scholarly journals Creation of a new genus in the family Secoviridae substantiated by sequence variation of newly identified strawberry latent ringspot virus isolates

2019 ◽  
Vol 165 (1) ◽  
pp. 21-31 ◽  
Author(s):  
A. M. Dullemans ◽  
M. Botermans ◽  
M. J. D. de Kock ◽  
C. E. de Krom ◽  
T. A. J. van der Lee ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Complete Genome ◽  
New Genus ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Ringspot Virus ◽  
Genome Sequences ◽  
The Family ◽  
Virus Isolates

Abstract To obtain insight into the sequence diversity of strawberry latent ringspot virus (SLRSV), isolates from collections and diagnostic samples were sequenced by high-throughput sequencing. For five SLRSV isolates, the complete genome sequences were determined, and for 18 other isolates nearly complete genome sequences were determined. The sequence data were analysed in relation to sequences of SLRSV and related virus isolates available in the NCBI GenBank database. The genome sequences were annotated, and sequences of the protease-polymerase (Pro-Pol) region and coat proteins (CPs) (large and small CP together) were used for phylogenetic analysis. The amino acid sequences of the Pro-Pol region were very similar, whereas the nucleotide sequences of this region were more variable. The amino acid sequences of the CPs were less similar, which was corroborated by the results of a serological comparison performed using antisera raised against different isolates of SLRSV. Based on these results, we propose that SLRSV and related unassigned viruses be assigned to a new genus within the family Secoviridae, named “Stralarivirus”. Based on the phylogenetic analysis, this genus should include at least three viruses, i.e., SLRSV-A, SLRSV-B and lychnis mottle virus. The newly generated sequence data provide a basis for designing molecular tests to screen for SLRSV.

scholarly journals Halocins, Bacteriocin-Like Antimicrobials Produced by the Archaeal Domain: Occurrence and Phylogenetic Diversity in Halobacteriales

2020 ◽  
Author(s):  
Afef Najjari ◽  
Hiba Mejri ◽  
Marwa Jabbari ◽  
Haitham Sghaier ◽  
Ameur Cherif ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Complete Genome ◽  
Halophilic Archaea ◽  
Amino Acid Sequences ◽  
Genome Sequences ◽  
Encoding Gene ◽  
New Research ◽  
Shed Light

Members of extremely halophilic archaea, currently consisting of more than 56 genera and 216 species, are known to produce their specific bacteriocin-like peptides and proteins called halocins, synthesized by the ribosomal pathway. Halocins are diverse in size, consisting of proteins as large as 35 kDa and peptide “microhalocins” as small as 3.6 kDa. Today, about fifteen halocins have been described and only three genes, halC8, halS8 and halH4, coding C8, S8 and H4 halocins respectively have been identified. In this study, a total of 1858 of complete and nearly complete genome sequences of Halobacteria class members were retrieved from the IMG and Genbank databases and then screened for halocin encoding gene content, based on the BLASTP algorithm. A total of 61 amino acid sequences belonging to three halocins classes (C8, HalH4 and S8) were identified within 15 genera with the abundance of C8 class. Phylogenetic analysis based on amino acids sequences showed a clear segregation of the three halocins classes. Halocin S8 was phylogenetically more close to HalH4. No clear segregation on species and genera levels was observed based on halocin C8 analysiscontrary to HalH4 based analysis. Collectively, these results give an overview on halocins diversity within halophilic archaea which can open new research topics that will shed light on halocins as marker for haloarchaeal phylogentic delineation.

scholarly journals Complete Genome Sequences of Two Hydrangea Ringspot Virus Isolates from Japan

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Akira Yusa ◽  
Nozomu Iwabuchi ◽  
Hiroaki Koinuma ◽  
Takuya Keima ◽  
Yutaro Neriya ◽  
...  
Keyword(s):  
Complete Genome ◽  
Rna Virus ◽  
Nucleotide Sequences ◽  
Ringspot Virus ◽  
Genomic Sequences ◽  
Genome Sequences ◽  
Hydrangea Macrophylla ◽  
Hydrangea Ringspot Virus ◽  
Virus Isolates

Hydrangea ringspot virus (HdRSV) is a plant RNA virus, naturally infecting Hydrangea macrophylla . Here, we report the first genomic sequences of two HdRSV isolates from hydrangea plants in Japan. The overall nucleotide sequences of these Japanese isolates were 96.0 to 96.3% identical to those of known European isolates.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

scholarly journals Single Passage of Human Metapneumovirus in LLC-MK2 Cells Does Not Affect Viral Protein-Coding Capacity

