جستجوی مقالات مرتبط با کلیدواژه « فیلوژنی » در نشریات گروه « گیاهپزشکی »

More than 80 viral diseases of grapevines have been reported worldwide. The infectious degeneration disease complex causes growth reduction, stunting, shortening of internodes, bushy growth and decline in susceptible vines. Grapevine fanleaf viruses (GFLV), arabis mosaic virus (ArMV), grapevine deformation virus (GDefV), tomato ring spot virus (ToRSV) and tobacco ring spot virus (TRSV), which belong to the genus Nepovirus, are known to cause infectious degeneration. The genus Nepovirus has been divided into three subgroups A, B and C based on genome length, genomic organization, serological relationships, proteinase cleavage sites and the phylogenetic relationship of their coat protein (CP) gene. GDefV with the new name Nepovirus deformationis belongs to subgroup A of the genus Nepovirus and is closely related to ArMV and GFLV. Prevalence of GFLV in the vineyards of Iran raises the possibility that a mixed infection of GFLV and GDefV is also present in these areas. In Khorasan-Razavi Province, Iran's third-largest grape production center, research has addressed grape-affecting viruses with potential economic consequences, including reduced yield and product quality. Studying the distribution and genetic diversity of GDefV and other grape viruses is crucial for developing effective management and prevention strategies in the region's vineyards. In this study, GDefV was identified in the vineyards of Khorasan-Razavi province in Northeastern Iran and its complete genome was sequenced. In addition, the phylogenetic relationship of these isolates to other GDefV isolates deposited in GenBank was analyzed.

Samples from three grapevines were collected from a vineyard in Kashmer, Khorasan-Razavi Province; total RNA was extracted from the petiole of young leaves using the CTAB-PVPP method., GDefV and mixed infections of GDefV/GFLV were detected by PCR using specific primers. The PCR products were electrophoresed in a 1% agarose gel and sequenced. The miRNAs were extracted from grapevine petiole tissue using the modified CTAB method, and small RNA libraries were prepared using the TruSeq Small RNA Sample Prep Kit and sequenced on the Illumina Novaseq 6000 platform. After trimming the reads, contigs were generated using k-mer 15 in Velvet assembler 0.7.31. Contigs were verified using BLASTn and BLASTx in NCBI, and reconstruction of the GDefV genome from the NGS reads was performed using CLC Genomics Workbench (CLC Bio) software. Phylogenetic trees were generated in MEGA7 using the maximum likelihood (ML) method with 1000 replicates in the bootstrap test. The occurrence of possible recombinations in the GDefV genome was analyzed using the RDP v.6 package.

