylogenetic analysis based on S gene sequences showed that most of the nine PEDV isolates sequenced belonged to the G2a clade and were most closely related to variant strains of PEDV. However, two strains from Shaanxi (CH-SX1-2023 and CH-SX2-2023) belonged to the G2b subtype, and one strain from Henan (CH-HNC2-2023) belonged to the S-INDEL branch. Amino acid sequence comparisons showed that there were several amino acid substitutions and deletions in the S and ORF3 proteins of the PEDV strains from Henan and Shaanxi compared to the CV777 vaccine strain. Some of these mutations occurred in neutralizing epitopes, particularly COE and might therefore be associated with the ineffective protection provided by existing vaccines. These results will provide insights for better understanding of the epidemiological situation of PEDV in Henan and Shaanxi provinces between 2022 and 2023, and this information also contributes to the development of new strategies for the prevention and control of variant PEDV strains.

Biophysical and molecular evolutionary analysis reveals evidence of micro-evolution in the seminal fluid protein-Diazepam-binding inhibitor (DBI) of a Heliothine insect Helicoverpa armigera

Biophysical and molecular evolutionary analysis reveals evidence of micro-evolution in the seminal fluid protein-Diazepam-binding inhibitor (DBI) of a Heliothine insect Helicoverpa armigera

Genomics of a sexually selected sperm ornament and female preference in Drosophila.

Our understanding of animal ornaments and the mating preferences driving their exaggeration is limited by knowledge of their genetics. Post-copulatory sexual selection is credited with the rapid evolution of female sperm-storage organ morphology and corresponding sperm quality traits across diverse taxa. In Drosophila, the mechanisms by which longer flagella convey an advantage in the competition among sperm for limited storage space in the female, and by which female sperm-storage organ morphology biases fertilization in favour of longer sperm have been resolved. However, the evolutionary genetics underlying this model post-copulatory ornament and preference system have remained elusive. Here we combined comparative analyses of 149 Drosophila species, a genome-wide association study in Drosophila melanogaster and molecular evolutionary analysis of ~9,400 genes to elucidate how sperm and female sperm-storage organ length co-evolved into one of nature's most extreme ornaments and preferences. Our results reveal a diverse repertoire of pleiotropic genes linking sperm length and seminal receptacle length expression to central nervous system development and sensory biology. Sperm length development appears condition-dependent and is governed by conserved hormonal (insulin/insulin-like growth factor) and developmental (including Notch and Fruitless) pathways. Central developmental pathway genes, including Notch, also comprised the majority of a restricted set of genes contributing to both intraspecific and interspecific variation in sperm length. Our findings support 'good genes' models of female preference evolution.

Isolation, Identification, and Molecular Evolutionary Analysis of Infectious Hematopoietic Necrosis Virus (IHNV) from Farmed Rainbow Trout in Southwest China

IHNV troubled the salmon breeding industry in China for years, and it often causes large-scale deaths. To study the disease characteristics of IHNV and its epidemiology in China， this study isolated and sequenced the Whole genome of an IHNV strain (IHNV-SCCD) (GenBank No： OQ801357) from farmed diseased rainbow trout in Chengdu and compared 99 IHNV strains from China by mega.11. The IHNV-SCCD strain was isolated by using EPC cells. The complete genome sequence was determined and deposited in the NCBI database. Phylogenetic analysis showed that IHNV-SCCD belongs to the typical J gene group, recently with Sichuan strains. Except for BjLL strain and LN12-17 strain, the remaining 98 strains followed a single evolutionary path. Note that IHNV in Liaoning province is the fastest evolutionary. In addition to the geographical differences, the Xinjiang strains were closely related to the Yunnan strains, and some strains from Beijing were closely related to some strains from Sichuan. There were two evolutionary branches in Gansu and Qinghai; QH17, isolated from Qinghai, was most closely related to SX1704 from Shaanxi. These results suggest that the prevalence of IHNV in China was extremely wide, and the evolution rate was fast. It is necessary to strengthen the monitoring and prevention methods.