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Simon Loevenich ◽  
Aleksandr Ianevski ◽  
Eneli Oitmaa ◽  
Denis E. Kainov ◽  
Marit W. Anthonsen
Keyword(s):  
Amino Acid ◽  
Viral Protein ◽  
Complete Genome ◽  
Human Metapneumovirus ◽  
Amino Acid Sequences ◽  
Paired Comparisons ◽  
Genome Sequences ◽  
Protein Coding ◽  
Single Passage ◽  
Coding Capacity

ABSTRACT Here, we report the complete genome sequences of human metapneumovirus (HMPV) prior to and after passaging in LLC-MK2 cells. Paired comparisons of the 13,335-nucleotide genomes revealed that the virus acquired the T10736C transition in its genome, which did not affect the amino acid sequences of HMPV proteins.

Deniquelata barringtoniae gen. et sp. nov., associated with leaf spots of Barringtonia asiatica

Phytotaxa ◽  
2013 ◽  
Vol 105 (1) ◽  
pp. 11 ◽  
Author(s):  
HIRAN A. ARIYAWANSA ◽  
SAJEEWA S.N. MAHARACHCHIKUMBURA ◽  
SAMANTHA C.KARUNARATHNE ◽  
EKACHAI CHUKEATIROTE ◽  
ALI H. BAHKALI ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Sequence Data ◽  
Molecular Data ◽  
The Other ◽  
New Genus And Species ◽  
Leaf Spots ◽  
The Family ◽  
Pathogenicity Testing

Deniquelata barringtoniae gen. et sp. nov. (Montagnulaceae) forms numerous ascomata on distinct zonate leaf spots of Barringtonia asiatica (Lecythidaceae). We isolated this taxon and sequenced the 18S and 28S nrDNA. The result of phylogenetic analysis based on 18S and 28S nrDNA sequence data indicate that the genus belongs in the family Montagnulaceae, Dothideomycetes, Ascomycota. The ascomata are immersed, dark brown to black, with bitunicate asci and brown, muriform ascospores. Deniquelata is distinguished from the other genera in Montagnulaceae based on its short, broad, furcate and pedicellate asci, verruculose ascospores with short narrow pseudoparaphyses with parasitic naturee and this is also supported by molecular data. A new genus and species is therefore introduced to accommodate this taxon. We used isolates of this species to show via pathogenicity testing that the taxon is able to cause leaf spots when leaves are pin pricked.

scholarly journals Complete Genome Sequences of 11 Newcastle Disease Virus Isolates of Subgenotype VII.2 from Indonesia

2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Iryna V. Goraichuk ◽  
Dawn Williams-Coplin ◽  
Michael H. Wibowo ◽  
Peter A. Durr ◽  
Widya Asmara ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Complete Genome ◽  
Class Ii ◽  
Genome Sequences ◽  
Layer Chickens ◽  
Virus Isolates

We report the complete genome sequences of 11 virulent Newcastle disease viruses. The isolates were obtained from vaccinated broiler and layer chickens in three different provinces of Indonesia in 2013 and 2014. Phylogenetic analysis revealed that all isolates belong to subgenotype VII.2 in the class II cluster.

scholarly journals Enteractinococcus coprophilus gen. nov., sp. nov., of the family Micrococcaceae , isolated from Panthera tigris amoyensis faeces, and transfer of Yaniella fodinae Dhanjal et al. 2011 to the genus Enteractinococcus as Enteractinococcus fodinae comb. nov.

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2710-2716 ◽  
Author(s):  
Yan-Ru Cao ◽  
Yi Jiang ◽  
Rong-Xian Jin ◽  
Li Han ◽  
Wen-Xiang He ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Type Strain ◽  
New Genus ◽  
Sequence Data ◽  
Rrna Gene ◽  
Panthera Tigris ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Phosphatidylinositol Mannosides

