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1. Complete genome sequence of Antarcticibacterium flavum JB01H24T from an Antarctic marine sediment

Author:
Lee, Yung Mi; Jin, Young Keun; Shin, Seung Chul
Source:
Marine genomics 2020 v.50 pp. 100695
ISSN:
1874-7787
Subject:
open reading frames,   etc   ; chromosomes; genome; genomics; marine sediments; sequence analysis; Antarctic region; Antarctica;     Show all 8 Subjects
Abstract:
... Antarcticibacterium flavum JB01H24ᵀ was isolated from a marine sediment of the Ross Sea, Antarctica. Whole-genome sequencing of the strain Antarcticibacterium flavum JB01H24ᵀ was achieved using PacBio RS II platform. The resulting complete genome comprised of one closed, complete chromosome of 4,319,074 base pairs with a 40.87% G + C content, where genomic analyses demonstrated that it is constitu ...
DOI:
10.1016/j.margen.2019.100695

2. A Comparative Characterization of the Mitochondrial Genomes of Paramoeba aparasomata and Neoparamoeba pemaquidensis (Amoebozoa, Paramoebidae)

Author:
Bondarenko, Natalya; Volkova, Ekaterina; Masharsky, Alexey; Kudryavtsev, Alexander; Smirnov, Alexey
Source:
Thejournal of eukaryotic microbiology 2020 v.67 no.2 pp. 167-175
ISSN:
1066-5234
Subject:
open reading frames,   etc   ; Neoparamoeba; Paramoeba; codon usage; endosymbionts; gene order; mitochondrial genome; ribosomal RNA; transfer RNA;     Show all 9 Subjects
Abstract:
... Marine amebae of the genus Paramoeba (Amoebozoa, Dactylopodida) normally contain a eukaryotic endosymbiont known as Perkinsela‐like organism (PLO). This is one of the characters to distinguish the genera Neoparamoeba and Paramoeba from other Dactylopodida. It is known that the PLO may be lost, but PLO‐free strains of paramoebians were never available for molecular studies. Recently, we have descri ...
DOI:
10.1111/jeu.12767

3. Genome Resource for the Huanglongbing Causal Agent ‘Candidatus Liberibacter asiaticus’ Strain AHCA17 from Citrus Root Tissue in California, USA

Author:
Cai, Weili; Nunziata, Schyler; Costanzo, Stefano; Kumagai, Lucita; Rascoe, John; Stulberg, Michael J.
Source:
Plant disease 2020 v.104 no.3 pp. 627-629
ISSN:
0191-2917
Subject:
open reading frames,   etc   ; Candidatus Liberibacter asiaticus; Citrus; epidemiology; genes; greening disease; metagenomics; pathogens; pummelos; trees; California;     Show all 11 Subjects
Abstract:
... ‘Candidatus Liberibacter asiaticus’ is the unculturable causative agent of citrus huanglongbing disease. Here, we report the first citrus root metagenome sequence containing the draft genome of ‘Ca. L. asiaticus’ strain AHCA17, obtained from a pummelo tree in California. The assembled genome was 1.2 Mbp and resulted in 37 contigs (N₅₀ = 158.7 kbp) containing 1,057 predicted open reading frames and ...
DOI:
10.1094/PDIS-08-19-1735-A

4. The Architecture of SARS-CoV-2 Transcriptome

Author:
Kim, Dongwan; Lee, Joo-Yeon; Yang, Jeong-Sun; Kim, Jun Won; Kim, V. Narry; Chang, Hyeshik
Source:
Cell 2020 v.181 no.4 pp. 914-921.e10
ISSN:
0092-8674
Subject:
open reading frames,   etc   ; Betacoronavirus; Coronavirus infections; DNA; genome; genomics; messenger RNA; nanopores; pandemic; pathogenicity; sequence analysis; transcription (genetics); transcriptome; transcriptomics;     Show all 14 Subjects
Abstract:
... SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic. Although the SARS-CoV-2 genome was reported recently, its transcriptomic architecture is unknown. Utilizing two complementary sequencing techniques, we present a high-resolution map of the SARS-CoV-2 transcriptome and epitranscriptome. DNA nanoball sequencing shows that the transcriptome is highly complex owing to numerous disc ...
DOI:
10.1016/j.cell.2020.04.011
PubMed:
32330414
PubMed Central:
PMC7179501

