Baculovirus Kimura two-parameter species demarcation criterion is confirmed by the distances of 38 core gene nucleotide sequences

Abstract We report the genome sequence of a putative new foveavirus infecting non-cultivated Vitis vinifera, tentatively named “grapevine foveavirus A” (GFVA). This virus was identified by high-throughput sequencing analysis of a European wild Vitis collected in Switzerland. Phylogenetic analysis revealed that this virus clustered with known grapevine virus T (GVT) isolates but was clearly distinct from any of them. If considering the International Committee of Taxonomy of Viruses (ICTV)-suggested foveavirus species demarcation criterion based on sequence similarity in the replicase gene/protein, this virus should be considered a member of a new species closely related to GVT. On the other hand, comparison of capsid gene/protein sequences using the same criteria indicates that GFVA is at the border of species demarcation. Whether this virus represents a highly divergent GVT isolate or a member of a distinct but closely related species is discussed.

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De Novo Assembly and Species-Specific Marker Development as a Useful Tool for the Identification of Scutellaria L. Species

Current Issues in Molecular Biology ◽

10.3390/cimb43030152 ◽

2021 ◽

Vol 43 (3) ◽

pp. 2177-2188

Author(s):

Hakjoon Choi ◽

Wan Seok Kang ◽

Jin Seok Kim ◽

Chang-Su Na ◽

Sunoh Kim

Keyword(s):

De Novo ◽

Dna Barcode ◽

Core Gene ◽

Nucleotide Sequences ◽

Specific Marker ◽

Sequencing Platform ◽

Pcr Product ◽

A Genome ◽

Folk Remedy ◽

Species Specific

Scutellaria L. (family Lamiaceae) includes approximately 470 species found in most parts of the world and is commonly known as skullcaps. Scutellaria L. is a medicinal herb used as a folk remedy in Korea and East Asia, but it is difficult to identify and classify various subspecies by morphological methods. Since Scutellaria L. has not been studied genetically, to expand the knowledge of species in the genus Scutellaria L., de novo whole-genome assembly was performed in Scutellaria indica var. tsusimensis (H. Hara) Ohwi using the Illumina sequencing platform. We aimed to develop a molecular method that could be used to classify S.indica var. tsusimensis (H. Hara) Ohwi, S. indica L. and three other Scutellaria L. species. The assembly results for S.indica var. tsusimensis (H. Hara) Ohwi revealed a genome size of 318,741,328 bp and a scaffold N50 of 78,430. The assembly contained 92.08% of the conserved BUSCO core gene set and was estimated to cover 94.65% of the genome. The obtained genes were compared with previously registered Scutellaria nucleotide sequences and similar regions using the NCBI BLAST service, and a total of 279 similar nucleotide sequences were detected. By selecting the 279 similar nucleotide sequences and nine chloroplast DNA barcode genes, primers were prepared so that the size of the PCR product was 100 to 1000 bp. As a result, a species-specific primer set capable of distinguishing five species of Scutellaria L. was developed.

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Nanopore sequencing of tomato mottle leaf distortion virus, a new bipartite begomovirus infecting tomato in Brazil

10.21203/rs.3.rs-291179/v1 ◽

2021 ◽

Author(s):

Thais Pereira Martins ◽

Tadeu Araujo Souza ◽

Patricia Santos Silva ◽

Erich Yukio Tempel Nakasu ◽

Fernando Lucas Melo ◽

...

Keyword(s):

Nucleotide Identity ◽

Species Demarcation Criterion ◽

Bipartite Begomovirus ◽

Nanopore Sequencing ◽

Demarcation Criterion ◽

A Genome ◽

Tomato Field ◽

Identity Match ◽

Leaf Deformation ◽

Leaf Distortion

Abstract During a survey in a tomato field in Luziânia (Goiás State, Brazil), a plant showing mottling, chlorotic spots, and leaf distortion was found. A new bipartite begomovirus was found by Nanopore sequencing, and the full DNA-A sequence was confirmed by Sanger sequencing. The highest nucleotide identity match of this DNA-A genome (2596 bases) was 81.65% with tomato golden leaf deformation virus (HM357456). Due to the current species demarcation criterion of 91% of nucleotide identity (DNA-A), we propose it as a new member of the genus Begomovirus, named Tomato mottle leaf distortion virus.

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Identification and Genetic Characterization of a Novel Respirovirus in Alpine Chamois (Rupicapra rupicapra rupicapra)

Animals ◽

10.3390/ani10040704 ◽

2020 ◽

Vol 10 (4) ◽

pp. 704

Author(s):

Camilla Luzzago ◽

Erika Ebranati ◽

Antonio Lavazza ◽

Martina Besozzi ◽

Gianguglielmo Zehender ◽

...

