scholarly journals Molecular Characterisation of a Novel and Highly Divergent Passerine Adenovirus 1

Viruses ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 1036
Author(s):  
Ajani Athukorala ◽  
Jade K. Forwood ◽  
David N. Phalen ◽  
Subir Sarker
Keyword(s):  
Complete Genome ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Passerine Bird ◽  
The Novel ◽  
Transmembrane Helices ◽  
Novel Genes ◽  
Separate Species ◽  
Natural Host Species ◽  
Genes Encoding

Wild birds harbour a large number of adenoviruses that remain uncharacterised with respect to their genomic organisation, diversity, and evolution within complex ecosystems. Here, we present the first complete genome sequence of an atadenovirus from a passerine bird that is tentatively named Passerine adenovirus 1 (PaAdV-1). The PaAdV-1 genome is 39,664 bp in length, which was the longest atadenovirus to be sequenced, to the best of our knowledge, and contained 42 putative genes. Its genome organisation was characteristic of the members of genus Atadenovirus; however, the novel PaAdV-1 genome was highly divergent and showed the highest sequence similarity with psittacine adenovirus-3 (55.58%). Importantly, PaAdV-1 complete genome was deemed to contain 17 predicted novel genes that were not present in any other adenoviruses sequenced to date, with several of these predicted novel genes encoding proteins that harbour transmembrane helices. Subsequent analysis of the novel PaAdV-1 genome positioned phylogenetically to a distinct sub-clade with all others sequenced atadenoviruses and did not show any obvious close evolutionary relationship. This study concluded that the PaAdV-1 complete genome described here is not closely related to any other adenovirus isolated from avian or other natural host species and that it should be considered a separate species.

scholarly journals Blastococcus jejuensis sp. nov., an actinomycete from beach sediment, and emended description of the genus Blastococcus Ahrens and Moll 1970

2006 ◽  
Vol 56 (10) ◽  
pp. 2391-2396 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Beach Sediment ◽  
Actinomycete Strain ◽  
Type Strains

A novel actinomycete, strain KST3-10T, was isolated from sand sediment of a beach in Jeju, Korea, and was subjected to polyphasic taxonomic characterization. The organism produced circular, smooth, translucent, apricot-coloured colonies comprising coccoid- or rod-shaped cells. Phylogenetic analyses based on 16S rRNA gene sequences showed that the organism belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch outside the radiation of the genus Blastococcus. The organism showed 16S rRNA gene sequence similarity values of 98.2 % with respect to Blastococcus aggregatus DSM 4725T and 98.1 % with respect to Blastococcus saxobsidens BC444T. The type strains of the two Blastococcus species shared 98.2 % sequence similarity with respect to each other, whereas the levels of sequence similarity between the novel organism and the type strains of the less closely related neighbours, Modestobacter multiseptatus and Geodermatophilus obscurus, were in the range 96.2–96.9 %. The physiological, biochemical and chemotaxonomic data revealed that the novel organism can be readily differentiated from members of the genus Blastococcus and that it merits separate species status. On the basis of the phenotypic and genotypic evidence, strain KST3-10T represents a novel species of the genus Blastococcus, for which the name Blastococcus jejuensis sp. nov. is proposed. The type strain is KST3-10T (=NRRL B-24440T=KCCM 42251T).

scholarly journals Coevolution of the Spexin/Galanin/Kisspeptin Family: Spexin Activates Galanin Receptor Type II and III

Endocrinology ◽  
2014 ◽  
Vol 155 (5) ◽  
pp. 1864-1873 ◽  
Author(s):  
Dong-Kyu Kim ◽  
Seongsik Yun ◽  
Gi Hoon Son ◽  
Jong-Ik Hwang ◽  
Cho Rong Park ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
G Protein Coupled Receptors ◽  
Receptor Interaction ◽  
The Novel ◽  
Natural Ligands ◽  
Peptide Gene ◽  
Relationship Of ◽  
G Protein Coupled ◽  
Syntenic Analysis

