جستجوی مقالات مرتبط با کلیدواژه "phylogenetic analysis" در نشریات گروه "کشاورزی"

In spring and summer 2023, a survey of plant samples from green spaces and ornamental greenhouses, along with adjacent weeds in Yazd City, showed symptoms likely linked to phytoplasma disease. Notable symptoms included stem flattening, phyllody, and yellowing observed in Angelica archangelica, Ligustrum sp., Mirabilis jalapa, and Hibiscus cannabinus. Five samples from each plant were sent to the Plant Virology Research Center at Shiraz University for DNA extraction via the CTAB method. Polymerase chain reaction (PCR) was conducted using general primers (P1/P7) and nested primers (R16MF2/R16MR2) specific for phytoplasma. As expected, fragments of 1800 bp and 1250 bp were amplified with the general and nested primers, respectively. These fragments were excised from the gel, purified, and sent to Sinohe Company for sequencing. Comparison of the sequences with those in the NCBI database using BLAST showed that the phytoplasmas from Angelica archangelica, Ligustrum sp., Mirabilis jalapa, and Hibiscus cannabinus were closely related to Indian (MH393563.1; host: Datura stramonium; identity: 98.94%), Turkish (HE649495.1; host: Ligustrum sp.; identity: 99.24%), Ugandan (HE649495.1; host: Hibiscus rosae; identity: 99.14%), and Iranian (KX685880.1; host: Eucalyptus sp.; identity: 98.64%) isolates. A phylogenetic tree was created to compare Iranian isolates with similar global isolates using MEGA 8.0 software.

 Vinca minor or lesser periwinkle is a perennial, herbaceous and creeping plant belonging to the genus Vinca and the family Apocynaceae. In addition to being an ornamental and cover plant, V. minor is a valuable herbal plant in traditional medicine, and it also acts as a natural source for the industrial manufacture of brain blood flow stimulants. Periwinkle contains more than 150  alkaloids, which have been isolated from the aerial parts and roots of the plant, so far (Proksa et al.,1988), consisting of vincaminorine, vincaminoreine, minovine, minovincine, vincamine, which has antihypoxic and neuroprotective properties as well as modulatory effects on brain circulation and neuronal homeostasis (Farahanikia et al., 2011). Vinca mosaic virus (VMV), belonging to the genus Potyvirus and the family Potyviridae, causes severe to mild mosaic symptoms, yellowing, blistering and leaf curl in the leaves of the periwinkle plant. In this study, the molecular and phylogenetic characteristics of two isolates of VMV were investigated via analysis of p1 and cp genes.

 Virus-like symptoms, such as mosaic and mottling, yellowing, blistering and leaf curling were found on the leaves of V. minor plants in the pardis campus of Ferdowsi University of Mashhad, Razavi Khorasan, Iran, during a survey in September 2019. Total RNA was extracted from the leaves with the SV Total RNA Isolation Kit to determine the causal agent(s) (Promega, USA). Deep sequencing was carried out on the samples by Macrogen Company in South Korea. Analysis of the results with CLC Genomics Workbench v.12.0.3 software showed that these plants were infected with two isolates of VMV. The cp and p1 gene sequences of VMV isolates were determined. Clustal Omega software was used to compare multiple sequence alignments among sequences and determine the percentage of identities at the nucleotide and amino acid levels. To determine phylogenetic relationships and evolutionary origin of Iranian VMV isolates, phylogenetic tree was drawn based on nucleotide and amino acid sequences of cp and p1 genes using MEGA 7 software and Maximum-Likelihood (ML) method with 1000 replications (Bootstrap). The SDT software (v.1.2) and Muscle sequencing were used to plot the similarity matrix among the isolates at the nucleotide and amino acid levels.

