Evolutionary Genetics Analysis Research Articles

Positive selection analyses identify a single WWE domain residue that shapes ZAP into a more potent restriction factor against alphaviruses.

The host interferon pathway upregulates intrinsic restriction factors in response to viral infection. Many of them block a diverse range of viruses, suggesting that their antiviral functions might have been shaped by multiple viral families during evolution. Host-virus conflicts have led to the rapid adaptation of host and viral proteins at their interaction hotspots. Hence, we can use evolutionary genetic analyses to elucidate antiviral mechanisms and domain functions of restriction factors. Zinc finger antiviral protein (ZAP) is a restriction factor against RNA viruses such as alphaviruses, in addition to other RNA, retro-, and DNA viruses, yet its precise antiviral mechanism is not fully characterized. Previously, an analysis of 13 primate ZAP orthologs identified three positively selected residues in the poly(ADP-ribose) polymerase-like domain. However, selective pressure from ancient alphaviruses and others likely drove ZAP adaptation in a wider representation of mammals. We performed positive selection analyses in 261 mammalian ZAP using more robust methods with complementary strengths and identified seven positively selected sites in all domains of the protein. We generated ZAP inducible cell lines in which the positively selected residues of ZAP are mutated and tested their effects on alphavirus replication and known ZAP activities. Interestingly, the mutant in the second WWE domain of ZAP (N658A) is dramatically better than wild-type ZAP at blocking replication of Sindbis virus and other ZAP-sensitive alphaviruses due to enhanced viral translation inhibition. The N658A mutant is adjacent to the previously reported poly(ADP-ribose) (PAR) binding pocket, but surprisingly has reduced binding to PAR. In summary, the second WWE domain is critical for engineering a more potent ZAP and fluctuations in PAR binding modulate ZAP antiviral activity. Our study has the potential to unravel the role of ADP-ribosylation in the host innate immune defense and viral evolutionary strategies that antagonize this post-translational modification.

Genetic diversity and prevalence of emerging Rickettsiales in Yunnan Province: a large-scale study

BackgroundRickettsia and related diseases have been identified as significant global public health threats. This study involved comprehensive field and systematic investigations of various rickettsial organisms in Yunnan Province.MethodsBetween May 18, 2011 and November 23, 2020, field investigations were conducted across 42 counties in Yunnan Province, China, encompassing small mammals, livestock, and ticks. Preliminary screenings for Rickettsiales involved amplifying the 16S rRNA genes, along with additional genus- or species-specific genes, which were subsequently confirmed through sequencing results. Sequence comparisons were carried out using the Basic Local Alignment Search Tool (BLAST). Phylogenetic relationships were analyzed using the default parameters in the Molecular Evolutionary Genetics Analysis (MEGA) program. The chi-squared test was used to assess the diversities and component ratios of rickettsial agents across various parameters.ResultsA total of 7964 samples were collected from small mammals, livestock, and ticks through Yunnan Province and submitted for screening for rickettsial organisms. Sixteen rickettsial species from the genera Rickettsia, Anaplasma, Ehrlichia, Neoehrlichia, and Wolbachia were detected, with an overall prevalence of 14.72%. Among these, 11 species were identified as pathogens or potential pathogens to humans and livestock. Specifically, 10 rickettsial organisms were widely found in 42.11% (24 out of 57) of small mammal species. High prevalence was observed in Dremomys samples at 5.60%, in samples from regions with latitudes above 4000 m or alpine meadows, and in those obtained from Yuanmou County. Anaplasma phagocytophilum and Candidatus Neoehrlichia mikurensis were broadly infecting multiple genera of animal hosts. In contrast, the small mammal genera Neodon, Dremomys, Ochotona, Anourosorex, and Mus were carrying individually specific rickettsial agents, indicating host tropism. There were 13 rickettsial species detected in 57.14% (8 out of 14) of tick species, with the highest prevalence (37.07%) observed in the genus Rhipicephalus. Eight rickettsial species were identified in 2375 livestock samples. Notably, six new Rickettsiales variants/strains were discovered, and Candidatus Rickettsia longicornii was unambiguously identified.ConclusionsThis large-scale survey provided further insight into the high genetic diversity and overall prevalence of emerging Rickettsiales within endemic hotspots in Yunnan Province. The potential threats posed by these emerging tick-borne Rickettsiales to public health warrant attention, underscoring the need for effective strategies to guide the prevention and control of emerging zoonotic diseases in China.Graphical

Insecticide resistance status and bar-codingof dengue vectors in three districts of Tamil Nadu, India.