Analysis of the variations within Q. ilex L. and the evaluation of morphological types based on chloroplast and nuclear DNA sequences

Q. ilex evaluated within evergreen has wide geographic distribution in Mediterranean basin. Hybridization and gene flow are effective and frequently observed mechanisms in Q. ilex. Moreover, weak reproductive barrier between closely related taxa in the zones with geographical contact is another important state that increase genetic diversity within Q. ilex and then taxonomic problems. Two morphological types known as rotundifolia and ilex are defined based on the variations between Q. ilex populations appearing as a result of all these factors. However, it is still controversial situation whether morphological types: ilex and rotundifolia are subspecies of Q. ilex or two separate species. In this study, short DNA sequences that consist of matK gene-partial trnK gene intron of chloroplast DNA and ITS1-5.8S rRNA gene-ITS2 of nuclear DNA were used to overcome such difficulties and to reveal the variations between Q. ilex populations. All populations belonging to Q. ilex based on both barcoding regions were determined and examined using the Molecular Evolutionary Genetics Analysis (MEGA 11). The analysis such as base substitutions, variable and parsim-info sites, transitional and transversional base substitution ranges (%) and nucleotide frequencies (%) were performed and finally, Maximum Parsimony (MP) dendrograms for both barcoding regions were drawn to evaluate the populations belonging to Q. ilex in terms of their variations, phylogenetic-evolutionary relationships and taxonomic statues. Although both barcoding regions support the separation of Q. ilex populations based on different morphological types, especially, matK gene-partial trnK gene intron sequences exhibited more clear and informative results than ITS1-5.8S rRNA gene-ITS2 sequences.

First Molecular Characterization of Small Ruminant Lentiviruses in Hungarian Goat Population.

In 2023, a molecular study was conducted on the Hungarian goat population to determine genotypes and subtypes of small ruminant lentiviruses (SRLV) infecting these herds. Ten goat herds seropositive for SRLV infection according to a serosurvey conducted earlier in Hungary were selected, and 135 adult goats (>1 year old) were blood sampled. The two-stage nested real-time PCR (nRT-PCR) was used to detect proviral DNA of SRLV and distinguish between two main viral genotypes (A and B). PCR products were submitted for Sanger dideoxy sequencing, and phylogenetic and molecular evolutionary analyses were conducted on the 200-250 bp-long proviral DNA sequences from the end of long terminal repeat (LTR) region and beginning of gag gene using the MEGA11 software. Reference strains included strains most identical to Hungarian sequences according to the Standard Nucleotide BLAST and prototypic strains for the relevant genotypes and subtypes. Proviral DNA of SRLV was detected in goats from all ten tested herds. A single SRLV genotype was detected in 6 herds-genotype A in three herds and B also in three herds. In four herds, mixed infection with genotypes A and B was confirmed. In total, 110/135 seropositive goats tested positive in the nRT-PCR (81.5%): 49/110 goats (44.5%) for genotype A, 54/110 goats (49.1%) for genotype B, and 7/110 goats (6.4%) for both genotypes. Hungarian sequences belonged to subtypes A1/A18, A2, and subtype B1. This is the first study which shows that Hungarian goats are infected by SRLV belonging to both genotypes A and B.

The herd-level prevalence of caprine arthritis-encephalitis and genetic characteristics of small ruminant lentivirus in the Lithuanian goat population

Caprine arthritis-encephalitis (CAE) is a progressive disease of goats caused by small ruminant lentivirus (SRLV) and is considered as one of the most important threats for goat farming in developed countries. The disease prevalence has never been investigated in the Lithuanian goat population. Therefore, a descriptive cross-sectional study was carried out in 2021–2022 to determine if SRLV infection was present in the Lithuanian goat population and, in the case of a positive result, to estimate the true herd-level prevalence of SRLV infection and specify genotypes and subtypes of SRLV responsible for the infection. Thirty goat herds counting >5 adult goats were randomly selected and, in each herd, a representative sample of adult goats was blood-sampled and tested serologically for SRLV infection using a commercial ELISA. The herd was considered infected if at least one goat tested positive and the true herd-level prevalence of SRLV infection was estimated using the Bayesian approach. Seropositive animals were found in 17 / 30 herds (57 %; 95 % confidence interval: 39 %, 73 %). The true herd-level prevalence was 56 % (95 % credible interval: 36 %, 76 %). In 10 / 17 seropositive herds whose owners consented for resampling of seropositive goats, 1–5 seropositive goats were tested using the nested real-time PCR (nRT-PCR). Goats from 9 seropositive herds tested positive in the nRT-PCR: in 4 herds for genotype A, in 4 herds for genotype B, and in 1 herd – 2 goats for genotype B and 1 goat for genotype A. From each of 9 nRT-PCR-positive herds, 1 PCR product of each genotype was sequenced using Sanger method and the phylogenic tree was constructed using the neighbor-joining method in the Molecular Evolutionary Genetics Analysis software. Four herds turned out to be infected with B1 subtype (91 % identity with the prototypic strain), 3 herds with A2 subtype (90 %-92 % identity), and a herd with mixed infection was infected with B1 (91 % identity) and A2 subtype (90 % identity). In one herd, the only seropositive goat was found to be infected with the strain most closely related to the A1 subtype (80 % identity). This study shows for the first time that SRLV infection is present and widespread in the Lithuanian goat population and both classical SRLV genotypes, represented by quite typical subtypes A2 and B1, appear to be responsible for the infection.