 The identities between the cp gene of two Iranian VMV isolates (VMV-IR-1 and VMV-IR-2) at the nucleotide (nt) and amino acid (aa) levels were 93.11% and 97.00% respectively. For the p1 gene, the obtained results showed 68.35% identity at the nt level and 97.00% at the aa level. The highest percent of nt identity of the VMV cp with other potyviruses in the GenBank was with ASV1 (asparagus virus 1) (75.00% with VMV-IR-1 and 73.82% with VMV-IR-2) VMV-IR-1 and VMV-IR-2 showed the highest aa identity with VDMV (vanilla distortion mosaic virus) (70.39%). The highest nt and aa identity of p1 gene of VMV isolates was with CatMV (catharanthus mosaic virus) (52.29% VMV-IR-1 and 51.31% with VMV-IR-2) and ZTMV (zucchini tigre mosaic virus) (28.70%), respectively. Protected motifs were also identified in the cp and p1 gene sequences. Dendrograms obtained from phylogenetic analysis based on nt and aa acid sequences of these genes placed two Iranian VMV isolates, along with other species of potyviruses in the GenBank, viruses in two and three separate groups respectively. Based on cp gene sequences, at the aa level Iranian VMV isolates is most closely related to yam mosaic virus (YMV) virus, and at the nt level with the closest viruses are include sweet potato virus 2 (SPV2), sugarcane mosaic virus (SCMV), onion yellow dwarf virus (OYDV) and johnsongrass mosaic virus (JGMV) in the same group. Based on the p1 gene sequences, VMV isolates at the nt level were most closely related to the JGMV virus and at the aa level were most closely related to the YMV and celery mosaic virus (CeMV) viruses.

 In this study, for the first time, the molecular properties of VMV isolates were determined based on the cp and p1 genes, and the phylogenetic position of two Iranian VMV isolates was drown. The results showed that the cp gene can be used for taxonomic purposes. Considering the medicinal and ornamental properties of periwinkle and effect of the viruses on its properties, special attention should be paid to viral diseases of this plant.

The aim of this investigation was to examine the alterations in the nucleotide sequence of CAPN2 and CAPN3 genes among a population consisting of nine Japanese quails. The study also aimed at determining the genetic diversity within these populations, as well as establishing their phylogeny relationship with other species. To achieve these goals, data on nucleotide sequences for both CAPN2 and CAPN3 were extracted from 62 different species available in World Gene Bank (NCBI), alongside that found for Japanese quail samples and analyzed using DnaSP software coupled with MEGA program techniques. The results showed that CAPN2 gene polymorphism was more than the CAPN3 gene in Japanese quail and as a result, the conserved regions in CAPN3 gene were more compared to the CAPN2 gene. The numerical value of dN/dS ratio for Japanese quail was estimated in the CAPN3 gene (0.94) and in the CAPN2 gene 0.68, which respectively indicate neutral selection and purifying selection on these two genes during evolution. The results of the neutral evolution test (Tajima's D) for CAPN2 and CAPN3 genes in all the discussed species were positive and more than one, which indicates positive selection for these genes in all the studied species. The findings of this investigation can aid in identifying the areas within CAPN2 and CAPN3 genes linked to distinct phenotypic traits seen in the examined species. Analysis of phylogeny revealed that these two genes have displayed varying evolutionary responses along different studied species,

The Saffron Latent Virus (SaLV) is new species in the Potyvirus genus, which has been recently characterized from Iran. Even though most of the symptoms on infected plants remain hidden, it causes considerable damage to saffron fields. There is no data available on the phylogenetic relationship among different strains of this virus based on its coat protein, despite its high incidence and economic significance. To address this, we collected 152 samples of saffron leaves, flowers, and corms from fields in South Khorasan and Razavi Khorasan provinces, both with and without symptoms like stunting, yellowing, and twisting. After extracting RNA, the presence of SaLV was examined using reverse transcription-polymerase chain reaction (RT-PCR) with specific primers targeting the coat protein. The findings revealed that 92 out of 152 samples (60%) were infected with the virus. Subsequently, seven representative samples, each from a selected region were sequenced. Phylogenetic analysis using MEGAX software showed that the virus strains formed two distinct groups, and the strains studied were placed in the second group. Interestingly, strains from the same geographical region and product were distributed among different groups, suggesting that geographical separation and host type did not significantly impact the viral diversity. This study is the first in detecting of SaLV in saffron flowers and corms and pinpointing the diversity of its new strains based on the coat protein in Iran.