Occurrence and distribution of vector population are crucial for entomological study in context of prevention, control and elimination of vector-borne diseases. To update some entomological aspects in three districts of Tamil Nadu state namely Kumbakonam, Nagapattinam and Thriuvarur districts, the study was undertaken. The objective of the study was to understand the prevalence of mosquitoes; to assess insecticide resistance and phylogenetic analysis of dengue vectors [Aedes (Ae.) aegypti and Ae.albopictus]. The immature stages of mosquitoes were collected from different localities by standard WHO methods marking with GPS and mapping was done using ArcGIS 10.4 software for all three districts. Insecticide resistance test was conducted using WHO susceptibility test kits. The F1 generation of female adult mosquitoes of Ae. aegypti and Ae. albopictus were exposed to DDT 4% and Malathion 5% with the control paper of Risella oil and olive oil respectively. Further, genomic DNA of individual mosquito was isolated, and the sequencingwas done through Eurofins, Bangalore, India. The FASTA sequence was analyzed and the phylogenic tree was constructed using the Maximum likelihood method in Molecular Evolutionary Genetics Analysis (MEGA) software (version 10.0). A totally 5307 specimens were collected through expanded survey in all three study areas. The collection yielded 16 species from six genera of mosquitoes. In total collection, the Ae. albopictus was the dominant species in Kumbakonam and Thiruvarur districts and Ae. aegypti was dominant in Nagapattinam district. The predominant breeding sources were discarded tyre with rainwater, plastic cups, coconut shells, aluminum vessels, sliver containers, bottles, grinding stones and earthen pots etc. The study revealed high pupal indices in all three study areas. Insecticide resistance monitoring revealed possible resistance in Ae. aegypti against DDT in all three districts whereas against Malathion, possible resistance was recorded in Kumbakonam and Nagapattinam and in Thiruvarur district, the species was found to be susceptible. Ae. albopictus showed resistance against DDT in all three districts but susceptible to Malathion. The sequences obtained for Dengue vectors showed 99% similar with Genbank. The phylogenetic tree was constructed using COI region sequences. Certainly, observed the different genetic relationship among Ae. aegypti and Ae. albopictus between the study areas. The study confirmed the presence of Ae. aegypti and Ae. albopictus in all three districts. The study further revealed that these vectors are susceptible to Malathion but resistance to DDT. The continue surveillance of dengue vector and monitoring of insecticide resistance will strengthen the control programme for appropriate vector control measurements.

Functional analysis of basidiomycete specific chitin synthase genes in the agaricomycete fungus Pleurotus ostreatus

Chitin is an essential structural component of fungal cell walls composed of transmembrane proteins called chitin synthases (CHSs), which have a large range of reported effects in ascomycetes; however, are poorly understood in agaricomycetes. In this study, evolutionary and molecular genetic analyses of chs genes were conducted using genomic information from nine ascomycete and six basidiomycete species. The results support the existence of seven previously classified chs clades and the discovery of three novel basidiomycete-specific clades (BI–BIII). The agaricomycete fungus Pleurotus ostreatus was observed to have nine putative chs genes, four of which were basidiomycete-specific. Three of these basidiomycete specific genes were disrupted in the P. ostreatus 20b strain (ku80 disruptant) through homologous recombination and transformants were obtained (Δchsb2, Δchsb3, and Δchsb4). Despite numerous transformations Δchsb1 was unobtainable, suggesting disruption of this gene causes a crucial negative effect in P. ostreatus. Disruption of these chsb2–4 genes caused sparser mycelia with rougher surfaces and shorter aerial hyphae. They also caused increased sensitivity to cell wall and membrane stress, thinner cell walls, and overexpression of other chitin and glucan synthases. These genes have distinct roles in the structural formation of aerial hyphae and cell walls, which are important for understanding basidiomycete evolution in filamentous fungi.

ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets.

Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.

Molecular Identification of Dominant Microbes in Kola nut (Cola nitida)

Kola nut is an important dehiscent fruit but its supply fails to meet the demand due to limitations such as inadequate post-harvest practices leading to spoilage during transportation and storage. Identification of microbial contaminants is a necessary step in reducing the loss. Hence, this work aimed at characterizing the genome of dominant fungus and bacteria associated with kola nut (Cola nitida). Samples of kola nuts were collected from Oje and Oja-oba markets in Ibadan, Nigeria. Isolates were extracted from the lesion region of the samples using the standard method. Macro-morphological and micro-morphological observations of the pure culture of the isolates were conducted. After genomic DNA extraction of fungal and bacterial isolates, Polymerase Chain Reaction (PCR) was carried out using Internal Transcribed Sequence (ITS 1 and ITS 4) and 27F primers for fungal and bacterial genome respectively. Sanger sequencing of the purified DNA fragments was conducted utilizing the Nimagen, BrilliantDye™ Terminator Cycle Sequencing Kit V3.1, BRD3-100/1000. Molecular Evolutionary Genetics Analysis (MEGA version 6) was used for phylogenetic analysis. The result revealed that one fungus and two bacteria were associated with kola nuts. The fungal isolate showed 100% identity with Aspergillus wentii from the National Center for Biotechnology Information data base. The fungus showed a good relationship with A. dimorphicus and A. europaeus. The two bacterial isolates were also identified through the phylogenic analysis as Bacillus cereus and B. subtilis. B. cereus is closely related to B. thuringiensis. This research provides background information on the Kola nut microbial contaminant. Keywords: Bacteria, Contaminant, Fungus, Identification, Primers, Sequencing

Analyses and Insights into Genetic Reassortment and Natural Selection as Key Drivers of Piscine orthoreovirus Evolution.

Piscine orthoreovirus (PRV) is a pathogen that causes heart and skeletal muscle inflammation in Salmo salar and has also been linked to circulatory disorders in other farmed salmonids, such as Oncorhynchus kisutch and Oncorhynchus mykiss. The virus has a segmented, double-stranded RNA genome, which makes it possible to undergo genetic reassortment and increase its genomic diversity through point mutations. In this study, genetic reassortment in PRV was assessed using the full genome sequences available in public databases. This study used full genome sequences that were concatenated and genome-wide reassortment events, and phylogenetic analyses were performed using the recombination/reassortment detection program version 5 (RDP5 V 5.5) software. Additionally, each segment was aligned codon by codon, and overall mean distance and selection was tested using the Molecular Evolutionary Genetics Analysis X software, version 10.2 (MEGA X version 10.2). The results showed that there were 17 significant reassortment events in 12 reassortant sequences, involving genome exchange between low and highly virulent genotypes. PRV sequences from different salmonid host species did not appear to limit the reassortment. This study found that PRV frequently undergoes reassortment events to increase the diversity of its segmented genome, leading to antigenic variation and increased virulence. This study also noted that to date, no reassortment events have been described between PRV-1 and PRV-3 genotypes. However, the number of complete genomic sequences within each genotype is uneven. This is important because PRV-3 induces cross-protection against PRV-1, making it a potential vaccine candidate.