The samples showed leaf deformation, shortening of internodes, bushy growth, stunting and decline, but these symptoms are probably related to GFLV, and GDefV only causes leaf deformation in the infected vine. The PCR amplification and sequencing of a segment of the coat protein gene revealed a co-infection of GDefV and GFLV in the samples. GFLV is widely distributed in Iranian vineyards, GDefV has also been previously reported in the vineyards of northwestern Iran, but this is the first report of GDefV in the vineyards of Khorasan-Razavi Province.After refining the reads, approximately 15 million reads (92-99.7% of the original reads) remained for further analysis. The read sequences of each library were deposited in the Sequence Read Archive (SRA) under the accession number SAMN33747579-81. Three Iranian GDefV isolates obtained from three miRNA libraries were deposited in GenBank (accession numbers **-**).RNA1 and RNA2 of the three Iranian GDefV isolates had a length of 7386 and 3753 nucleotides, respectively. The RNA1 in GDefV had an open reading frame (ORF) of 6852 nucleotides in length, which started with the start codon AUG at position 288 and ended with the stop codons UAA or UAG at position 7142. The 5' end of the genome had 287 nucleotides long and contained two repeating sequences of 15 nucleotides that formed stem-loop structures. The length of the non-coding region at the 3' end had 244 nucleotides. Translation of RNA1 of the GDefV genome produces a polyprotein (p1) of 2285 amino acids (approximately 252 kda). The polyprotein p1 comprises the cofactor proteins proteinase, helicase, VPg, proteinase and polymerase with approximate weights of 45, 88, 3, 25 and 91 kDa, respectively. RNA2 also has one ORF, located between nucleotides 237 and 3560. This open reading frame also produces a 122 kDa polyprotein (P2) with 1108 amino acids. The second fragment of the GDeFV genome had 236 nucleotides as a 5'-noncoding region with three repeating sequences of 15 nucleotides that produced stem-loop structures with a 3-nucleotide loop and a 6bp stem. The 3'-noncoding region was also 193 nucleotides long. Polyprotein P2 comprised protein 2A, movement protein (MP) and coat protein (CP). The GDefV polyproteins had cysteine/alanine (C/A) and arginine/glycine (R/G) cleavage sites similar to those of the GFLV polyprotein. Comparison of the RNA1 sequences from three Iranian GDefV isolates with other GDefV isolates available in GenBank showed that the Iranian isolates had 88.1-92.2 % nucleotide identity with each other and 90.3-93.9 % with GenBank isolates at the nucleotide level. At the amino acid level, the Iranian isolates were 86.6-91.6 % identity with each other and 88.9-92.7 % with GenBank isolates. For RNA2, the Iranian isolates showed 89.4-92 % similar to each other and 89.6-94.2 % similar to GenBank isolates at the nucleotide level. The amino acid similarity between the Iranian GDefV isolates was 85-88.6 %. In the phylogenetic tree based on the nucleotide and amino acid sequences of RNA1 and RNA2 of the GDefV genome, the Iranian isolates of this study were clustered in a distinct clade than other GDefV isolates from Turkey (HE613269 and NC017939).GDefV was reported in 2003 and no further information is available on its distribution in vineyards around the world. GDefV has already been reported from Turkey and Iran, but the complete genome sequence of the Iranian GDefV isolate is being reported for the first time. Further studies on the population diversity of GDefV isolates in different regions of Iran are required to gain more insight into the mechanisms affecting the dynamics of GDefV populations.

The ant Cataglyphis bazoftensis Khalili-Moghadam Salata & Borowiec, 2021 has been recently described in Iran. Here, new materials of C. bazoftensis were collected from five new localities in Chaharmahal and Bakhtiari provinces, Iran. All the specimens examined were morphologically consistent with the description of C. bazoftensis. At the molecular level, based on a phylogenetic trees obtained from the mitochondrial Cytochrome C oxidase subunit I gene (COI), C. bazoftensis appears as the sister taxon of Cataglyphis kurdistanica Pisarski, 1965, separated from each other by a genetic distance of 9.79 %

Ash trees (Fraxinus spp.) are one of the most important ornamental trees in the green space of cities. To evaluate the fungi associated with decline and dieback of ash trees, the symptomatic samples from branches, trunks, and roots of two species of Fraxinus (European Fraxinus, F. excelsior and Van, F. rotundifolia) were collected from Ardabil and Namin during the summer and autumn of 2018–2019. From the 60 samples, 81 fungal isolates were recovered. Based on morphological features of all isolates together with sequence data of tef-1α gene and specific primers of some Fusarium and Neocosmospora species, 21 fungal species were identified, i.e., Alternaria, Chaetomium, Clonostachys, Cytospora, Fusarium, Microascus, Microsphaeropsis, Neocosmospora, Peyronellaea and Phialophora. Neocosmospora solani, Cytospora chrysosperma and F. oxysporum had the highest abundance, respectively. Pathogenicity test was performed by excised shoot for F. cerealis, F. equiseti, F. oxysporum and N. solani excided shoot method and for C. chrysosperma on excided shoot method and also on two years old ash saplings in greenhouse. Our results showed that all examined species except F. cerealis and F. equiseti cause discoloration of wood texture at the inoculation site. According to our knowledge, most of the fungal species identified in this study, are reported for the first time on ash trees worldwide. Besides, F. denticulatum is a new record to the Iranian mycobiota.

