scholarly journals Full length genome sequence of Polish isolate of Beet soil-borne virus confirms low level of genetic diversity.

2009 ◽  
Vol 56 (4) ◽  
Author(s):  
Natasza Borodynko ◽  
Beata Hasiów-Jaroszewska ◽  
Natalia Rymelska ◽  
Henryk Pospieszny
Keyword(s):  
Genetic Diversity ◽  
Genome Organization ◽  
Selective Pressure ◽  
Triple Gene Block ◽  
Synonymous Substitutions ◽  
Gene Block ◽  
Synonymous Mutations ◽  
High Level ◽  
Full Length Genome ◽  
First Time

The complete nucleotide sequence of a Polish isolate of Beet soil-borne virus was determined for the first time. The genome organization was identical with those previously established for isolates from Germany and China. A comparison of the Polish isolate with others deposited in GenBank revealed high level of nucleotide identity, about 98-100%, throughout the genome analyzed. The ratio between non-synonymous and synonymous substitutions was rather low suggesting a negative selective pressure. The non-synonymous mutations were particulary frequent in triple gene block.

scholarly journals Complete Genome Sequence of aLily virus XIsolate from Japan

2018 ◽  
Vol 6 (4) ◽  
Author(s):  
Takamichi Nijo ◽  
Yukari Okano ◽  
Masayoshi Kondo ◽  
Hiroaki Okuhara ◽  
Hiroyo Sekimura ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Triple Gene Block ◽  
Start Codon ◽  
Gene Block ◽  
First Time ◽  
Triple Gene Block Protein

ABSTRACTThe complete genome sequence ofLily virus X(LVX), which infects lilies, was determined for the first time from lilies in Japan. As with previous reports, the genome of the Japanese LVX isolate lacked an AUG start codon for the triple gene block protein 3-like region.

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

2018 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph D. Postman ◽  
Robert R. Martin ◽  
Ioannis E. Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus tentatively named as blackcurrant virus A (BCVA) has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase and RNA dependent RNA polymerase (RdRp) domains. The other four putative proteins exhibit no significant homology to other virus proteins. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement. Phylogenetic analysis using replicase conserved motifs loosely placed BCVA within the Betaflexiviridae whereas it was evolutionarily distant to existing members of the family when using the putative TGBp 1-like and coat protein sequences. Our analysis strongly suggests that BCVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family in the order Tymovirales.

scholarly journals Intraspecific functional and genetic diversity ofPetriella setifera

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4420 ◽  
Author(s):  
Giorgia Pertile ◽  
Jacek Panek ◽  
Karolina Oszust ◽  
Anna Siczek ◽  
Magdalena Frąc
Keyword(s):  
Genetic Diversity ◽  
Functional Diversity ◽  
Quinic Acid ◽  
Significant Degree ◽  
Fungal Species ◽  
Intraspecific Diversity ◽  
Metabolic Diversity ◽  
Biolog System ◽  
High Level ◽  
First Time

The aim of the study was an analysis of the intraspecific genetic and functional diversity of the new isolated fungal strains ofP. setifera. This is the first report concerning the genetic and metabolic diversity ofPetriella setiferastrains isolated from industrial compost and the first description of a protocol for AFLP fingerprinting analysis optimised for these fungal species. The results showed a significant degree of variability among the isolates, which was demonstrated by the clearly subdivision of all the isolates into two clusters with 51% and 62% similarity, respectively. For the metabolic diversity, the BIOLOG system was used and this analysis revealed clearly different patterns of carbon substrates utilization between the isolates resulting in a clear separation of the five isolates into three clusters with 0%, 42% and 54% of similarity, respectively. These results suggest that genetic diversity does not always match the level of functional diversity, which may be useful in discovering the importance of this fungus to ecosystem functioning. The results indicated thatP. setiferastrains were able to degrade substrates produced in the degradation of hemicellulose (D-Arabinose, L-Arabinose, D-Glucuronic Acid, Xylitol, γ-Amino-Butyric Acid, D-Mannose, D-Xylose and L-Rhamnose), cellulose (α-D-Glucose and D-Cellobiose) and the synthesis of lignin (Quinic Acid) at a high level, showing their importance in ecosystem services as a decomposer of carbon compounds and as organisms, which make a significant contribution to carbon cycling in the ecosystem.The results showed for the first time that the use of molecular biology techniques (such as AFLP and BIOLOG analyses) may allow for the identification of intraspecific diversity of as yet poorly investigated fungal species with favourable consequences for our understanding their ecosystem function.