Exploring the Relationship Between Growth Hormone Secretagogue Receptor (GHSR) Gene and Body Proportions in Bangkok Chickens: Insights from DNA Sequencing and Hin6I Enzyme-Restricted PCR-RFLP Analysis

The purpose of this study was to determine the diversity of the growth hormone secretagogue receptor (GHSR) gene and also to analyze the association of the GHSR gene with the body proportions of Bangkok chickens. A total of 125 Bangkok chickens were reared, and blood samples were taken. Bangkok chickens were kept in colony cages with ad libitum feeding and drinking. The GHSR gene polymorphism was determined using the PCR-RFLP method. The restriction enzyme used in this study was Hin6I. The data analyzed were indicators of body proportions, which included data on body weight, carcass weight, and commercial cut weight. Single nucleotide polymorphism (SNP) identification using the Molecular Evolutionary Genetics Analysis 7 program with reference number AB095994.1. Allele frequency values, genotype frequencies, and Hardy-Weinberg balance values were also analyzed. The association between the GHSR gene and the traits observed in Bangkok chickens was analyzed using the T-test. The results of the study showed that the GHSR gene in Bangkok chickens had two genotypes, namely TT and CT. The values for Ho and He were 0.224 and 0.198, respectively. The genotype frequencies of TT and CT were 0.776 and 0.224, respectively. The two genotypes were associated with body weight, carcass weight, and commercial weight (p < 0.05). For all measured criteria, the TT genotype showed a higher weight value than the CT genotype. The GHSR gene has the potential to be used as a genetic marker for the selection process on body weight, carcass weight, and commercial weight traits.

Application of Nested-qPCR-High Resolution Melting (HRM) Technology on Strongyloides stercoralis Isolates from Iran.

Strongyloides stercoralis is a parasite with special characteristics presenting it as a unique nematode. Iran is an endemic area for S. stercoralis. In this study, nested-qPCR-high resolution melting (HRM) technology was applied on some human isolates of S. stercoralis from this country by focusing on evolutionary genetics analysis. Twelve human isolates of S. stercoralis were collected from four endemic provinces of Iran. Genomic DNA was extracted from a single filariform larva for every isolate. Using specific primers targeting partial regions in cox1 gene, nested-qPCR-HRM was performed and melting-curve profiles were analyzed alongside the evaluation of genetic proximity and phylogenetic analysis using MEGA7 and DnaSP5 software. The melting temperature (Tm) values of the isolates were 77.9°C-78.3°C. All isolates from Guilan, Mazandaran, and Khouzestan Provinces shared Tm values of 78.2°C to 78.3°C, while the isolates from Hormozgan Province showed Tm values of 77.9°C, 78.0°C, and 78.1°C. The phylogenetic tree illustrated that thesequences of the current study included nine haplotypes. Tajima's D index analyses showed that cox1 gene in S. stercoralis isolates was negative (Tajima's D = - 0.27). The isolates were divided into five temperature groups. Although HRM assay compared to PCR sequencing identified more limited genetic changes, it revealed that the mean of Tm of the isolates from Hormozgan Province was lower than those of other provinces and represented specific haplotypes for this geographical region on the phylogenetic tree.

Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia.

The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia. In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software. Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.

Diversity of astroviruses in wild animals in Yunnan province, China

BackgroundAstroviruses (AstVs) are single-stranded RNA viruses that have been detected in a wide range of mammals and birds. They are associated with numerous interspecies transmissions and viral recombination events, posing a threat to human and animal health.MethodsWe collected 1,333 samples from wild animals, including bats, rodents, wild boars, and birds, from various states and cities in the Yunnan Province, China, between 2020 and 2023 to investigate the presence of AstVs. AstVs were detected using a polymerase chain reaction targeting the RdRp gene. Finally, the Molecular Evolutionary Genetics Analysis software was used to construct the phylogenetic tree.ResultsThe overall positivity rate for AstVs was 7.12% in four species, indicating their widespread occurrence in the region. High genetic diversity among AstVs was observed in different animal species, suggesting the potential for interspecies transmission, particularly among rodents and birds. Additionally, we identified a novel AstV strain and, for the first time, provided information on the presence of bastroviruses in Yunnan, China.ConclusionsThe widespread distribution and high genetic diversity of AstVs, along with the observed potential for interspecies transmission, highlight the importance of further investigation and surveillance in the region. The findings emphasize the need for increased attention to AstVs and their potential impact on human and animal health in Yunnan and other regions.

