scholarly journals Illumina Sequencing Reveals the First Near-Complete Genome Sequence of Ugandan Passiflora Virus

2019 ◽  
Vol 8 (20) ◽  
Author(s):  
E. K. Mbeyagala ◽  
S. Maina ◽  
M. W. Macharia ◽  
S. B. Mukasa ◽  
T. Holton
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Amino Acid Identity ◽  
Passion Fruit ◽  
Passiflora Edulis ◽  
Content Type ◽  
Acid Identity ◽  
Symptomatic Sample

Here, we present the first near-complete genome of Ugandan Passiflora virus (UPV) sequenced from a symptomatic sample of KH7 passion fruit (Passiflora edulis Sims) variety. UPV had limited amino acid identity with other potyviruses known to cause passion fruit woodiness disease (PWD).

scholarly journals Complete Genome Sequence of Sulfurospirillum Strain ACSTCE, a Tetrachloroethene-Respiring Anaerobe Isolated from Contaminated Soil

2020 ◽  
Vol 9 (40) ◽  
Author(s):  
Leitao Huo ◽  
Yi Yang ◽  
Yan Lv ◽  
Xiuying Li ◽  
Frank E. Löffler ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Contaminated Soil ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Amino Acid Identity ◽  
Circular Chromosome ◽  
Content Type ◽  
Acid Identity ◽  
Circular Plasmid

ABSTRACT Here, we report the complete genome sequence of the tetrachloroethene-to-trichloroethene dechlorinator Sulfurospirillum sp. strain ACSTCE. The genome consists of a 38.05-kb circular plasmid and a 2.69-Mb circular chromosome, which encodes 3 identical reductive dehalogenases with 91.47% amino acid identity to the PceA of Sulfurospirillum multivorans strain DSM 12446.

scholarly journals Complete Genome Sequence of Serratia marcescens Myophage Moabite

2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Lyndsey Price ◽  
Matthew Rohren ◽  
Heather Newkirk ◽  
Mei Liu ◽  
Jolene Ramsey
Keyword(s):  
Serratia Marcescens ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Amino Acid Identity ◽  
Trna Genes ◽  
Nosocomial Pathogen ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired

Serratia marcescens is a Gram-negative nosocomial pathogen causing various hospital-acquired infections. Here, we describe the complete genome sequence of S. marcescens myophage Moabite. The genome of Moabite is 273,933 bp long, with 337 predicted coding sequences and two tRNA genes, and it shares its highest amino acid identity with Serratia phage 2050HW.

scholarly journals Complete Genome Sequence of Salmonella enterica Siphophage Shemara

2020 ◽  
Vol 9 (6) ◽  
Author(s):  
Michael Chung ◽  
Yicheng Xie ◽  
Heather Newkirk ◽  
Mei Liu ◽  
Jason J. Gill ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Amino Acid Levels

Here, we present the annotated genome of Shemara, a siphophage of Salmonella enterica. The Shemara genome is 44 kb with 83 predicted protein-coding genes. At the nucleotide and amino acid levels, Shemara is most similar to phages in the Guernseyvirinae subfamily.

scholarly journals Genome Sequence of Leuconostoc mesenteroides LK-151 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids

2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Shiro Kato ◽  
Tadao Oikawa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Acid Production ◽  
Leuconostoc Mesenteroides ◽  
Amino Acid Production ◽  
Content Type

ABSTRACT Here, we report the complete genome sequence of strain LK-151 of Leuconostoc mesenteroides, which was isolated from a Japanese sake cellar and has the potential to produce large amounts of d-amino acids, namely, d-Ala and d-Glu. The genome contains 4 genes related to d-amino acid production.

scholarly journals Characterization of the Complete Genome and P0 Protein for a Previously Unreported Genotype of Cotton Leafroll Dwarf Virus, an Introduced Polerovirus in the United States

Plant Disease ◽  
2020 ◽  
Vol 104 (3) ◽  
pp. 780-786 ◽  
Author(s):  
Sofia Avelar ◽  
Roberto Ramos-Sobrinho ◽  
Kassie Conner ◽  
Robert L. Nichols ◽  
Kathy Lawrence ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome ◽  
The United States ◽  
Amino Acid Identity ◽  
Full Length ◽  
Dwarf Virus ◽  
Nucleotide Identity ◽  
Acid Identity ◽  
Cotton Leafroll Dwarf Virus

Virus-like disease symptoms consisting of leaf cupping, shortened internodes, and overall stunting were observed in commercial cotton fields in Alabama in 2017 to 2018. To determine the complete genome sequence of the suspected causal polerovirus, symptomatic leaf samples were collected in Macon County, Alabama, and subjected to Illumina RNA sequencing. Based on BLASTn analysis, the Illumina contig of 5,771 nt shared the highest nucleotide identity (approximately 95%) with members of the species Cotton leafroll dwarf virus (CLRDV) (genus Polerovirus; family Luteoviridae) from Argentina and Brazil. The full-length viral genome sequence was verified by reverse transcription (RT)-PCR amplification, cloning, and Sanger sequencing. The complete CLRDV genome of 5,865 nt in length shared 94.8 to 95.2% nucleotide identity with six previously reported CLRDV isolates. The genome of the CLRDV isolate amplified from Alabama samples (CLRDV-AL) has seven predicted open reading frames (ORFs). Viral proteins 1 to 5 (P1 to P5) shared 91.9 to 99.5% amino acid identity with the six CLRDV isolates from Argentina and Brazil. However, P0, the suppressor of host gene silencing, shared 82.4 to 88.5% pairwise amino acid identity with the latter CLRDV isolates. Phylogenetic analysis of the seven full-length CLRDV genomes resolved three sister clades: CLRDV-AL, CLRDV-typical, and CLRDV-atypical, respectively. Three recombination events were detected by the recombination detection program among the seven CLRDV isolates with breakpoints occurring along the genome. Pairwise nucleotide identity comparisons of ORF0 sequences for the three CLRDV-AL field isolates indicated that they were >99% identical, suggesting that this previously unknown CLRDV genotype represents a single introduction to Alabama.