5. The mitochondrial genome of Morchella importuna (272.2 kb) is the largest among fungi and contains numerous introns, mitochondrial non-conserved open reading frames and repetitive sequences

Author:
Liu, Wei; Cai, Yingli; Zhang, Qianqian; Chen, Lianfu; Shu, Fang; Ma, Xiaolong; Bian, Yinbing
Source:
International journal of biological macromolecules 2020 v.143 pp. 373-381
ISSN:
0141-8130
Subject:
open reading frames,   etc   ; DNA; Morchella; developmental stages; enzymes; introns; medicinal fungi; mitochondria; mitochondrial genome; repetitive sequences; ribosomal RNA; vegetative growth;     Show all 12 Subjects
Abstract:
... The complete mitochondrial genome of Morchella importuna, the famous edible and medicinal mushroom, was assembled as a 272,238 bp single circular dsDNA. As the largest mitogenome among fungi, it exhibits several distinct characteristics. The mitogenome of M. importuna encoded 14 core conserved mitochondrial protein-coding genes and 151 mitochondrial non-conserved open reading frames (ncORFs) were ...
DOI:
10.1016/j.ijbiomac.2019.12.056

6. Genome sequence analysis of 91 Salmonella Enteritidis isolates from mice caught on poultry farms in the mid 1990s

Author:
Guard, Jean; Cao, Guojie; Luo, Yan; Baugher, Joseph D.; Davison, Sherrill; Yao, Kuan; Hoffmann, Maria; Zhang, Guodong; Likens, Nathan; Bell, Rebecca L.; Zheng, Jie; Brown, Eric; Allard, Marc
Source:
Genomics 2020 v.112 no.1 pp. 528-544
ISSN:
0888-7543
Subject:
open reading frames,   etc   ; Salmonella Enteritidis; algorithms; farms; feral animals; genome; genomics; genotype; humans; mice; mutation; phenotype; poultry; sequence analysis; Pennsylvania;     Show all 15 Subjects
Abstract:
... A total of 91 draft genome sequences were used to analyze isolates of Salmonella enterica serovar Enteritidis obtained from feral mice caught on poultry farms in Pennsylvania. One objective was to find mutations disrupting open reading frames (ORFs) and another was to determine if ORF-disruptive mutations were present in isolates obtained from other sources. A total of 83 mice were obtained betwee ...
DOI:
10.1016/j.ygeno.2019.04.005

7. Conserved Secondary Structures in Viral mRNAs

Author:
Kiening, Michael; Ochsenreiter, Roman; Hellinger, Hans-Jörg; Rattei, Thomas; Hofacker, Ivo; Frishman, Dmitrij
Source:
Viruses 2019 v.11 no.5
ISSN:
1999-4915
Subject:
open reading frames,   etc   ; databases; messenger RNA; prediction; virus replication; viruses;     Show all 6 Subjects
Abstract:
... RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, ...
DOI:
10.3390/v11050401
PubMed:
31035717
PubMed Central:
PMC6563262

8. Efficient transposition of Tn4556 by alterations in inverted repeats using a delivery vector carrying a counter-selectable marker for Streptomyces

Author:
Sota, Masahiro; Sakoda, Akiko; Ikeda, Haruo
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 477-482
ISSN:
1367-5435
Subject:
open reading frames,   etc   ; Streptomyces; methyltransferases; sequence analysis; transposons;     Show all 5 Subjects
Abstract:
... A 6625-base pair transposon, Tn4556, was initially isolated from a Streptomyces strain and a sequence analysis was performed; however, its annotation data remain incomplete. At least three positions were identified as frameshift and base-exchange errors by resequencing. The revised sequence revealed that Tn4556 contains four open reading frames that encode transposase, methyltransferase, isoprenyl ...
DOI:
10.1007/s10295-018-2101-x
PubMed:
30460506
PubMed Central:
PMC6403206

9. Characteristics of lytic phage vB_EcoM-ECP26 and reduction of shiga-toxin producing Escherichia coli on produce romaine