Avian infectious bronchitis virus (AIBV) review by continent.

Infectious bronchitis virus (IBV) is a positive-sense, single-stranded, enveloped RNA virus responsible for substantial economic losses to the poultry industry worldwide by causing a highly contagious respiratory disease. The virus can spread quickly through contact, contaminated equipment, aerosols, and personal-to-person contact. We highlight the prevalence and geographic distribution of all nine genotypes, as well as the relevant symptoms and economic impact, by extensively analyzing the current literature. Moreover, phylogenetic analysis was performed using Molecular Evolutionary Genetics Analysis (MEGA-6), which provided insights into the global molecular diversity and evolution of IBV strains. This review highlights that IBV genotype I (GI) is prevalent worldwide because sporadic cases have been found on many continents. Conversely, GII was identified as a European strain that subsequently dispersed throughout Europe and South America. GIII and GV are predominant in Australia, with very few reports from Asia. GIV, GVIII, and GIX originate from North America. GIV was found to circulate in Asia, and GVII was identified in Europe and China. Geographically, the GVI-1 lineage is thought to be restricted to Asia. This review highlights that IBV still often arises in commercial chicken flocks despite immunization and biosecurity measures because of the ongoing introduction of novel IBV variants and inadequate cross-protection provided by the presently available vaccines. Consequently, IB consistently jeopardizes the ability of the poultry industry to grow and prosper. Identifying these domains will aid in discerning the pathogenicity and prevalence of IBV genotypes, potentially enhancing disease prevention and management tactics.

Mycotoxic effects of entomopathogenic fungi of fall armyworm (Spodoptera frugiperda J.E. Smith) on poultry feed safety

This study was carried out to analyze mycotoxins of entomopathogenic fungi of fall armyworm (Spodoptera frugiperda J.E. Smith) and poultry feed safety. An experiment was set up to assess the types of mycotoxins produced by entomopathogenic fungal parasite of fall armyworm larvae and their subsequent effect on the safety of the larvae as a feed ingredient. Molecular characterization was done to estimate the diversity of entomopathogenic fungi on fall armyworm larvae specimens from the treatment plots. Sequenced data was analyzed and processed using Molecular Evolutionary Genetic Analysis 6.0 software. The results showed relative diversity of fall armyworm larvae with 11 species isolated belonging to Aspergillus, Penicillium, Fusarium, Trichoderma, Bipolaris and Irpex genus. Some of these are potential mycotoxin producing fungi. Although isolated fungi potentially produce Ochratoxin, Fumonisin, Zearalenone and Trichothecene mycotoxins, only aflatoxins were analyzed in this study. About 3.98 μg /kg of aflatoxin was observed using the ELISA total assay which is within the threshold toxicity levels set in Kenya for feed of about 20 μg /kg. While this is under the threshold set by Kenya, it is still enough to cause concern as the cumulative exposure of even low doses can have impacts. This study therefore concludes that, Spodoptera frugiperda can be potentially contaminated with aflatoxins and when formulating poultry diets, there is need to monitor production so that the quality is not compromised and feed safety is ensured. Further studies are recommended to determine how much produced aflatoxins are then transferred into the poultry products such as eggs and meat.

