Phylogenetic analyses and genomic variation of the 2019-nCoV

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

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Characterization of Novel Erwinia amylovora Jumbo Bacteriophages from Eneladusvirus Genus

Viruses ◽

10.3390/v12121373 ◽

2020 ◽

Vol 12 (12) ◽

pp. 1373

Author(s):

Sang Guen Kim ◽

Sung Bin Lee ◽

Sib Sankar Giri ◽

Hyoun Joong Kim ◽

Sang Wha Kim ◽

...

Keyword(s):

Genome Size ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Gc Content ◽

Genomic Analysis ◽

Open Reading Frames ◽

Comparative Genomic ◽

Limited Information ◽

High Sequence Similarity ◽

A Genome

Jumbo phages, which have a genome size of more than 200 kb, have recently been reported for the first time. However, limited information is available regarding their characteristics because few jumbo phages have been isolated. Therefore, in this study, we aimed to isolate and characterize other jumbo phages. We performed comparative genomic analysis of three Erwinia phages (pEa_SNUABM_12, pEa_SNUABM_47, and pEa_SNUABM_50), each of which had a genome size of approximately 360 kb (32.5% GC content). These phages were predicted to harbor 546, 540, and 540 open reading frames with 32, 34, and 35 tRNAs, respectively. Almost all of the genes in these phages could not be functionally annotated but showed high sequence similarity with genes encoded in Serratia phage BF, a member of Eneladusvirus. The detailed comparative and phylogenetic analyses presented in this study contribute to our understanding of the diversity and evolution of Erwinia phage and the genus Eneladusvirus.

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Genomic variance of the 2019-nCoV coronavirus

10.1101/2020.02.02.931162 ◽

2020 ◽

Cited By ~ 12

Author(s):

Carmine Ceraolo ◽

Federico M. Giorgi

Keyword(s):

Scientific Community ◽

Sequence Similarity ◽

Molecular Characteristics ◽

Genomic Information ◽

High Sequence Similarity ◽

Sequence Identity ◽

Genomic Variance ◽

Global Concern ◽

Novel Coronavirus ◽

Bat Coronavirus

AbstractThere is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.

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Molecular Characteristics of Carnivore Protoparvovirus 1 With High Sequence Similarity Between Wild and Domestic Carnivores in Taiwan

10.20944/preprints202104.0600.v1 ◽

2021 ◽

Author(s):

Ai-Mei Chang ◽

Chen-Chih Chen

Keyword(s):

Dna Sequences ◽

Gastrointestinal Disease ◽

Sequence Similarity ◽

Domestic Dogs ◽

Molecular Characteristics ◽

High Sequence Similarity ◽

Vp2 Gene ◽

Pcr Screening ◽

Wild Carnivores ◽

Domestic Carnivores

Carnivore protoparvovirus 1 (CPPV-1) is a DNA virus causing gastrointestinal disease and immunosuppression in various terrestrial carnivores. Domestic dogs and cats are considered the primary CPPV-1 reservoirs. The habitat overlaps of wild carnivores and free-roaming dogs increases the threat of CPPV-1 transmission between them. This study explored the CPPV-1 distribution among wild carnivores through PCR screening and compared the DNA sequences of the partial capsid protein (VP2) between wild and domestic carnivores. In total, 181 samples were screened for the CPPV-1 VP2 gene, including 32 masked palm civets (Paguma larvata), 63 Chinese ferret badgers (Melogale moschata), and 86 crab-eating mongooses (Herpestes urva), from 2015 to 2019 in Taiwan. The average prevalence of CPPV-1 was 17.7% (32/181), with the highest prevalence in masked palm civets (37.5%). In addition, a masked palm civet was coinfected with two CPPV-1 strains. Among the 33 partial VP2 gene sequences, 23 were identical to sequences amplified from domestic dogs and cats in Asia and the remaining 10 were identified for the first time. This study demonstrated that CPPV-1 has circulated between domestic and wild carnivores in rural Taiwan. Therefore, further population control and health management of free-roaming domestic carnivores are recommended.

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Coevolution ofaah: Adps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

The Scientific World JOURNAL ◽

10.1100/2012/504905 ◽

2012 ◽

Vol 2012 ◽

pp. 1-9 ◽

Cited By ~ 2

Author(s):

Liyan Ping ◽

Matthias Platzer ◽

Gaiping Wen ◽

Nicolas Delaroque

Keyword(s):

Stop Codon ◽

Sequence Similarity ◽

General Pattern ◽

Genomic Analysis ◽

Dna Binding Proteins ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Host Bacterium ◽

High Sequence Similarity ◽

Lepidopteran Larvae

A protein named AAH was isolated from the bacteriumMicrobacterium arborescensSE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell) but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of theaahgene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny ofdps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. Theaahgene had evolved new function but still retained the typical dodecameric structure.