A novel actinobacterium, designated strain YIM 100590T, was isolated from Panthera tigris amoyensis faeces collected from Yunnan Wild Animal Park in Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequence data showed that strain YIM 100590T is a member of the family Micrococcaceae . Cells were coccoid to oval (0.7–1.5 µm in diameter) occurring singly or in clusters. Growth was observed at 10–37 °C (optimum 28 °C) and at pH 7.0–11.0 (optimum pH 8.0). The major fatty acids were iso-C15 : 0 (32.22 %), anteiso-C15 : 0 (31.64 %) and iso-C16 : 0 (17.38 %). The peptidoglycan was of A4α type (l-Lys–Gly–l-Glu). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, dimannosyl diacylglycerol, an unknown glycolipid and two unknown phospholipids. The quinone system comprised menaquinones MK-7 (91.9 %) and MK-8 (8.3 %). The DNA G+C content of strain YIM 100590T was 56.2 mol%. Chemotaxonomic data indicated that the strain belongs to the family Micrococcaceae . On the basis of morphological and chemotaxonomic data and phylogenetic analysis, strain YIM 100590T is considered to represent a novel species of a new genus within the family Micrococcaceae , for which the name Enteractinococcus coprophilus gen. nov., sp. nov. is proposed. The type strain of Enteractinococcus coprophilus is YIM 100590T ( = DSM 24083T = JCM 17352T). Yaniella fodinae DSM 22966T was transferred to the new genus as Enteractinococcus fodinae comb. nov. (type strain G5T = DSM 22966T = JCM 17931T = MTCC 9846T).

scholarly journals Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama

2013 ◽  
Vol 94 (1) ◽  
pp. 128-135 ◽  
Author(s):  
Junichi Soma ◽  
Hiroshi Tsunemitsu ◽  
Takeshi Miyamoto ◽  
Goro Suzuki ◽  
Takashi Sasaki ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
High Identity ◽  
Rotavirus A ◽  
Bovine Rotavirus ◽  
Epidemiological Impact

Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.

Lapidia, a new monotypic genus of Asteraceae (Eupatorieae) from Brazil, and its phylogenetic placement

Phytotaxa ◽  
2017 ◽  
Vol 291 (1) ◽  
pp. 1 ◽  
Author(s):  
NÁDIA ROQUE ◽  
SILVANA C. FERREIRA ◽  
CÁSSIO VAN DEN BERG
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Sequence Data ◽  
Sister Group ◽  
Species Number ◽  
Monotypic Genus ◽  
Campos Rupestres ◽  
Chapada Diamantina ◽  
Phylogenetic Placement ◽  
The Family

Asteraceae is the family with the highest species number in the rocky fields (campos rupestres) of the Chapada Diamantina, Bahia, Brazil. On the basis of several collections from this area, we are proposing a new genus of Asteraceae based on morphology and phylogeny, to accommodate a species newly described here. Lapidia apicifolia is a loosely ramified shrub 2–4 m high, stem tomentose, leaves opposite-decussate, laminae conduplicate, petiolate, receptacle flat, epaleaceous, glabrous, and pappus of bristles fused at base, irregular in length, fringed and purplish. In a phylogenetic analysis using sequence data from ITS and trnL-trnF of selected members of Eupatorieae, Lapidia is indicated as sister group of a highly supported clade with Morithamnus, Bahianthus and Catolesia. This group is composed by loosely branched shrubs, most with leaves that are lax, stems, leaves and involucral bracts that are viscid (Bahianthus and Morithamnus) and, if not, trichomes (tomentose indumentum) are developed (Lapidia), to protect against both solar radiation and loss of water. A description, illustrations, and a discussion about related and sympatric genera are presented.

Paradictyocheirospora tectonae, a novel genus in the family Dictyosporiaceae from India

Phytotaxa ◽  
2021 ◽  
Vol 509 (3) ◽  
Author(s):  
KUNHIRAMAN C. RAJESHKUMAR ◽  
RAJNISH K. VERMA ◽  
SARANYAPHAT BOONMEE ◽  
SAJINI CHANDRASIRI ◽  
KEVIN D. HYDE ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Record ◽  
New Genus ◽  
Sequence Data ◽  
Novel Genus ◽  
The Family ◽  
Distinct Lineage

This study introduces, Paradictyocheirospora, a new genus, belonging to the family Dictyosporiaceae with evidence from morphology and phylogenetic analysis of a combined ITS, LSU and TEF1α sequence data. Paradictyocheirospora can be distinguished from allied taxa based on dictyosporous, cheiroid conidia with suprabasal bubble-like hyaline appendages and cylindrical, reduced conidiophores. The new genus is similar to Dictyocheirospora; however, the conidia are smaller with fewer rows (3–6) and have globose, supra-basal appendages. Paradictyocheirospora tectonae forms a distinct lineage basal to Digitodesmium and Dictyocheirospora. Additional new collections from Thane, Maharashtra were morphologically identical and phylogenetically related to Dictyocheirospora nabanheensis, and the latter is a new record from India.

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