PHYLOGENETIC RELATIONSHIP BETWEEN RABIES VIRUS (RABIES LYSSAVIRUS) VARIANTS FROM TWO DIFFERENT HOST SPECIES

Rabies is a fatal zoonotic disease that affects several mammals. Bats are recognized hosts of the rabies virus, and their main food source is the blood of other mammals, particularly cattle. During feeding, bats transmit the virus to cattle, which are victims of the disease, contributing to economic losses and increasing the risk of infection for humans. Based on this affinity in the rabies cycle between bats and cattle, the objective of this study was to analyze the phylogenetic relationships of rabies virus samples in cattle and bats. The G gene of the rabies virus was chosen for this study because it is directly related to the infection process. Nucleotide sequences of the viral G gene were selected from GenBank for samples obtained from infected cattle and bats. Maximum parsimony analyses were conducted using the Molecular Evolutionary Genetics Analysis software. The Maxima Parsimony tree indicated a phylogenetic relationship between the G genes of both hosts, indicating that the virus evolved from bats to cattle. Analysis of parsimoniously informative sites revealed that the viral G gene carried specific mutations in each host. Knowledge of the evolutionary relationships between the rabies virus and its hosts is critical for identifying potential new hosts and the possible routes of infection for humans.

The interest of informative ancestry markers (AIM) and their fields of application

This review focuses on the study of biogeographic ancestry using the Accurate Ancestry Identification Panel. Autosomal markers may provide little information about the nature of an individual's admixture due to ongoing human recombination and migration. Biogeographic ancestry assessment (BGA) is a term used to describe ancestry through DNA testing. This is usually accomplished by testing specific regions of DNA called ancestry information markers (AIMs). AIMs are chosen because they expose significantly different frequencies between different populations in different parts of the world. The panels of these AIMs can be assessed using next-generation sequencing (NGS) to predict the geographical origins of a person of interest's ancestors, usually in terms of continent of origin, and sometimes by smaller geographic regions. The use of ancestry informative markers (AIM) to identify genomic ancestry can be useful for a variety of studies in evolutionary genetics, biomedical research, and forensic analyses. However, there remains a major challenge in determining AIMs for populations with complex and highly mixed ancestry.

Molecular characterization of the ligninolytic Sundarban mangrove isolate Stenotrophomonas maltophilia GD1 and its promising applications in the dye and fiber industry

Lignocellulolytic biocatalysts, including laccase, cellulase, and pectinase, have high potential for degrading lignocellulosic biomass (LCB). Jute and banana are fiber-producing LCBs that hold significant economic value. Nevertheless, certain parts of these plants are utilized as waste material due to their low-quality fiber, which causes losses for the industry. These waste portions can be processed and biologically converted into high-value fiber. A bacterial strain called Stenotrophomonas maltophilia GD1, which can produce several proteins, was isolated from the Sundarban mangrove ecosystem in West Bengal, India, and genetically analyzed via 16S rRNA sequencing. The strain exhibited the ability to produce all three necessary lignocellulolytic enzymes, with the highest levels of laccase and minimal cellulase and pectinase activity. The strain modified the fibers extensively, as determined by Young’s modulus, and removed the color from the toxic industrial dyes. This demonstrates the broad potential of this strain for waste valorization and environmental remediation. Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) confirmed the enhanced fiber quality. Microbial phylogenetic relationships were established using Molecular Evolutionary Genetics Analysis version 11 (MEGA 11).

Single Nucleotide Polymorphism R25C and R25H on Leptin gene and their association with body weight and measurements of Pasundan cattle