The novel neuropeptide spexin (SPX) was discovered using bioinformatics. The function of this peptide is currently under investigation. Here, we identified SPX along with a second SPX gene (SPX2) in vertebrate genomes. Syntenic analysis and relocating SPXs and their neighbor genes on reconstructed vertebrate ancestral chromosomes revealed that SPXs reside in the near vicinity of the kisspeptin (KISS) and galanin (GAL) family genes on the chromosomes. Alignment of mature peptide sequences showed some extent of sequence similarity among the 3 peptide groups. Gene structure analysis indicated that SPX is more closely related to GAL than KISS. These results suggest that the SPX, GAL, and KISS genes arose through local duplications before 2 rounds (2R) of whole-genome duplication. Receptors of KISS and GAL (GAL receptor [GALR]) are phylogenetically closest among rhodopsin-like G protein-coupled receptors, and synteny revealed the presence of 3 distinct receptor families KISS receptor, GALR1, and GALR2/3 before 2R. A ligand-receptor interaction study showed that SPXs activate human, Xenopus, and zebrafish GALR2/3 family receptors but not GALR1, suggesting that SPXs are natural ligands for GALR2/3. Particularly, SPXs exhibited much higher potency toward GALR3 than GAL. Together, these results identify the coevolution of SPX/GAL/KISS ligand genes with their receptor genes. This study demonstrates the advantage of evolutionary genomics to explore the evolutionary relationship of a peptide gene family that arose before 2R by local duplications.

scholarly journals Arcanobacterium bialowiezense sp. nov. and Arcanobacterium bonasi sp. nov., isolated from the prepuce of European bison bulls (Bison bonasus) suffering from balanoposthitis, and emended description of the genus Arcanobacterium Collins et al. 1983

2006 ◽  
Vol 56 (4) ◽  
pp. 861-866 ◽  
Author(s):  
Alexandra Lehnen ◽  
Hans-Jürgen Busse ◽  
Kai Frölich ◽  
Malgorzata Krasinska ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
European Bison ◽  
Rrna Gene ◽  
The Novel ◽  
Bison Bonasus ◽  
Bacterial Strains ◽  
Separate Species ◽  
Arcanobacterium Pyogenes

A taxonomic study was performed on 13 bacterial strains isolated from preputial swabs of European bison (Bison bonasus) bulls suffering from balanoposthitis. The isolates were Gram-positive, non-motile, facultatively anaerobic, diphtheroid-shaped cells. Based on biochemical profiles and BOX-PCR-generated genomic fingerprints, the isolates were grouped into two clusters represented by four and nine strains, respectively. Strains 1(W3/01)T and 2(W106/04)T, selected as representatives of the two clusters, shared 97·2 % 16S rRNA gene sequence similarity. The highest gene sequence similarities found (95·5–96·4 %) were to Arcanobacterium pyogenes DSM 20630T and Arcanobacterium bernardiae DSM 9152T, demonstrating that the novel strains are members of the genus Arcanobacterium, but are not members of a recognized species. The polar lipid profiles of the two novel strains displayed the major characteristics also found in A. pyogenes DSM 20630T and Arcanobacterium haemolyticum DSM 20595T. Detection of a quinone system with MK-10(H4) as the predominant compound confirmed phylogenetic relatedness of the novel strains to A. pyogenes and separated them from the type species of the genus, A. haemolyticum, which contains MK-9(H4) as the predominant quinone. Results from DNA–DNA hybridizations clearly demonstrated that strains 1(W3/01)T and 2(W106/04)T represent separate species. Based on these data, two novel species of the genus Arcanobacterium are described, for which the names Arcanobacterium bialowiezense sp. nov. [type strain 1(W3/01)T=DSM 17162T=NCTC 13354T] and Arcanobacterium bonasi sp. nov. [type strain 2(W106/04)T=DSM 17163T=NCTC 13355T] are proposed.

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Phylogenetic relationships of endornaviruses in common bean from the western highlands of Kenya and global sequences

2018 ◽  
Author(s):  
James M Wainaina ◽  
Elijah Ateka ◽  
Timothy Makori ◽  
Monica A Kehoe ◽  
Laura M Boykin
Keyword(s):  
Phaseolus Vulgaris ◽  
Complete Genome ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Current Knowledge ◽  
Sequence Similarity ◽  
Evolutionary Relationship ◽  
Sub Saharan Africa ◽  
Complete Genomes ◽  
Sub Saharan