Author:
Park, Do-Won; Lim, Ga-yeon; Lee, Young-duck; Park, Jong-Hyun
Source:
Applied biological chemistry 2020 v.63 no.1 pp. 19
ISSN:
2468-0834
Subject:
open reading frames,   etc   ; Escherichia coli O157; Myoviridae; diarrhea; genes; hemolytic uremic syndrome; host range; humans; lettuce; nucleotides; pH; pathogens; phages; phylogeny; temperature; viral morphology;     Show all 16 Subjects
Abstract:
... Foodborne Shiga toxin-producing Escherichia coli (STEC) cause severe diarrhea and hemolytic uremic syndrome (HUS) in humans. However, traditional methods for STEC sterilization are difficult to apply to fresh food. To control the pathogen, phage infecting E. coli O157:H7 were isolated and characterized. The isolated phage vB_EcoM-ECP26 had an icosahedral head and a contractile tail, and was classi ...
DOI:
10.1186/s13765-020-00502-4

10. A novel β-catenin from Apostichopus japonicus mediates Vibrio splendidus-induced inflammatory-like response

Author:
Zhang, Zhen; Lv, Zhimeng; Zhang, Weiwei; Guo, Ming; Li, Chenghua
Source:
International journal of biological macromolecules 2020 v.156 pp. 730-739
ISSN:
0141-8130
Subject:
open reading frames,   etc   ; Apostichopus japonicus; Vibrio splendidus; amino acids; apoptosis; beta catenin; genes; immune response; intestines; messenger RNA; phosphorylation; sequence analysis; signal transduction;     Show all 13 Subjects
Abstract:
... β-catenin, an adaptor molecule in Wnt/β-catenin signaling pathway, is associated with different physiological processes such as intestinal immune, apoptosis, and inflammation-associated response. However, the function of β-catenin is still largely unknown in Apostichopus japonicus. In the present study, we cloned and characterized β-catenin gene from A. japonicus by RNA-seq and RACE approaches. Th ...
DOI:
10.1016/j.ijbiomac.2020.04.103

11. Bacteriophage-mediated extracellular DNA release is important for the structural stability of aerobic granular sludge

Author:
Wang, Yi-qiao; Li, Wei; Zhuang, Jin-long; Liu, Yong-di; Shapleigh, James P.
Source:
The Science of the total environment 2020 v.726 pp. 138392
ISSN:
0048-9697
Subject:
open reading frames,   etc   ; Actinobacteria; Bacteroidetes; CRISPR sequences; CRISPR-Cas systems; DNA; Proteobacteria; bacteriophages; deoxyribonuclease I; enzymatic hydrolysis; gene editing; genome; metagenomics; prediction; proteins; sludge;     Show all 16 Subjects
Abstract:
... The aim of this study was to investigate the microbial characteristics and the structural role of exDNA in different size AGSs. Metagenomic results showed that exDNA has a significantly lower GC content, ~46.0%, than the ~65.0% GC of intracellular DNA (inDNA). Taxonomic predictions showed most of the reads from the exDNA that could be taxonomically assigned were from members of the phyla Bacteroid ...
DOI:
10.1016/j.scitotenv.2020.138392

12. Identification of a novel bacterial taxon associated with bovine mastitis showing a close evolutionary relationship with Elizabethkingia sp

Author:
Pan, Zihao; Zhou, Qian; Ma, Hui; Gong, Qianmei; Wang, Suchun; Yao, Huochun; Ma, Jiale; Wang, Kaicheng
Source:
Microbiological research 2020 v.236 pp. 126443
ISSN:
0944-5013
Subject:
open reading frames,   etc   ; Holstein; Riemerella; agar; bovine mastitis; color; genes; milk; pathogenicity; pathogens; phylogeny; ribosomal RNA; sequence analysis; sheep; single nucleotide polymorphism; China;     Show all 16 Subjects
Abstract:
... Recently, the characteristics of prevalent bacterial pathogens causing bovine mastitis have become increasingly complicated, and many commensal or unusual bacterial species have been isolated from milk samples of cows with mastitis. Strain JS20170427COW was isolated dominantly from the milk of Holstein Friesian cows with mastitis in Jiangsu province in China. Colonies of this strain showed a hillo ...
DOI:
10.1016/j.micres.2020.126443