Abstract. Hilmia N, Ramdani D, Hidayat R, Widyastuti R, Hernaman I, Dudi, Edianingsih P, Arifin J. 2023. Single Nucleotide Polymorphism R25C and R25H on Leptin gene and their association with body weight and measurements of Pasundan cattle. Biodiversitas 24: 6310-6315. The Leptin gene is a potential candidate for genetic selection in livestock. Nonsynonimous Single Nucleotide Polymorphisms (SNP) Arg25Cys/R25C in Leptin gene associated with fat deposition mainly. This study aimed to identify polymorphism of Leptin Gene based on SNPs of Pasundan cattle and their association with body weight and measurements. This research used 64 DNA samples along with the corresponding body weight and measurement data from Pasundan cattle. About 9 and 7 DNA samples from Bali and Ongole cross (PO) cattle respectively, were also collected as comparisons. The DNA along 620 bp was multiplied by PCR. The SNPs in the Leptin gene on exon two were identified, followed by direct sequencing of the PCR product. The sequencing results were analyzed by BioEdit and Molecular Evolutionary Genetic Analysis (MEGA) 4.0. The General Linear Model analyzed the association between SNPs and body weight and measurements. The results showed there were two nonsynonymous SNP in the Leptin gene on exon two, i.e. g.1047C>T/Arg25Cys/R25C (T allele) that changed amino acid Arginine to Cysteine and g.1048G>A/Arg25His/R25H (A allele) which changed Arginine to Histidine. The frequency of the C allele in the Leptin gene on Pasundan cattle (0.54) was higher than mutation alleles, i.e. T ( 0.29) and A allele (0.17). There were six genotypes: CC (0.266), CT (0.390), CA (0.156), TT, TA, and AA 0.063 respectively. The Leptin gene mutation at the 25th position of amino acids, which changed Arginin to Cystein or Histidin (R25C and R25H), did not affect body weight and measurement in Pasundan Cattle. Therefore, nonsynonymous SNP R25C and R25H could not be used as marker genetic selection in Pasundan cattle.

Barkodlama Bölgesi Olarak Potentilla L. Cinsinde psbA-trnH IGS Sekanslarının Değerlendirmesi

Barkodlama Bölgesi Olarak Potentilla L. Cinsinde psbA-trnH IGS Sekanslarının Değerlendirmesi

Molecular cloning and heterologous expression analysis of 1-Deoxy-D-Xylulose-5-Phosphate Synthase gene in Centella asiatica L.

Many genes involved in triterpenoid saponins in plants control isoprenoid flux and constitute the precursor pool, which is channeled into various downstream pathways leading to the synthesis of triterpenoid saponins in C. asiatica. Full-length 1-Deoxy-D-Xylulose-5-Phosphate-Synthase (CaDXS) gene was isolated for the study from the previously annotated Centella asiatica leaves transcriptomic data. The CaDXS gene sequence was submitted to the NCBI databases with GenBank accession number MZ997832. The full-length CaDXS gene contained a 2244 base pair open reading frame that encoded a 747 amino acid polypeptide. The predicted molecular weight (MW) and theoretical pI of DXS are 76.28 kDa and 6.86, respectively. Multiple amino acid sequence alignment of amino acids and phylogenetic studies suggest that CaDXS shares high similarities with DXS from other plants DXS belonging to different families. A phylogenetic tree was constructed using Molecular Evolutionary Genetic Analysis (MEGA) version 10.1.6. Structural analysis provided fundamental information about the three-dimensional features and physicochemical parameters of the CaDXS protein. Quantitative expression analysis showed that CaDXS transcripts were maximally expressed in leaf, followed by petiole, roots, and node tissues. CaDXS was cloned into the expression vector pET28a, expressed heterologously in DH5α bacteria, confirmed by sequencing, and subsequently characterized by protein expression and functional complementation. The study focused on understanding the protein structure, biological significance, regulatory mechanism, functional analysis, and gene characterization of the centellosides biosynthetic pathway gene DXS for the first time in the plant. It would provide new information about the metabolic pathway and its relative contribution to isoprenoid biosynthesis.

Morphogenetic Sharks of Genus Carcharinus Traded at Southwest Aceh Fish Landing Sites

Research on the types of sharks traded at the Southwest Aceh fish landing site was conducted in September 2022. The purpose of this study is to analyze the morphology and genetic analysis of sharks. Sampling uses purposive sampling techniques, for morphological analysis refers to shark identification books, while genetic analysis uses the Sanger method used at the sequencing stage. Morphological data analysis using Image-j software, for genetic analysis, using Mega 6 (Molecular Evolutionary Genetic Analysis). Morphological analysis was carried out at the Laboratory of Biosystematics and Marine Genetics, Faculty of Fisheries and Marine Sciences, Teuku Umar University. Genetic analysis was carried out at the Denpasar Biodiversity Laboratory, Bali. The results of this study found two species of sharks with a total of 8 individuals from the genus Carcharinus