Grapevine virus A (GVA) belongs to Vitivirus genus and is one of the most important causes of wood rugose in grapes. During the years 2019 to 2021, a total of 79 leaf samples showing symptoms of leaf yellowing and reddening from vineyards of Khorasan Razavi Province (including Bardaskan, Kashmar, Khalilabad, and Mohammadiyeh) were collected. The initial infection of the samples to GVA was directly checked using an ELISA test, and the final confirmation of results was performed by RT-PCR with specific primers. Total RNA extraction was performed from scraped bark of young stems using CTAB method. GVA was detected in 14 samples through the ELISA test, and a fragment of 238 base pairs from the p10 protein was amplified in these 14 samples using RT-PCR. The amplified products from four samples were ligated into the pTG19-T vector, and the recombinant plasmids were sequenced bidirectionally. The obtained sequences were compared with the other GVA sequences in GenBank using BlastN tool and the nucleotide similarity was 85.7-95%. The phylogenetic tree based on p10 protein showed there are four main groups, and Khorasan Razavi isolates classified within the fourth group. Comparison of p10-protein sequence of Iranian isolates with other isolates showed there is a conserved region in N-terminal region, which includes an arginine-rich motif followed by a zinc-finger motif. There have been many studies on other viruses of grape in this province, but this is the first study on ithe phylogenyof GVA isolates in the vineyards of Khorasan Razavi province.

AT-hook motif nuclear localization (AHL) proteins play a critical role in plant biological processes, and it is highly conserved in terrestrial plants. In Arabidopsis thaliana this gene family data is available. We used this data to detect and interpret the AHL gene family in the Cardamine hirsuta. In Silico analysis was launched and initially 29 AHL genes were detected. Phylogenetic analysis afterward exhibits that AHL in C. hirsuta has been grouped into two clades, clade B with 3-5 introns, and clade A intron-free similar to A. thaliana. According to the combination of AT-hook motif(s) and PPC domain, AHL proteins are divided into three subclades (sub-clades-I/-II/-III). Subclades-I are related to Clade-A, while subclades-II and subclades-III are related to Clade-B. The motif analysis exhibits that the three genes including AHL1, AHL10, and AHL11, although had the AT-hook motifs, lacked the PCC domain, and therefore the actual number of AHL family genes decreased to 26. Looking at duplication events in the AHL gene family in C. hirsuta, 16 homologous genes were found due to segmental duplication, and no tandem sequences were observed in these genes. In-depth inspection showed that segment genomic duplication events could cause the expansion of these genes. Examining ratios of non-synonymous (Ka) and synonymous (Ks) substitution rates, i.e. Ka/Ks, in 5 pairs of homologous genes showed those with Ka/Ks < 1 were exposed to the adverse selection. These findings reveal a possible evolutionary relationship for the AHL gene family in C. hirsuta, providing helpful information for future analysis to investigate their biological functions.

In the visits of the spring, summer, and autumn of 2021 and 2022 to the orchards of stone fruit trees in Golestan province, suspected symptoms of phytoplasma disease such as yellowness, deterioration, reddening, and small leaves were observed, and 28 samples of leaves from different hosts of stone fruit trees were collected. P1/P7 general primers were used for general PCR, and R16F2n/R16R2 primers were used for nested PCR. Infected samples amplified 1800 bp fragments in general PCR and 1250 bp fragment in nested PCR. Out of the 28 samples collected, 3 samples of peach trees had a band in the target area. The nested PCR product after sequencing was registered in the World Gene Bank with accession numbers OQ945143 and OP055811. At the same time, transplanting was done on the benchmark plant, Periwinkle, with the aim of gene storage and observation of phytoplasma symptoms. The comparison of the obtained sequences with the sequences available on the NCBI by the BLAST showed the most similarity to Aster yellows phytoplasmas, and the phylogenetic analysis of the target sequence with the maximum likelihood estimation algorithm in comparison with the different phytoplasma subgroups reported in Iran also showed the results confirmed the blast. Also, the comparison of patterns obtained from virtual RFLP identified the most similar reference pattern of the 16SrI group, subtype AD (GenBank accession: DQ286577), with a similarity coefficient of 0.77, which indicates that this strain may represent a new group. The results of this study confirm the presence of phytoplasma in peach trees in Golestan province for the first time and indicate the presence of a phytoplasma species close to Candidatus phytoplasma asteris in Golestan province.