Comparison of Barley Stripe Mosaic Virus Strains

2008 ◽  
Vol 63 (3-4) ◽  
pp. 271-276 ◽  
Author(s):  
Elsayed E. Hafez ◽  
Engy E. Abdel Aleem ◽  
Faiza A. Fattouh
Keyword(s):  
Mosaic Virus ◽  
Phylogenetic Trees ◽  
Triple Gene Block ◽  
Northern Blotting ◽  
Barley Stripe Mosaic Virus ◽  
Evolutionary Divergence ◽  
Gene Block ◽  
Virus Particles ◽  
Distinct Cluster ◽  
High Level

BSMV (barley stripe mosaic virus) particles were obtained in a pure state from infected host plant tissues of Hordeum vulgare. The three genomic parities (α, β and γ) were amplified by PCR using specific primers for each particle; each was cloned. Partial sequence of the α, β and γ segments was determined for the Egyptian isolate of barley stripe mosaic virus (BSMV AE1). Alignment of nucleotide sequences with that of other known strains of the virus, BSMV type strains (CV17, ND18 and China), and the generation of phylogenetic trees was performed. A low level of homology was detected comparing 467 bp of the α and 643 bp of the segments to that of the other strains, and thus BSMV α and β segments were in separate clusters. However, 1154 bp of the γ segments of BSMV AE1 showed a high level of homology especially to strain BSMV ND18, as they both formed a distinct cluster. Northern blotting of pure BSMV AE1 virus and H. vulgare-infected tissue were compared using an α ND18 specific probe. Western blotting using antibodies specific for the coat protein (CP) and the triple gene block 1 (TGB1) protein, which are both encoded by the β ND18 segment, still indicated a high level of similarity between proteins produced by BSMV ND18 and AE1. We suggest that the BSMV AE1 isolate is a distinct strain of BSMV which reflects the genetic evolutionary divergence among BSMV strains and members of the Hordeivirus group

scholarly journals A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 406 ◽  
Author(s):  
Thanuja Thekke-Veetil ◽  
Thien Ho ◽  
Joseph Postman ◽  
Robert Martin ◽  
Ioannis Tzanetakis
Keyword(s):  
Genome Organization ◽  
High Throughput Sequencing ◽  
Triple Gene Block ◽  
Open Reading Frames ◽  
Methyl Transferase ◽  
Gene Block ◽  
New Family ◽  
Molecular Features ◽  
Genome Features ◽  
Novel Virus

A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

scholarly journals RAPD-analysis of Fagopyrum species and cultivars genome polymorphism

2008 ◽  
Vol 6 (3) ◽  
pp. 3-10
Author(s):  
Guzel D Kadyrova ◽  
Fanusya Z Kadyrova ◽  
Natalia N Ryzhova ◽  
Elena Z Kochieva
Keyword(s):  
Genetic Diversity ◽  
Related Species ◽  
Rapd Analysis ◽  
Natural Populations ◽  
Genomic Polymorphism ◽  
Genome Variability ◽  
Genome Polymorphism ◽  
Close Relationship ◽  
High Level ◽  
First Time

RAPD-analysis of biodiversity in cultivated annual buckwheat species Fagopyrum esculentum, F. tataricum and related species F. giganteum and F. cymosum has been performed. Close relationship between F. cymosum, F. giganteum и F. tataricum has been confirmed. Intraspecific genome variability of F. tataricum accessions (0,01-0,15) is lower than in F. esculentum (0,10-0,33). For the first time genetic diversity in Russian buckwheat cultivars has been investigated. The high level of genomic polymorphism in F. esculentum cultivars (0,10-0,29) that is comparable to the variability in natural populations is shown.