Keyword(s):

Genetic Characterization ◽

Phylogenetic Analyses ◽

Amino Acid Sequences ◽

Species Demarcation Criterion ◽

Demarcation Criterion ◽

Protein Amino Acid ◽

Rupicapra Rupicapra ◽

Separate Branch ◽

Alpine Chamois

The Respirovirus genus, family Paramamixoviridae, includes respiratory viral pathogens. Here we report the identification and genetic characterization of a respirovirus in an Alpine chamois showing interstitial pneumonia associated with catarrhal bronchopneumonia. The full-genome characterization of this respirovirus, named ChamoisRV/IT2014, revealed low similarities to caprine respirovirus (77.1%), bovine respirovirus (74.5%) and human respirovirus (72.0%). The phylogenetic analyses based on the full-length genome sequence of the novel isolate and reference respirovirus strains showed that ChamoisRV/IT2014 clustered with caprine respirovirus but formed a separate branch. The phylogenetic tree topology of complete large protein amino acid sequences, representing the current species demarcation criterion for Respirovirus genus, showed a 0.05 branch length of ChamoisRV/IT2014 sequence between the nearest node and the tip of the branch, suggesting that this virus belongs to a novel species. This new isolate in a new host species raises several questions to be addressed on the epidemiological role of chamois and the risks of cross-transmission between wild ruminants and livestock.

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Partial molecular characterization of begomoviruses isolated from weeds collected in tomato crops in the southeast of Valle del Cauca, Colombia

Revista Colombiana de Ciencias Hortícolas ◽

10.17584/rcch.2020v14i1.10434 ◽

2020 ◽

Vol 14 (1) ◽

Author(s):

Juan Carlos Vaca-Vaca ◽

Frenyiline Jara-Tejada ◽

Karina López-López

Keyword(s):

Nucleotide Sequence ◽

Mosaic Virus ◽

Molecular Characterization ◽

Yellow Mosaic Virus ◽

Nucleotide Sequence Analysis ◽

Species Demarcation Criterion ◽

Demarcation Criterion ◽

Sequence Identity ◽

Valle Del Cauca ◽

Leaf Distortion

Weeds are usually considered as a source of new viruses but are often neglected during diversity studies. Previously eleven samples of weeds were collected along the edges of a tomato crop field located in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the Southeast of Valle del Cauca. These samples were positive for begomoviruses but their molecular characterization had not been done until now. For each sample, DNA fragments were cloned, sequenced and analyzed. Nucleotide sequence analysis of viral fragments showed the presence of six different begomoviruses: two virus isolated from Lantana camara, Desmodium sp. and Amaranthus dubius were previously described as potato yellow mosaic virus (PYMV) and passionfruit leaf distortion virus (PLDV), respectively; other four virus which were isolated from L. camara, A. dubius, Rivina humilis, Desmodium sp., Rhynchosia minima, Hybanthus attenuatus, Verbena sp., Croton hirtus and Caesalpinia sp., showed its highest nucleotide sequence identity (89%) with bean chlorotic mosaic virus (BChMV), datura leaf distortion virus (DaLDV) and rhynchosia golden mosaic Yucatan virus (RhGMYV). Cloned viruses fragments from these weeds could be new begomoviruses not previously reported before, this in accordance with the ICTV species demarcation criterion for the genus Begomovirus (≥91 % sequence identity). Mixed infections of begomoviruses in Desmodium sp. and A. dubius weeds also was found in this analysis. Finally, this paper reports by the first time to three alternative begomoviruses weeds hosts that infect tomato and passion fruit crops: A. dubius for PYMV, and L. camara and Desmodium sp. for PLDV, respectively.

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Some results of the Barbier-Chalonge-Divan system of stellar classification

Symposium - International Astronomical Union ◽

10.1017/s0074180900053250 ◽

1966 ◽

Vol 24 ◽

pp. 77-90 ◽

Cited By ~ 1

Author(s):

D. Chalonge

Keyword(s):

Early Type ◽

Parameter System ◽

Early Type Stars ◽

Two Parameter

Several years ago a three-parameter system of stellar classification has been proposed (1, 2), for the early-type stars (O-G): it was an improvement on the two-parameter system described by Barbier and Chalonge (3).

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Subjective Time Preference and Willingness to Pay for an Energy-Saving Durable Good

Zeitschrift für Sozialpsychologie ◽

10.1024//0044-3514.32.3.133 ◽

2001 ◽

Vol 32 (3) ◽

pp. 133-141 ◽

Cited By ~ 4

Author(s):

Gerrit Antonides ◽

Sophia R. Wunderink

Keyword(s):

Willingness To Pay ◽

Energy Saving ◽

Subjective Time ◽

Durable Good ◽

Discount Function ◽

Hyperbolic Discount ◽

The One ◽

Two Parameter ◽

Difference Effect ◽

Better Than

Summary: Different shapes of individual subjective discount functions were compared using real measures of willingness to accept future monetary outcomes in an experiment. The two-parameter hyperbolic discount function described the data better than three alternative one-parameter discount functions. However, the hyperbolic discount functions did not explain the common difference effect better than the classical discount function. Discount functions were also estimated from survey data of Dutch households who reported their willingness to postpone positive and negative amounts. Future positive amounts were discounted more than future negative amounts and smaller amounts were discounted more than larger amounts. Furthermore, younger people discounted more than older people. Finally, discount functions were used in explaining consumers' willingness to pay for an energy-saving durable good. In this case, the two-parameter discount model could not be estimated and the one-parameter models did not differ significantly in explaining the data.

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