Phylogenetic analysis of selected species of Asteraceae on the basis of RPS 11 Gene

The Asteraceae family is a prominent group of flowering plants found across the globe, with the exception of Antarctica. The Asteraceae family is a largest flowering family pivotal group in plant evolution and diversification. Despite its importance, the genetic diversity within this family remains understudied. We focused on the rps-11 gene, a chloroplast marker previously utilized in phylogenetic studies, to investigate its potential in resolving Asteraceae relationships. The focus was on examining genetic diversity within sixteen specifically chosen species from the Asteraceae family. This assessment was based on an analysis of a chloroplast gene responsible for encoding the ribosomal protein of the smaller subunit 11 (rps 11). Nearly 417 bp of rps 11 gene was amplified, sequenced, computationally translated into amino acid sequence and the data was used for phylogenetic analysis as well as for rps 11 protein structure predictions. Based on nucleotide and amino acid sequences phylograms were drawn with the help of Molecular Evolutionary Genetic Analysis (MEGA 6), which exhibited clear genetic relationship among species under investigation. The observed genetic distance was 0.02 for Maximum likelihood tree based on nucleotide sequences whereas it was 0.05 for phylogram based on amino acid sequences. These values revealed that amino acid-based tree has demonstrated greater diversity among selected species in comparison to nucleotides-based tree. On the basis of pair wise distance calculations, genetic divergence values were found within the range of 0.015–0.309. Moreover, 3D protein modeling for rps 11 protein of sixteen selected species was also carried out by iterative threading assembly refinement (I-Tasser) software. The models exhibiting the highest C-score were picked with satisfactory plot statistics (> 90%) and structurally validated by PROCHECK. Furthermore, Ramachandran plots displayed that the rps 11 protein structures of Tagetes minuta, Xanthium strumarium, Lactuca sativa and Chrysanthemum indicum have best feature models with > 90% of residues in the allowed region and ≤ 2% in the disallowed region. The research is not enough to stand alone to validate the viability of the rps11 gene as a prospective contender for phylogenetic analysis. İn future we will focus on the maximum genetic diversity theory for phylogenetic analysis of this family.

Evolutionary origins of the lysosome-related organelle sorting machinery reveal ancient homology in post-endosome trafficking pathways

The major organelles of the endomembrane system were in place by the time of the last eukaryotic common ancestor (LECA) (~1.5 billion years ago). Their acquisitions were defining milestones during eukaryogenesis. Comparative cell biology and evolutionary analyses show multiple instances of homology in the protein machinery controlling distinct interorganelle trafficking routes. Resolving these homologous relationships allows us to explore processes underlying the emergence of additional, distinct cellular compartments, infer ancestral states predating LECA, and explore the process of eukaryogenesis itself. Here, we undertake a molecular evolutionary analysis (including providing a transcriptome of the jakobid flagellate Reclinomonas americana), exploring the origins of the machinery responsible for the biogenesis of lysosome-related organelles (LROs), the Biogenesis of LRO Complexes (BLOCs 1,2, and 3). This pathway has been studied only in animals and is not considered a feature of the basic eukaryotic cell plan. We show that this machinery is present across the eukaryotic tree of life and was likely in place prior to LECA, making it an underappreciated facet of eukaryotic cellular organisation. Moreover, we resolve multiple points of ancient homology between all three BLOCs and other post-endosomal retrograde trafficking machinery (BORC, CCZ1 and MON1 proteins, and an unexpected relationship with the "homotypic fusion and vacuole protein sorting" (HOPS) and "Class C core vacuole/endosomal tethering" (CORVET) complexes), offering a mechanistic and evolutionary unification of these trafficking pathways. Overall, this study provides a comprehensive account of the rise of the LROs biogenesis machinery from before the LECA to current eukaryotic diversity, integrating it into the larger mechanistic framework describing endomembrane evolution.