A Confrontation between Two Doctrines: The Birth of Struggle for Hegemony in Hebrew Children's Literature during the 1930s and 1940s

2008 ◽  
Vol 1 (2) ◽  
pp. 139-155 ◽  
Author(s):  
YAEL DARR
Keyword(s):  
Children's Literature ◽  
Educational System ◽  
Single Channel ◽  
Children’S Literature ◽  
The Political ◽  
Literary Creation ◽  
History Of ◽  
High Level ◽  
First Time ◽  
Literary Quality

This article describes a crucial and fundamental stage in the transformation of Hebrew children's literature, during the late 1930s and 1940s, from a single channel of expression to a multi-layered polyphony of models and voices. It claims that for the first time in the history of Hebrew children's literature there took place a doctrinal confrontation between two groups of taste-makers. The article outlines the pedagogical and ideological designs of traditionalist Zionist educators, and suggests how these were challenged by a group of prominent writers of adult poetry, members of the Modernist movement. These writers, it is argued, advocated autonomous literary creation, and insisted on a high level of literary quality. Their intervention not only dramatically changed the repertoire of Hebrew children's literature, but also the rules of literary discourse. The article suggests that, through the Modernists’ polemical efforts, Hebrew children's literature was able to free itself from its position as an apparatus controlled by the political-educational system and to become a dynamic and multi-layered field.

Genetic Diversity of Basil (Ocimum spp. - Lamiaceae) Based on RAPD Markers and Volatile Oil Constituents

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 492f-493
Author(s):  
Roberto F. Vieira ◽  
James E. Simon ◽  
Peter Goldsbrough ◽  
Antonio Figueira
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Rapd Markers ◽  
Volatile Oil ◽  
Essential Oil Composition ◽  
Oil Composition ◽  
Traditional Medicines ◽  
The Tropics ◽  
High Degree ◽  
First Time

Essential oils extracted from basil (Ocimum spp.) by steam distillation are used to flavor foods, oral products, in fragrances, and in traditional medicines. The genus Ocimum contains around 30 species native to the tropics and subtropics, with some species naturalized and/or cultivated in temperate areas. Interand intraspecific hybridization have created significant confusion in the botanical systematics of this genus. Taxonomy of basil (O. basilicum) is also complicated by the existence of numerous varieties, cultivars, and chemotypes within the species that do not differ significantly in morphology. In this study we are using RAPD markers and volatile oil composition to characterize the genetic diversity among the most economically important Ocimum species. We hypothesize that the genetic similarity revealed by molecular markers will more accurately reflect the morphological and chemical differences in Ocimum than essential oil composition per se. Preliminary research using five Ocimum species, four undetermined species, and eight varieties of O. basilicum (a total of 19 accessions) generated 107 polymorphic fragments amplified with 19 primers. RAPDs are able to discriminate between Ocimum species, but show a high degree of similarity between O. basilicum varieties. The genetic distance between nine species and among 55 accessions within the species O. americanum, O. basilicum, O. campechianum, O. × citriodorum, O. gratissimum, O. kilimandscharium, O. minimum, O. selloi, and O. tenuiflorum will be analyzed by matrix of similarity and compared to the volatile oil profile. This research will for the first time apply molecular markers to characterize the genetic diversity of Ocimum associate with volatile oil constituent.

scholarly journals The LEPR Gene Is Associated with Reproductive Seasonality Traits in Rasa Aragonesa Sheep

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2448
Author(s):  
Kenza Lakhssassi ◽  
Malena Serrano ◽  
Belén Lahoz ◽  
María Pilar Sarto ◽  
Laura Pilar Iguácel ◽  
...  
Keyword(s):  
Amino Acid Change ◽  
Leptin Receptor ◽  
Extreme Values ◽  
Reproductive Traits ◽  
Reproductive Seasonality ◽  
Synonymous Substitutions ◽  
Lepr Gene ◽  
Exon 20 ◽  
First Time

The aim of this study was to characterize and identify causative polymorphisms in the leptin receptor (LEPR) gene responsible for the seasonal variation of reproductive traits in sheep. Three reproductive seasonality traits were studied: the total days of anoestrous (TDA), the progesterone cycling months (P4CM) and the oestrous cycling months (OCM). In total, 18 SNPs were detected in 33 ewes with extreme values for TDA and OCM. Six SNPs were non-synonymous substitutions and two of them were predicted in silico as deleterious: rs596133197 and rs403578195. These polymorphisms were then validated in 239 ewes. The SNP rs403578195, located in exon 8 and leading to a change of alanine to glycine (Ala284Gly) in the extracellular domain of the protein, was associated with the OCM trait, being the G allele associated with a decrease of 12 percent of the OCM trait. Haplotype analyses also suggested the involvement of other non-synonymous SNP located in exon 20 (rs405459906). This SNP also produces an amino acid change (Lys1069Glu) in the intracellular domain of the protein and segregates independently of rs403578195. These results confirm for the first time the role of the LEPR gene in sheep reproductive seasonality.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

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