Saffron is the most expensive spice in the world. The economic value of saffron is due to the existence of apocarotenoids in its stigma. Therefore, the isolation and characterization of genes involving in apocarotenoids metabolism is on particular importance. In this research, beacause the importance of CsUGT gene in crocin biosynthesis, it was isolated, cloned the E.coli strain DH5α. The full length gene was sequenced and registered in the NCBI. In order to characterize CsUGT gene, first the protein sequence was obtained, and then the physical and chemical characteristics and physiology of the CsUGT protein were analyzed by Protparam, SOPMA, ProtScale, Pfam, ProtComp, SignalP, TMHMM and ChloroP servers and tools. Also, using the Swiss-Model server, the 3D structure of this protein was investigated and Ramachandran diagram was drawn to validate the 3D drawn model structure. According to the results, CsUGT protein with 462 amino acids has the conserved sequence of glycosyltransferase family proteins and was identified as a polar protein, stable at high temperatures and without hydrophobic domain. CsUGT protein has no peptide signal or binding signals and has a cytoplasmic location. This research made it possible to isolate the CsGTS gene of saffron and optimized the conditions of its transfer into a vector. In addition, the results of CsUGT protein structure analysis provide the basis for future functional studies and can also provide valuable information regarding the behavior and reaction of this enzyme in the synthesis of saffron apocarotenoids. In addition, these results can be useful in the future programs of Iranian saffron genetic modification.

DNA Mitochondria is one of the most commonly molecular markers for phylogenetic studies in animals due to its simple genome structure, which presents an ideal model to study evolution and genetic similarity. The aim of the present study was to investigate the divergence and percentage of genetic similarity along with the phylogenetic analysis of the eight species of wild and domestic goat based on the complete sequence of the mitochondrial genome and the separate sequences of 13 protein-coding genes for each genome.

In the present study, complete mitochondrial genome sequences along with separate sequences of 13 protein-coding genes per each genome from seven wild species of goat including Markhor (C. falcoeri), Capra ibex, Capra nubiana, Capra pyrenaica, Capra sibirica, Capra caucasica, Capra aegagrus, and domesticated species of goat (Capra hircus) were retrieved from NCBI database and compared to each other. Mitochondrial genomes and genes alignment were accomplished by the MegAlign module of DNASTAR software and compared by the Clustal W method. The Sequence Distances sub-section of the MegAlign module of DNASTAR also was used for the analysis of complete genome and gene sequences divergence and similarity percentage. For phylogenetic analysis, complete mitochondrial genomes and protein-coding genes’ sequences were aligned using MEGA7 software.

Based on the analysis, it was found that the highest similarity between the nucleotide sequences of the complete genome (99.50) of domestic goat (Capra hircus) and wild Capra aegagrus goat and the lowest percentage of similarity (93.79) between the nucleotide sequences of the complete genome of the breed Capra nubiana) with wild goat Capra sibirica goat. Also, based on the results of the phylogenetic tree, it was found that domestic goat breeds (Capra hircus) and wild Capra aegagrus goat are divided into one group and wild Capra ibex and Capra pyrenaica breeds are divided into another distinct cluster.

In this study, all the results obtained from complete sequences of the mitochondrial genome analysis are consistent with the results obtained from the sequence of 13 protein coding genes per each genome, which indicates the correct clustering of wild and domestic goat breeds. Therefore, mitochondrial genome sequences could be used as a suitable genetic marker for accurate phylogenetic analysis and clustering of different species of sheep.