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Phylogenetic Analysis of Spike and Envelope Proteins for a Number of Bat Coronaviruses for Understanding the Hypothesis of Possible Origin for the Novel 2019-nCoV

Kurdistan Journal of Applied Research ◽

10.24017/science.2020.ichms2020.15 ◽

2020 ◽

pp. 137-144

Author(s):

Salar Ibrahim Ali

Keyword(s):

Hong Kong ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Tree ◽

Envelope Protein ◽

Spike Protein ◽

Phylogenetic Tree Analysis ◽

Tree Analysis ◽

Close Relationship ◽

Bat Coronavirus

Coronavirus Disease 19 (COVID-19) emergence reveals globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV; moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade.

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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

10.21203/rs.3.rs-33194/v1 ◽

2020 ◽

Author(s):

Tingting Li ◽

Dongxia Liu ◽

Yadi Yang ◽

Jiali Guo ◽

Yujie Feng ◽

...

Keyword(s):

Phylogenetic Tree ◽

Common Ancestor ◽

Virus Disease ◽

Evolutionary Relationship ◽

Critical Issue ◽

Last Common Ancestor ◽

Genome Sequences ◽

Phylogenetic Tree Analysis ◽

Origin And Evolution ◽

Bat Coronavirus

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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Identification of a novel receptor for an invertebrate oxytocin/vasopressin superfamily peptide: molecular and functional evolution of the oxytocin/vasopressin superfamily

Biochemical Journal ◽

10.1042/bj20040555 ◽

2004 ◽

Vol 382 (1) ◽

pp. 231-237 ◽

Cited By ~ 27

Author(s):

Tsuyoshi KAWADA ◽

Atsuhiro KANDA ◽

Hiroyuki MINAKATA ◽

Osamu MATSUSHIMA ◽

Honoo SATAKE

Keyword(s):

Sequence Similarity ◽

Genomic Analysis ◽

Egg Laying ◽

Pcr Analysis ◽

High Sequence Similarity ◽

Calcium Dependent ◽

Functional Correlation ◽

Dependent Signal ◽

Egg Laying Behaviour

Annetocin is structurally related to an OT (oxytocin)/VP (vasopressin) family peptide, which has been isolated from the earthworm Eisenia foetida and has been shown to induce OT-like egg-laying behaviour. We now report the identification of an endogenous AnR (annetocin receptor). The deduced AnR precursor displays high sequence similarity with OT/VP receptors. Genomic analysis of the AnR gene revealed that the intron-inserted position is conserved between the AnR gene and the mammalian OT/VP receptor genes. These results indicate that AnR and mammalian OT/VP receptors share a common ancestor gene. Administration of annetocin to the AnR expressed in Xenopus oocytes induced a calcium-dependent signal transduction. Reverse transcriptase–PCR analysis and in situ hybridization showed that the AnR gene is expressed specifically in the nephridia located in the clitellum region, although the nephridia are distributed throughout the worm body. This result suggests that annetocin induces egg-laying behaviour through its action on the nephridia. This is the first description concerning the functional correlation between an invertebrate OT/VP-related peptide and egg-laying behaviour.

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High diversity of fungi associated with living parts of boreal forest bryophytes

Botany ◽

10.1139/b08-102 ◽

2008 ◽

Vol 86 (11) ◽

pp. 1326-1333 ◽

Cited By ~ 52

Author(s):

Håvard Kauserud ◽

Cecilie Mathiesen ◽

Mikael Ohlson

Keyword(s):

Boreal Forest ◽

Boreal Forests ◽

Fungal Diversity ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

High Sequence Similarity ◽

Operational Taxonomic Units ◽

Main Portion ◽

Similarity Searches ◽

Small Overlap

Bryophytes are a dominant and functionally important component of the forest floor vegetation in boreal forests, yet little is known about the fungal diversity associated with these abundant plants. Using molecular identification, we document an ecologically and phylogenetically diverse array of fungi associated with the living parts of three widespread and abundant boreal forest bryophytes, i.e., Hylocomium splendens (Hedw.) Schimp. in B.S.G., Pleurozium schreberi (Brid.) Mitt., and Polytrichum commune Hedw. From 376 cloned ITS sequences, 158 operational taxonomic units (OTUs), roughly corresponding to the number of species, were defined based on sequence similarity searches (Fasta) and phylogenetic analyses. A main portion (62.8%) of the OTUs belonged to Ascomycota, 32.0% to Basidiomycota, 3.9% to Chytridiomycota, and 1.3% to Glomeromycota. The most common orders were Helotiales (18.6%), Agaricales (11.5%), Chaetothyriales (9.6%), and Tremellales (9.0%). Frequently detected OTUs of potentially high ecologic importance included two with high sequence similarity (>99%) to the agaric Entoloma conferendum (Britzelm.) Noordel and the endophyte Lophodermium piceae (Fckl.) Hoehn., and various OTUs with affinity to the Helotian genus Hyphodiscus. Several ectomycorrhiza-forming basidiomycetes were also detected. Most OTUs (77.2%) were only detected once and a very small overlap in composition of OTUs was observed among the three bryophytes, indicating the occurrence of an immense fungal diversity associated with boreal forest bryophytes that deserves further study.