Fusarium rot is one of the most important diseases of beans (Phaseolus vulgaris). In order to identify Fusaria that cause bean root rot in Markazi Province (Iran), in the summer of 2018 and 2019, several bean fields were visited and infected plants with root rot were sampled and the fungi were isolated in the laboratory. Based on morphological and sequencing characteristics of internal transcribed spacers of rDNA (ITS) and translation elongation factor 1-α (EF-1α) gene regions, 37 Fusarium isolates, including Fusarium oxysporum species complex, F. solani species complex, and F. lateritium species complex, as well as F. equiseti, F. acuminatum and F. redolens were identified. All isolates caused root rot on Sadry bean cultivar. Since F. solani isolates were the most common, twelve isolates of this group were selected and their phylogenetic relationships were studied. Of the three Clades of F. solani species complex, the isolates were placed in Clade 2 and 3. Only one isolate was found in Clade 2 whose properties matched those of F. brasiliense. The other isolates were classified in Clade 3 divided into two subgroups. In host range tests of F. solani isolates, none of the isolates was pathogenic on lentils, vetch and cowpea. A number of isolates caused root rot in chickpeas, soybeans, and potato tubers. F. lateritium, F. redolens and F. brasiliense are reported for the first time from Iran.

Endophytic and grapevine trunk diseases associated fungi were isolated from Zanjan province and their inhibitory effect on 2 grapevine fungal pathogens Cytospora chrysosperma and Fusarium sp. was investigated. A total of 95 fungal isolates were isolated, of which 63/54% were from healthy and 36.45% were from diseased tissues. Using strong disinfection steps, probability of isolation of saprophytic fungi was decreased to minimum; So, the fungi isolated from healthy and infected tissues considered as endophytes and grapevine trunk diseases associated fungi, respectively. Preliminary molecular identification of 13 representative isolates in terms of morphological characteristics was performed using nucleotide sequencing of ITS–rDNA region was done and 10 genera were identified. The taxa of Alternaria malorum, Alternaria sp., Allocanariomyces tritici, Aaosphaeria arxii, Clonostachys rosea, Chaetomium sp., Daldinia loculata, Daldinia sp., Fusarium oxysporum, Fusarium sp., Macrophomina phaseolina, Phaeoacremonium minimum and Stromatinia narciss were identified. Pathogenicity of A. tritici, C. rosea and F. oxysporum was confirmed. Antagonistic activity of 13 fungal isolates against pathogenic fungi of grapevine trunk diseases (GTDs) including C. chrysosperma and Fusarium sp. using dual–culture method showed that species of F. oxysporum, P. minimum and C. rosea had the greatest potential as biocontrol agents. In this study, two species of A. arxii and S. narcissi were isolated from healthy grape tissue and to the best of our knowledge; are reported for the first time as endophytic fungi of grapevine trees in the world. D. loculata was isolated from infected tissues of grape trunk and is reported for the first time as a fungi associated with grapevine trunk diseases from the world. Moreover, the pathogenicity of A. tritici and F. oxysporum, was proved in green house condition and are reported for the first time as grapevine pathogens from the world.

Grapevine trunk diseases are destructive fungal diseases that have considerably increased in the recent decades worldwide. More than 130 fungal species were associated with grapevine trunk diseases worldwide; however, the pathogenicity tests have not been conducted for some fungal species. From 2018 to 2020, grapevines with stunted growth, yellowing, branch dieback, and discoloration of the wood tissues symptoms were observed during field observation in the Fars province of Iran. This study aims to isolate, identify and characterize the fungal agents that cause these diseases using a combination of the morphological and molecular approaches.

Grapevines with stunted growth, yellowing, branch dieback, and discoloration of the wood tissues symptoms were used for the isolation of fungal strains. Small pieces of infected wood tissues taken from the margin of symptomatic and approximately healthy parts were surface sterilized and plated onto potato dextrose agar and malt extract agar media amended with ampicillin. Fungal colonies were purified using single spore and hyphal tip methods. Isolates were identified using morphological characteristics as well as sequencing of different gene regions. The pathogenicity of the isolates was tested in greenhouse conditions using one-year-old seedlings of grapevine. To complete Koch's Postulates, fungal agents were re-isolated from inoculated plants and identified.

166 fungal isolates were obtained and identified using the morphological characteristics as well as sequencing of different gene regions. The isolates were identified as Botryosphaeria dothidea, Cytospora chrysosperma, Fomitiporia mediterranea, Kalmusia variispora, Macrophomina phaseolina, Phaeoacremonium minimum, and Phaeoacremonium parasiticum. Among the species, P. minimum (28.31%) and C. chrysosperma (5.42%) had the most and least frequency, respectively. Pathogenicity tests using one-year-old seedlings in glasshouse showed all tested isolates can cause grapevine trunk diseases and produced white rot (in F. mediterranea) or wood necrosis (in other species) on inoculated tissue, developing from the point of inoculation. 