Background: Endornaviruses are non-pathogenic viruses infecting multiple agricultural important crops including legumes, with global distribution. However, there is an absence on the complete genome of endornaviruses from legumes in particular with the sub-Saharan region. In this study, we report the first complete genomes of PvEV1 and PvEV2, and the evolutionary relationship of these genomes. Methods: Viral symptomatic common beans (Phaseolus vulgaris) showing Bean common mosaic necrosis virus (BCMNV) symptoms from Vihiga county, in the western highlands of Kenya were collected during field survey’s in the region. High throughput sequencing (RNA-Seq) was carried out on total RNA isolated from symptomatic leaf samples. Subsequently, de novo assembly and reference mapping was carried out to obtain the complete genomes of PvEV-1 and PvEV-2. Results: We identified the complete genome of Phaseolus vulgaris endornavirus 1 and 2 (PvEV-1 and PvEV-2) from sub-Saharan Africa (SSA). The average genome size of PvEV-1 was ~13,890 nucleotides (nt) while PvEV-2 was ~14,698 nt, encoding a single open reading frame (ORF). Single ORFs ranged from 4,632 to 4,633 aa in PvEV-1 and from 4,899 – to 4,954 aa in PvEV-2. Both ORFs encoded for the RNA-dependent RNA polymerase (RdRP) gene. The percentage sequence similarity between PvEV-1, PvEV-2 from this study GenBanks sequences was 29 % to 99 %. Bayesian phylogenetic analysis resolved in two well-supported monophyletic clades, with isolates from this study clustering with those from Brazil sequences. Discussion: This study provides the first insights into the evolutionary relationships of PvEV from SSA diverse and contributes towards filling the current knowledge gaps on endornaviruses

scholarly journals Search for genes encoding potentially amyloidogenic proteins involved in regulation of nonsense -suppresion in Sacharom yces cerevisiae

2011 ◽  
Vol 9 (4) ◽  
pp. 79-86
Author(s):  
Anton A Nizhnikov ◽  
Zalina M Magomedova ◽  
Alsu Faritovna Sayfitdinova ◽  
Sergey Georgievich Inge-Vechtomov ◽  
Aleksey Petrovich Galkin
Keyword(s):  
Genetic Background ◽  
Chimeric Protein ◽  
Nonsense Suppression ◽  
The Novel ◽  
Novel Genes ◽  
Gene Encoding ◽  
Amyloidogenic Proteins ◽  
Genes Encoding ◽  
Sup35 Gene

Previously, the deletion of SUP35N has been shown to create the genetic background for identification of the novel genes and epigenetic determinants controlling the nonsense-suppression. Here, using a genomic overexpression screen, we have found several genes encoding potentially amyloidogenic proteins, whose overexpression affects the suppressor phenotype in the strain producing the chimeric protein Aβ-Sup35MC on the background of the deletion of SUP35 gene encoding releasing factor eRF 3. It has been demonstrated the NAB2, NAB3 and VTS1 genes participate in the regulation of nonsense-suppression in S. cerevisiae.

scholarly journals Mucilaginibacter paludis gen. nov., sp. nov. and Mucilaginibacter gracilis sp. nov., pectin-, xylan- and laminarin-degrading members of the family Sphingobacteriaceae from acidic Sphagnum peat bog

2007 ◽  
Vol 57 (10) ◽  
pp. 2349-2354 ◽  
Author(s):  
Timofei A. Pankratov ◽  
Brian J. Tindall ◽  
Werner Liesack ◽  
Svetlana N. Dedysh
Keyword(s):  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
Peat Bog ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Phenotypic Differences ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains

Two facultatively aerobic, heterotrophic bacteria capable of degrading pectin, xylan, laminarin and some other polysaccharides were obtained from the acidic Sphagnum peat bog Bakchar, in western Siberia, Russia, and were designated strains TPT18T and TPT56T. Cells of these isolates are Gram-negative, non-motile, long rods that are covered by large capsules. On ageing, they transform into spherical L-forms. Strains TPT18T and TPT56T are acido- and psychrotolerant organisms capable of growth at pH 4.2–8.2 (with an optimum at pH 6.0–6.5) and at 2–33 °C (with an optimum at 20 °C). The major fatty acids are iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c); the quinones are MK-7 and MK-6. Comparative 16S rRNA gene sequence analysis revealed that the novel strains share 97 % sequence similarity and belong to the family Sphingobacteriaceae; however, they are related only distantly to members of the genera Pedobacter (91.8–93.3 % similarity) and Sphingobacterium (89.6–91.2 % similarity). The DNA G+C content of strains TPT18T and TPT56T is 42.4 and 46.1 mol%, respectively. The low DNA–DNA hybridization value (42 %) and a number of phenotypic differences between strains TPT18T and TPT56T indicated that they represent two separate species. Since the two isolates are clearly distinct from all currently described members of the family Sphingobacteriaceae, we propose a novel genus, Mucilaginibacter gen. nov., containing two novel species, Mucilaginibacter gracilis sp. nov. and Mucilaginibacter paludis sp. nov. The type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis are respectively TPT18T (=ATCC BAA-1391T =VKM B-2447T) and TPT56T (=ATCC BAA-1394T =VKM B-2446T).

scholarly journals Vibrio casei sp. nov., isolated from the surfaces of two French red smear soft cheeses