scholarly journals Complete Genome Sequence of a Novel Putative RNA Virus, RiPV-2, from the Bean Bug Riptortus pedestris

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Yi-Ting Yang ◽  
Se Jin Lee ◽  
Yu-Shin Nai ◽  
Jae Su Kim
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Entomopathogenic Fungus ◽  
Complete Genome ◽  
Rna Virus ◽  
Content Type ◽  
Riptortus Pedestris ◽  
Bean Bug

ABSTRACT A novel putative single-stranded RNA virus was discovered from the transcriptome of a bean bug, Riptortus pedestris, infected with the entomopathogenic fungus Beaveria bassiana JEF-007. The complete genome sequence was 9,915 nucleotides long and encoded a 2,916-amino-acid polyprotein. This virus belonged to Iflaviridae based on phylogenetic analysis and was named RiPV-2.

scholarly journals Draft Genome Sequence of a Novel Picornavirus Isolated from Japanese Eel (Anguilla japonica)

2020 ◽  
Vol 9 (42) ◽  
Author(s):  
Sachiko Terashima ◽  
Motoo Suzuki ◽  
Tomokazu Takano ◽  
Motoshige Yasuike ◽  
Tomomasa Matsuyama ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genome Sequence ◽  
Draft Genome ◽  
Amino Acid Identity ◽  
Anguilla Japonica ◽  
Japanese Eel ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Acid Identity

ABSTRACT We report the draft genome sequence of a novel member of the order Picornavirales that was obtained from the gills of farmed Japanese eel (Anguilla japonica). A putative polyprotein encoded by the genome was similar to that of other picornaviruses and shared 31% amino acid identity with that of eel picornavirus 1.

scholarly journals Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Shiro Kato ◽  
Tadao Oikawa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Lactobacillus Sakei ◽  
Content Type ◽  
Genes Encoding ◽  
Amino Acid Racemase

ABSTRACT This announcement reports the complete genome sequence of strain LK-145 of Lactobacillus sakei isolated from a Japanese sake cellar as a potent strain for the production of large amounts of d-amino acids. Three putative genes encoding an amino acid racemase were identified.

Complete genome sequence of a novel virus, classifiable within the Potyviridae family, which infects passion fruit (Passiflora edulis)

2018 ◽  
Vol 163 (11) ◽  
pp. 3191-3194 ◽  
Author(s):  
Sara Jover-Gil ◽  
Avital Beeri ◽  
Patricia Fresnillo ◽  
Alon Samach ◽  
Héctor Candela
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Passion Fruit ◽  
Passiflora Edulis ◽  
Novel Virus

scholarly journals Complete genome sequence of a Passion fruit yellow mosaic virus (PFYMV) isolate infecting purple passionfruit (Passiflora edulis f. edulis)

2019 ◽  
Vol 72 (1) ◽  
pp. 8643-8654 ◽  
Author(s):  
Helena Jaramillo Mesa ◽  
Mauricio Alejandro Marín Montoya ◽  
Pablo Gutiérrez Sánchez
Keyword(s):  
Mosaic Virus ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Plant Diseases ◽  
Passion Fruit ◽  
Yellow Mosaic Virus ◽  
Close Relative ◽  
Passiflora Edulis ◽  
The World

Purple passion fruit (Passiflora edulis f. edulis), also known as gulupa, is a vine plant of the familiy Passifloraceae, which in recent years has gained importance in the world fruit market due to its exotic nature and excellent organoleptic properties. Although the demand for gulupa in Colombia has increased significantly to become one of the most important fruit exports, the cultivated area has been in decline since 2009 due to the impact of plant diseases. Cucumber mosaic virus (CMV), soybean mosaic virus (SMV) and cowpea aphid borne mosaic virus (CABMV) are amongst the main viruses found infecting gulupa in Colombia. To further characterize the virome of gulupa, a deep sequencing transcriptome study was performed from a producing region in eastern Antioquia. Based on the results of next-generation sequencing (NGS), we report the genome sequence of a tymovirus infecting this plant. Phylogenetic analysis revealed this virus to be a close relative of Passion fruit yellow mosaic virus (PFYMV), Cassia yellow mosaic-associated virus (CYMaV) and Calopogonium yellow vein virus (CYVV). To date, only a 1115 nt segment comprising the RdRP-CP region of PFYMV has been reported; this sequence shares 84.79% and 95.24% identities at the nucleotide and amino acid levels with the purple passionfruit tymovirus suggesting that the detected virus is a PFYMV isolate (PFYMV_Antioquia). Finally, RT-qPCR and Sanger sequencing using specific primers confirmed the presence of PFYMV in different purple passionfruit crops in Antioquia. This is the first complete genome sequence of a PFYMV isolate reported in the world.

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