This study's results showed that grapevines in Fars province are infected with fungi causing trunk diseases, which were previously reported from other provinces of Iran and other countries. According to our knowledge, it is the first report of all species, except P. minimum and P. parasiticum, causing grapevine trunk diseases in Fars province. More studies are required to better understand the causal agents of grapevine trunk diseases in other parts of Iran and introduce chemical or natural components that can reduce the economic losses caused by grapevine trunk diseases.

The Karkheh protected area is considered as one of the protected areas of Iran, which harbors a remarkable diversity of vegetation. A population belonging to the genus Pratylenchus was recovered and identified as P. mediterraneus during a survey on the biodiversity of the plant-parasitic nematodes in this region of Khuzestan province. This study aims to characterize the population based on the morphological and morphometric characteristics and evaluate its phylogenetic affinities using LSU D2-D3 and ITS rDNA sequences. Moreover, its phylogenetic relationships were investigated with other relevant genera and species.

Several soil samples were collected from the rhizosphere of tamarisk trees in Karkheh protected area. The centrifugal-floatation and tray methods were used for extracting the nematodes from the soil samples. The collected specimens were fixed and transferred to the pure glycerin after extracting the nematodes by using the modified De Grisse method. Then, permanent microscopic slides were prepared from the processed nematodes. The species was identified by using a light microscope equipped with a drawing tube based on the morphological and morphometric characteristics, and valid keys. The molecular phylogenetic analyses were performed by using partial sequences of the D2-D3 expansion segments of  the large subunit, and internal transcribed spacer (LSU D2-D3 and ITS rDNA) regions based on the Bayesian inference under the GTR + G + I model.

A population of the genus Pratylenchus was recovered in the present study. The morphological, morphometric and molecular studies based on the D2-D3 domains of the 28S and ITS rRNA gene indicated that the recovered population belongs to P. mediterraneus. The morphological, morphometric, and molecular data of the Iranian population of the species were presented for the first time in this study. In the phylogenetic tree inferred using the 28S rRNA gene sequences, the newly generated sequence of the Iranian population of P. mediterraneus formed a clade with other sequences of the species, and some sequences assigned to P. thornei. All other sequences of P. thornei occupied a clade, in close phylogenetic relationship with the aforementioned clade. The newly generated sequence of the Iranian population formed a maximally supported clade with other sequences of the species in the phylogenetic tree inferred using the ITS rRNA gene.  

The two species P. thornei and P. mediterraneus are morphologically very similar and can mainly be separated from each other by presence/absence of male and a functional spermatheca. Their separation is further corroborated by using the partial sequences of 28S and ITS rDNA. The sequences of the two species form the separate clades, and the identification of some sequences occupying the same clade with the sequences of P. mediterraneus need further validations in lack of the morphological data.

The pathogens causing white blister rusts (Albuginales, Oomycota) comprises three genera including Albugo, Pustula and Wilsoniana infecting species of Brassicaceae, Caryophyllales and Asteridae, respectively. The current study contributes with new knowledge on Albuginales in Iran. An extensive survey for sampling white blister rust specimens was performed during the 2017-2020 growing season in some regions in Eastern and Northern Iran. Based on morphological and molecular (Cox2 and ITS) data Albugo lepidii on Lepidium sativum, A. koreana on Camelina transcaspica, Albugo arenosa on Strigosella africana, A. candida on various hosts, A. occidentalis on spinach and Wilsoniana portulacae on Portulaca sp. were identified. Our results, represent the first morphologically and molecularly verified report of A. candida on Goldbachia laevigata, Raphanus sativus, Eruca sativa from Iran and on Sinapis arvensis, Savignya parviflora, Isatis leuconeura and Sisymbrium altissimum worldwide. Sisymbrium septulatum is reported as Matrix nova for A. candida. White blister rust caused by A. candida is reported for the first time on a member of the genus Savignya in Iran. Albugo lepidii and A. koreana are new records for Iranian mycobiota. Detailed descriptions and illustrations along with phylogenetic placement here are provided for Wilsoniana portulacae and Albugo occidentalis.