2010 ◽  
Vol 60 (8) ◽  
pp. 1745-1749 ◽  
Author(s):  
Anne Bleicher ◽  
Klaus Neuhaus ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Separate Species

Three Gram-negative, rod-shaped, catalase- and oxidase-positive, facultatively anaerobic and motile bacteria, strains WS 4538, WS 4539T and WS 4540, were isolated from the surfaces of two fully ripened French red smear soft cheeses. Based on 16S rRNA gene sequence similarity, all three strains were shown to belong to the genus Vibrio. They are most closely related to Vibrio rumoiensis S-1T (96.3 % similarity) and Vibrio litoralis MANO22DT (95.9 %). DNA–DNA hybridization confirmed that all three isolates belong to the same species and clearly separated strain WS 4539T from V. rumoiensis DSM 19141T (38–42 % relatedness) and V. litoralis DSM 17657T (28–37 %). In contrast to their nearest relatives, the strains exhibited β-galactosidase and aesculin hydrolase activities. A 14 bp insertion in the 16S rRNA gene sequence forms an elongated structure at helix 10 in the rRNA molecule and provides a tool for PCR-based identification of the novel species. Partial sequences of the housekeeping genes atpA, recA, rpoA and pyrH supported the conclusion that the three isolates constitute a separate species within the genus Vibrio. The name Vibrio casei sp. nov. is proposed for the novel taxon. Strain WS 4539T (=DSM 22364T =LMG 25240T; DNA G+C content 41.8 mol%) is the type strain and WS 4540 (=DSM 22378 =LMG 25241) is a reference strain.

scholarly journals Complete Genome Sequence of the Novel Psychrobacter sp. Strain AJ006, Which Has the Potential for Biomineralization

2020 ◽  
Vol 9 (41) ◽  
Author(s):  
Jun Ho Lee ◽  
Pyung Cheon Lee
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
The Novel ◽  
Antarctic Soil ◽  
Circular Chromosome ◽  
Biomineralization Process ◽  
Chromosomal Genes ◽  
Genes Encoding ◽  
Single Circular Chromosome

ABSTRACT A novel Psychrobacter sp. strain, AJ006, was isolated from Antarctic soil. Its complete genome sequence consists of a single circular chromosome (3,032,533 bp; G+C content, 44.0%) and a single linear plasmid (49,070 bp; G+C content, 41.7%). Chromosomal genes encoding carbonic anhydrase and urease, key enzymes in a biomineralization process, were predicted.

scholarly journals Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov.

2005 ◽  
Vol 55 (2) ◽  
pp. 787-791 ◽  
Author(s):  
Deok-Chun Yang ◽  
Wan-Taek Im ◽  
Myung Kyum Kim ◽  
Sung-Taik Lee
Keyword(s):  
Fatty Acid ◽  
Xanthomonas Campestris ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
Biochemical Profiles ◽  
Pseudoxanthomonas Taiwanensis ◽  
Established Species

Gram-negative, non-spore-forming, rod-shaped bacteria, T7-09T and TR6-08T, were isolated from soil from a ginseng field in South Korea and characterized to determine their taxonomic position. 16S rRNA gene sequence analysis showed that the two isolates shared 99·5 % sequence similarity. Strains T7-09T and TR6-08T were shown to belong to the Proteobacteria and showed the highest levels of sequence similarity to Pseudoxanthomonas broegbernensis DSM 12573T (98·1 %), Pseudoxanthomonas mexicana AMX 26BT (97·4–97·5 %), Pseudoxanthomonas japonensis 12-3T (96·5–96·6 %), Pseudoxanthomonas taiwanensis ATCC BAA-404T (95·7 %) and Xanthomonas campestris ATCC 33913T (96·3–96·5 %). The sequence similarity values with respect to any species with validly published names in related genera were less than 96·5 %. The detection of a quinone system with Q-8 as the predominant compound and a fatty acid profile with C15 : 0 iso as the predominant acid supported the assignment of the novel isolates to the order ‘Xanthomonadales’. The two isolates could be distinguished from the established species of the genus Pseudoxanthomonas by the presence of quantitative unsaturated fatty acid C17 : 1 iso ω9c and by their unique biochemical profiles. The results of DNA–DNA hybridization clearly demonstrated that T7-09T and TR6-08T represent separate species. On the basis of these data, it is proposed that T7-09T (=KCTC 12208T=IAM 15116T) and TR6-08T (=KCTC 12207T=IAM 15115T) be classified as the type strains of two novel Pseudoxanthomonas species, for which the names Pseudoxanthomonas koreensis sp. nov. and Pseudoxanthomonas daejeonensis sp. nov., respectively, are proposed.

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