13. Tobacco curly shoot virus C3 protein enhances viral replication and gene expression in Nicotiana benthamiana plants

Author:
Sun, Miao; Jiang, Kairong; Li, Chunji; Du, Jiang; Li, Mingjun; Ghanem, Hussein; Wu, Gentu; Qing, Ling
Source:
Virus research 2020 v.281 pp. 197939
ISSN:
0168-1702
Subject:
open reading frames,   etc   ; DNA; Nicotiana benthamiana; Potato virus X; Tobacco curly shoot virus; amino acid sequences; crops; gene overexpression; leaves; mutants; mutation; proteins; start codon; virion; virus replication;     Show all 15 Subjects
Abstract:
... Geminiviruses are single-stranded DNA viruses that cause devastating diseases in many crops worldwide. The replication enhancer proteins (REn), encoded by the C3 (AC3, and AL3) ORFs of geminiviruses, have critical roles in viral DNA accumulation and symptom development in infected plants. In the current study, we have constructed an infectious clone of the Tobacco curly shoot virus (TbCSV) C3 muta ...
DOI:
10.1016/j.virusres.2020.197939

14. GenOMIC AND Phylogenetic analysis of TWO Guinea Pig Adenovirus STRAINS RECOVERED from archival LUNG tissue

Author:
Hofmann-Sieber, Helga; Gonzalez, Gabriel; Spohn, Michael; Dobner, Thomas; Kajon, Adriana E.
Source:
Virus research 2020 pp. 197965
ISSN:
0168-1702
Subject:
open reading frames,   etc   ; DNA; Mastadenovirus; animal models; animal viruses; cytosine; genome; genomics; genotype; guanine; high-throughput nucleotide sequencing; lungs; pathogenesis; phylogeny; pneumonia; viruses; Australia; Germany;     Show all 18 Subjects
Abstract:
... Next generation sequencing was used to determine the whole genome sequence for two different strains of guinea pig adenovirus (GPAdV) detected in association with outbreaks of pneumonia in Australia in 1996, and in Germany in 1997 using total DNA extracted from infected archival frozen lung tissue as a template. The length of the determined genomic sequences was 37,031 bp and 37,070 bp, respective ...
DOI:
10.1016/j.virusres.2020.197965

15. Characterization and genome analysis of B1 sub-cluster mycobacteriophage PDRPxv

Author:
Sinha, Avni; Eniyan, Kandasamy; Manohar, Prasanth; Ramesh, Nachimuthu; Bajpai, Urmi
Source:
Virus research 2020 v.279 pp. 197884
ISSN:
0168-1702
Subject:
open reading frames,   etc   ; DNA; Mycobacterium; Siphoviridae; adsorption; antibiotic resistance; genes; growth curves; mass spectrometry; mycobacteriophage; sequence analysis; structural proteins; temperature; therapeutics; transcription (genetics); transmission electron microscopy; India;     Show all 17 Subjects
Abstract:
... Mycobacteriophages are viruses specific to mycobacteria that have gained attention as alternative therapeutic strategies for treating antibiotic-resistant infections. Mycobacteriophages are highly diverse and have been grouped into 29 clusters, 71 sub-clusters and 10 singletons based on the genome sequence. Here, we annotate the genome of PDRPxv, a lytic mycobacteriophage isolated from New Delhi; ...
DOI:
10.1016/j.virusres.2020.197884

16. Characterization of sacbrood virus and its infection in Apis cerana in the Qiandao Lake region in Zhejiang Province, China

Author:
Dong, Jie; Guo, Rui; Huang, Minjie; Wang, Deqian; Huang, Jiaxing
Source:
Journal of Asia-Pacific entomology 2020 v.23 no.1 pp. 76-81
ISSN:
1226-8615
Subject:
open reading frames,   etc   ; Apis cerana; Sacbrood virus; amino acids; complementary DNA; genes; haplotypes; honey bees; lakes; nucleotides; phylogeny; rapid amplification of cDNA ends; sequence alignment; viruses; China;     Show all 15 Subjects
Abstract:
... Chinese sacbrood virus (CSBV) is a disastrous virus that fatally threatens honeybees (Apis cerana) in China. Here, we identified the complete genome of CSBV using the rapid amplification of cDNA ends (RACE) method and compared the obtained sequences with those of other SBVs through multiple sequence alignment. The results showed that the full-length of CSBV genome from Zhejiang Province (CSBV-ZJ) ...
DOI:
10.1016/j.aspen.2019.11.003

17. Identification and Functional Characterization of Two Novel Fatty Acid Genes from Marine Microalgae for Eicosapentaenoic Acid Production