THI1 Gene Evolutionary Trends: A Comprehensive Plant-Focused Assessment via Data Mining and Large-Scale Analysis.

Molecular evolution analysis typically involves identifying selection pressure and reconstructing evolutionary trends. This process usually requires access to specific data related to a target gene or gene family within a particular group of organisms. While recent advancements in high-throughput sequencing techniques have resulted in the rapid accumulation of extensive genomics and transcriptomics data and the creation of new databases in public repositories, extracting valuable insights from such vast data sets remains a significant challenge for researchers. Here, we elucidated the evolutionary history of THI1, a gene responsible for encoding thiamine thiazole synthase. The thiazole ring is a precursor for vitamin B1 and a crucial cofactor in primary metabolic pathways. A thorough search of complete genomes available within public repositories reveals 702 THI1 homologs of Archaea and Eukarya. Throughout its diversification, the plant lineage has preserved the THI1 gene by incorporating the N-terminus and targeting the chloroplasts. Likewise, evolutionary pressures and lifestyle appear to be associated with retention of TPP riboswitch sites and consequent dual posttranscriptional regulation of the de novo biosynthesis pathway in basal groups. Multicopy retention of THI1 is not a typical plant pattern, even after successive genome duplications. Examining cis-regulatory sites in plants uncovers two shared motifs across all plant lineages. A data mining of 484 transcriptome data sets supports the THI1 homolog expression under a light/dark cycle response and a tissue-specific pattern. Finally, the work presented brings a new look at public repositories as an opportunity to explore evolutionary trends to THI1.

Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the Embecovirus subgenus.

There are several examples of coronaviruses in the Betacoronavirus subgenus Embecovirus that have jumped from an animal to the human host. Studying how evolutionary factors shape coronaviruses in non-human hosts may provide insight into the coronavirus host-switching potential. Equids, such as horses and donkeys, are susceptible to equine coronaviruses (ECoVs). With increased testing prevalence, several ECoV genome sequences have become available for molecular evolutionary analyses, especially those from the United States of America (USA). To date, no analyses have been performed to characterize evolution within coding regions of the ECoV genome. Here, we obtain and describe four new ECoV genome sequences from infected equines from across the USA presenting clinical symptoms of ECoV, and infer ECoV-specific and Embecovirus-wide patterns of molecular evolution. Within two of the four data sets analyzed, we find evidence of intra-host evolution within the nucleocapsid (N) gene, suggestive of quasispecies development. We also identify 12 putative genetic recombination events within the ECoV genome, 11 of which fall in ORF1ab. Finally, we infer and compare sites subject to positive selection on the ancestral branch of each major Embecovirus member clade. Specifically, for the two currently identified human coronavirus (HCoV) embecoviruses that have spilled from animals to humans (HCoV-OC43 and HCoV-HKU1), we find that there are 42 and 2 such sites, respectively, perhaps reflective of the more complex ancestral evolutionary history of HCoV-OC43, which involves several different animal hosts.IMPORTANCEThe Betacoronavirus subgenus Embecovirus contains coronaviruses that not only pose a health threat to animals and humans, but also have jumped from animal to human host. Equids, such as horses and donkeys are susceptible to equine coronavirus (ECoV) infections. No studies have systematically examined evolutionary patterns within ECoV genomes. Our study addresses this gap and provides insight into intra-host ECoV evolution from infected horses. Further, we identify and report natural selection pattern differences between two embecoviruses that have jumped from animals to humans [human coronavirus OC43 and HKU1 (HCoV-OC43 and HCoV-HKU1, respectively)], and hypothesize that the differences observed may be due to the different animal host(s) that each virus circulated in prior to its jump into humans. Finally, we contribute four novel, high-quality ECoV genomes to the scientific community.