Squalane is an unsaturated triterpene that has wide applications in pharmaceuticals. In this research, the production of squalene and its bioinformatic analysis in four species of unicellular and multicellular eukaryotes and prokaryotes were investigated in order to determine the difference of this gene in eukaryotes and prokaryotes. The results of phylogenetic analysis showed that algae as multicellular eukaryotes, yeast as single-celled eukaryote and bacteria as single-celled prokaryote were placed in one group and plants were placed in a separate group. GC percentage of SQS protein was evaluated by GC Content Calculator, as well as aliphatic index and instability index by protparam. The results showed that the SQS gene is in a range from unstable to stable. The analysis of the presence of signal sequences and the analysis of the detection of the final location of the protein showed that the possibility of transferring the SQS protein to the mitochondria, chloroplast and secretory pathway is very low and it is not among the signal proteins. It was also found in Gymnema sylvestre that this protein has three protected domains. The comparison of the secondary structure of the protein confirmed the existence of alpha sheets. 3D modeling of this protein in plant was done by homology modeling method and using Swiss Model database after selecting a suitable model with high similarity which was extracted from PDB database. In order to validate the structure of the drawn three-dimensional model and stereochemical analysis, the Ramachandran diagram was drawn and the dihedral angles were calculated. The results of structural quality evaluation showed that the proposed models have good quality and stability. The study of the protein structure can help to understand the function of the protein, and studying the details of its structure can be useful in the studies of the active site of the protein and docking.

Iris spp. is reported to be affected by several viruses in the family Potyviridae including iris mild mosaic virus (IMMV), iris severe mosaic virus (ISMV), iris fulva mosaic virus,  bean yellow mosaic virus (BYMV), turnip mosaic virus (TuMV), ornithogalum mosaic virus (OrMV), narcissus latent virus (NLV), butterfly flower mosaic virus (BFMV), and gladiolus mosaic virus (tentative name). Narcissus latent virus (NLV) is a member of the genus Macluravirus in the family Potyviridae. It has non-enveloped flexuous filamentous virions of 657 nm long and 13 nm wide, which encapsidate a single-stranded, positive-sense RNA molecule of approximately 8,000 nt long. NLV is distributed widely throughout the major planting areas of Japan, New Zealand, and European countries. It is one of the most common viruses infecting narcissus, iris, gladiolus, and nerine, causing significant yield losses and quality deterioration in their bulbs and flowers. Due to the presence of asymptomatic infection of NLV in iris and narcissus, the relevance of its infection in host plants may be severely underrated. As Khorasan Razavi province is one of the major producing areas of ornamental plants in Iran, identification of this virus is a concern. In this study, we attempted to identify NLV infecting iris plants and compare Iranian NLV isolates with other sequences from different geographical regions to provide the first detailed information of phylogenetic characterization of this virus in Iran.

Iris leaf samples showing virus-like symptoms of leaf chlorosis and mosaic were collected from field-grown plants in Khorasan Razavi province. Total RNA was extracted from the field samples using Promega SV Total RNA Isolation Kit (USA). Reverse-transcription polymerase chain reaction (RT-PCR) was performed using specific primer pair CPU-F (5΄-CATTACACCCGACCTGGAACT-3΄) and CPU-R (5΄-CCATTTCAGGGCATTGGAGGA-3΄), which were designed to amplify a 1066 bp fragment of the 3΄-region of NLV genome (encompassing partial NIb (25 nt), complete CP (894 nt), and partial 3'UTR (147 nt)). PCR products and DNA ladder were separated by agarose gel electrophoresis, visualized using DNA Green viewer staining, and photographed with ultraviolet-illumination. Amplified fragments of the expected size were purified, cloned into pTG19-T vector and bi-directionally sequenced. Obtained sequences were phylogenetically compared with the corresponding isolates available in the GenBank after multiple alignments. The phylogenetic tree was constructed based on the nucleotide sequences of the CP-UTR using the neighbor-joining method by MEGA11.