Author:
Thiyagarajan S,; Arumugam M,; Kathiresan S,
Source:
Applied biochemistry and biotechnology 2020 v.190 no.4 pp. 1371-1384
ISSN:
0273-2289
Subject:
open reading frames,   etc   ; Escherichia coli; Isochrysis; Pavlova; biosynthesis; catalytic activity; docosahexaenoic acid; eicosapentaenoic acid; enzymes; eukaryotic cells; gene expression; genes; microalgae; polymerase chain reaction; substrate specificity;     Show all 15 Subjects
Abstract:
... Marine microalgae such as Isochrysis sp. and Pavlova sp. are the predominant source of polyunsaturated fatty acids (PUFAs) such as eicosapentaenoic acid (EPA, 20:5n–3) and docosahexaenoic acid (DHA, 22:6n–3). EPA biosynthesis pathway is predominant in lower eukaryotes, and its biosynthetic gene expressions are not well established. Till date, the C18 elongation enzymes for EPA biosynthesis have no ...
DOI:
10.1007/s12010-019-03176-x

18. Molecular characterization, tissue distribution, and functional analysis of the STAC3 gene in chicken

Author:
Yin, Huadong; Zhao, Jing; Han, Shunshun; Cui, Can; Wang, Yan; Li, Diyan; Zhu, Qing
Source:
3 Biotech 2020 v.10 no.4 pp. 171
ISSN:
2190-572X
Subject:
open reading frames,   etc   ; cell differentiation; chickens; cholecystokinin; gene overexpression; genes; messenger RNA; muscle development; reverse transcriptase polymerase chain reaction; sarcoma; skeletal muscle; tissue distribution;     Show all 12 Subjects
Abstract:
... The Src homology 3 and cysteine-rich domain 3 gene (STAC3) encodes a protein containing both a cysteine-rich domain and two Src (sarcoma) homology 3 domains (SH3). STAC3 is specifically expressed in skeletal muscle and plays an important role in skeletal muscle development, but the explicit sequence and function of chicken SATC3 remain unknown. In the current study, we found the full-length chicke ...
DOI:
10.1007/s13205-020-2161-2
PubMed:
32206505
PubMed Central:
PMC7078424

19. Near-perfect kinetic resolution of racemic p-chlorostyrene oxide by SlEH1, a novel epoxide hydrolase from Solanum lycopersicum with extremely high enantioselectivity

Author:
Hu, Bo-Chun; Hu, Die; Li, Chuang; Xu, Xiong-Feng; Wen, Zheng; Wu, Min-Chen
Source:
International journal of biological macromolecules 2020 v.147 pp. 1213-1220
ISSN:
0141-8130
Subject:
open reading frames,   etc   ; Escherichia coli; Solanum lycopersicum; catalytic activity; computer simulation; enantioselectivity; epoxide hydrolase; gel chromatography; genes; hydrolysis; pH; reverse transcriptase polymerase chain reaction; thermal stability;     Show all 13 Subjects
Abstract:
... An open reading frame of sleh1, a gene encoding for a novel epoxide hydrolase from Solanum lycopersicum (SlEH1), was amplified by RT-PCR and expressed in E. coli BL21(DE3). The substrate spectrum assay showed that E. coli/sleh1 had EH activities towards all tested substrates except for racemic (rac-) 5a, and the highest enantiomeric ratio (E > 200) towards rac-2a, retaining (R)-2a with 99.1% eeₛ a ...
DOI:
10.1016/j.ijbiomac.2019.10.091

20. Comparative genomic analysis identifies small open reading frames (sORFs) with peptide-encoding features in avian 16S rDNA

Author:
Mortz, Mathieu; Dégletagne, Cyril; Romestaing, Caroline; Duchamp, Claude
Source:
Genomics 2020 v.112 no.2 pp. 1120-1127
ISSN:
0888-7543
Subject:
open reading frames,   etc   ; amino acid sequences; amino acids; birds; genomics; humans; mitochondria; mitochondrial genome; peptides; proteins; ribosomal DNA; selection pressure; stop codon;     Show all 13 Subjects
Abstract:
... The mitochondrial genome (mt-DNA) functional repertoire has recently been enriched in mammals by the identification of functional small open reading frames (sORFs) embedded in ribosomal DNAs. Through comparative genomic analyses the presence of putatively functional sORFs was investigated in birds. Alignment of available avian mt-DNA sequences revealed highly conserved regions containing four puta ...
DOI:
10.1016/j.ygeno.2019.06.026