Forensic characteristics of 38 Y-STR loci in the Hui population from Shaanxi Province, Northwest China

In this study, we genotyped 939 unrelated healthy individuals to investigate the genetic polymorphisms of 38 Y chromosome short tandem repeats(Y-STRs) loci included in the Yfiler™ Platinum kit in the Hui population of Shaanxi Province. Comprehensive population comparisons were performed using analysis of molecular variance(AMOVA), multidimensional scaling(MDS), and molecular evolutionary genetics analysis(MEGA) to explore population relationships. The allele frequencies of the single-copy loci ranged from 0.001 to 0.940 (DYS645), while those of the multi-copy loci ranged from 0.001 to 0.138 (DYS527). The highest genetic diversity (GD) value was observed for DYS385 (0.9723), and the lowest for DYS645 (0.1138). A total of 849 distinct haplotypes were identified among the 939 Hui individuals, with 808 (95.2 %) being unique. Haplotype diversity (HD), haplotype match probability, and discriminatory power (DC) in the Shaanxi Hui population were 0.9996, 0.0015, and 0.9041, respectively. Interpopulation comparisons based on Rst genetic distance values, phylogenetic trees, and MDS indicated that the Shaanxi Hui population has a close genetic relationship with the Ningxia Hui, Qinghai Hui, Xinjiang Hui, and Yunnan Hui populations. The population genetic stratification largely coincides with geographic distribution and language families. Our study revealed that the 38 Y-STR loci exhibit high genetic polymorphisms in the Hui population from Shaanxi Province.

Genome-Wide Identification of the Remorin Gene Family in Poplar and Their Responses to Abiotic Stresses.

The Remorin (REM) gene family is a plant-specific, oligomeric, filamentous family protein located on the cell membrane, which is important for plant growth and stress responses. In this study, a total of 22 PtREMs were identified in the genome of Populus trichocarpa. Subcellular localization analysis showed that they were predictively distributed in the cell membrane and nucleus. Only five PtREMs members contain both Remorin_C- and Remorin_N-conserved domains, and most of them only contain the Remorin_C domain. A total of 20 gene duplication pairs were found, all of which belonged to fragment duplication. Molecular evolutionary analysis showed the PtREMs have undergone purified selection. Lots of cis-acting elements assigned into categories of plant growth and development, stress response, hormone response and light response were detected in the promoters of PtREMs. PtREMs showed distinct gene expression patterns in response to diverse stress conditions where the mRNA levels of PtREM4.1, PtREM4.2 and PtREM6.11 were induced in most cases. A co-expression network centered by PtREMs was constructed to uncover the possible functions of PtREMs in protein modification, microtube-based movement and hormone signaling. The obtained results shed new light on understanding the roles of PtREMs in coping with environmental stresses in poplar species.

Comparative Plastomics of Plantains (Plantago, Plantaginaceae) as a Tool for the Development of Species-Specific DNA Barcodes.

Plantago (plantains, Plantaginaceae) is a cosmopolitan genus including over 250 species used as functional foods, forage, and traditional medicine. Among them, Plantago lanceolata is commonly used as an ingredient of herbal products, but the close similarity to other Plantago species can cause misidentifications with potentially serious consequences for product safety/quality. To test the possibility of developing species-specific barcoding markers, we de novo assembled plastome sequences of individuals of Plantago argentea, Plantago atrata, P. lanceolata, and Plantago maritima. These genomes were characterized in comparison with both previously sequenced conspecific accessions and other publicly available plastomes, thus providing an assessment of both intraspecific and interspecific genetic variation in Plantago plastomes. Additionally, molecular evolutionary analyses indicated that eleven protein-coding genes involved in different plastid functions in Plantago plastomes underwent positive selection, suggesting they might have contributed to enhancing species' adaptation during the evolutionary history of Plantago. While the most variable mutational hotspots in Plantago plastomes were not suitable for the development of species-specific molecular markers, species-specific polymorphisms could discriminate P. lanceolata from its closest relatives. Taken together, these results highlight the potential of plastome sequencing for the development of molecular markers to improve the identification of species with relevance in herbal products.