Amplification product (1066 bp) was obtained from five infected samples, but not from healthy samples. The most typical symptoms in positive samples were mosaic, and interveinal chlorosis. Three selected PCR positive samples were cloned into the pTG19-T vector and sequenced. BLASTn analysis of the sequenced data revealed that the PCR-amplified fragments belonged to NLV. Three selected isolates which are referred to as IR, IR2, and IR3 were deposited in GenBank. The previously identified and conserved amino acid sequence motifs described in CP of macluraviruses were present in Iranian CP sequences. The phylogenetic tree placed the NLV sequences into two distinct phylogroups I and II; the Iranian isolates clustered together with isolates from Poland, New Zealand, and United Kingdom into group II. Phylogenetic analysis showed that Iranian isolates shared 77.47 to 98.12% nucleotide sequence identity and 77.70-99.34% amino acid sequence identity with other isolates of NLV. Also, identity of these three isolates in the nucleotide and amino acid levels ranged between 97 to 97.84% and 97.38 to 99.02%, with each other, respectively. Iranian isolates showed the highest nucleotide sequence identity with NLV5_1 isolate (JX270766) from Poland (between 97.65 to 98.12 %) and the lowest with NLV3 isolate (JX270762) from Poland (between 77.47 to 77.95 %).

NLV is a major constraint to iris and narcissus production worldwide. The phylogenetic analysis showed a low correlation between genetic and geographic distances which further emphasizing the importance of the exchange and use of virus-free propagating organs in preventing the dissemination of this virus. It seems that contaminated vegetative organs from some European countries (e.g. Netherlands), which are the major producer and the largest exporters of flowers and ornamentals in the world, can play a significant role in the worldwide distribution of the virus. Identification and the use of more isolates are recommended for a better understanding of the genetic structure and variation of NLV populations on a large geographical scale. The data obtained in this study will be beneficial to improve control strategies for this virus in Iran.

Diapause is a physiological adaptation that allows an organism to survive adverse environmental conditions. Sunn pest, Eurygaster integriceps (Heteroptera: Scutelleridae), is a key pest of wheat and barley and univoltine species and its life cycle has two different phases, reproductive phase, and adult stage diapause. In this study, the gene expression patterns of Hexamerin storage protein were evaluated by quantitative Real-Time PCR assay in diapause and non-diapause female insects, in the Sunn pest’s fat body. The Hexamerin gene expression in diapausing females of sunn pest was 6.4 times higher than in non-diapausing females. The results of subcellular localization and signal peptide prediction suggested that the protein was categorized as an extracellular protein. According to phylogenetic analysis and multiple alignment analysis of the Sunn pest’s Hexamerin amino acid sequence and other bugs belonging to the Hemiptera order, the amino acid sequence was placed at clade belonging to the Hemiptera order (with 100 bootstrap number) and revealed high similarity and closeness to brown marmorated stink bug, Halyomorpha halys Hexamerin gene amino acid sequence (identity 62.6%). Identifying the Hexamerin gene as a reliable biochemical indicator for Sunn pest diapause can be a proper and valuable candidate for further studies at the cellular and molecular levels in this pest.

Cucumber mosaic virus [CMV] is one of the most important viruses infecting cucurbits worldwide. To study CMV infections in cucurbit fields of Kavar region in Fars province, samples were collected from watermelon, melon and squash plants showing symptoms of mosaic, yellowing, necrotic spots and stunting. A total of 85 samples were collected during spring and summer 2014. The infection of samples was examined using DAS-ELISA and RT–PCR. The serological method confirmed the infection of 40 samples with CMV. The coat protein gene of the virus was amplified by RT-PCR, using primers P1 and P2, which confirmed the results of DAS-ELISA. The amplified genes of three isolates were sequenced and compared with 19 corresponding sequences from Genbank. Phylogenetic analysis was performed using MEGA6, by Neighbor-joining method. Sequenced were divided to two separate groups, and all Iranian sequences were placed in group A. The results of this study showed a significant infection with CMV in melon fields of Kavar region which may cause significant yield losses.