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Morphological and Molecular Characteristics of Pratylenchus coffeae from the Origin of Robusta Coffee Plantation in Malang, East Java

Jurnal Perlindungan Tanaman Indonesia ◽

10.22146/jpti.42481 ◽

2019 ◽

Vol 23 (2) ◽

pp. 211

Author(s):

Aris Budiman ◽

Supramana Supramana ◽

Giyanto Giyanto

Keyword(s):

Phylogenetic Tree ◽

Universal Primers ◽

Molecular Characteristics ◽

28S Rrna ◽

Coffee Plantation ◽

Phylogenetic Tree Analysis ◽

Morphometric Characters ◽

Pratylenchus Coffeae ◽

Robusta Coffee ◽

Molecular Characters

Pratylenchus coffeae is the most important plant-parasitic nematode in Robusta coffee plantations. Information regarding morphology, morphometric and molecular characters of P. coffeae has not been reported in Indonesia. This study is aimed to describe those characters of P. coffeae that attack Robusta coffee. Root samples were taken from Robusta coffee plantation in Malang, East Java. Nematode extractions was conducted using a mist chamber method. Morphology and morphometric characters were observed from the permanent nematode slides. Single nematode DNA extract was amplified at the D2D3 segment of 28S rRNA and ITS1-5.8S-ITS2 rRNA with universal primers. Amplicon was sequenced and analysed for phylogenetic tree relationships. Female morphological key character of P. coffeae observed are: lip with two annulations, four lateral lines, esophageal overlap with intestine ventrally, monodelphic, and truncated tail shape. Male spicules curved ventrally. Female morphometrics are: n=26, L = 556.4 μm, DGO = 2.4 μm, anterior gonad = 174.8 μm, a = 28.5, b = 6.1, b’ = 4.1, c = 20.1, c’ = 2.3, V = 81.7. A Male is smaller than a female with n=24, L = 505.9 μm, a = 32.3, b = 5.5, b '= 3.9, c = 15.3, c' = 2.8 and T = 40.6. The molecular characters of P. coffeae were investigated for two isolates, namely SA1 and SA2. Based on the D2D3 and ITS1-5.8S-ITS2 regions, isolate SA1 has similarity level of 99% and 97% to the P. coffeae from NCBI. Similar result was shown by Isolate SA2 with similarity of 100% and 100% respectively. Phylogenetic tree analysis using Maximum Likelihood at the D2D3 segment of 28S rRNA and ITS1-5.8S-ITS2 regions showed that P. coffeae in this study was included in one clade with P. coffeae from several countries.

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Filimonas effusa sp. nov., isolated from a freshwater river

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.003875 ◽

2020 ◽

Vol 70 (3) ◽

pp. 1508-1515 ◽

Cited By ~ 4

Author(s):

Wen-Ming Chen ◽

Tzu-Ying Chen ◽

Zhi-Hao Li ◽

Soon-Wo Kwon ◽

Shih-Yi Sheu

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Species ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Rrna Gene ◽

High Sequence Similarity ◽

Content Type ◽

Link Type ◽

Freshwater River

Strain TTM-71T, isolated from a freshwater river in Taiwan, was characterized using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain TTM-71T is affiliated with species in the genus Filimonas . The 16S rRNA gene sequence similarity indicated that strain TTM-71T is closely related to species within the genus Filimonas (94.7–95.5 % sequence similarity) and had a high sequence similarity with Filimonas endophytica SR 2-06T (95.5 %). Strain TTM-71T showed 70.3 % average nucleotide identity and 24.9 % digital DNA–DNA hybridization identity with Filimonas lacunae YT21T. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed beige-colored colonies. Optimal growth occurred at 20 °C, pH 8, and in the presence of 0.5 % NaCl. The major fatty acids of strain TTM-71T were iso-C15 : 0, iso-C15 : 1 G and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c). The predominant hydroxy fatty acid was iso-C17 : 0 3-OH. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, four uncharacterized aminophospholipids, one uncharacterized aminolipid, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamine was homospermidine. The only isoprenoid quinone was MK-7. Genomic DNA G+C content was 45.6 mol%. On the basis of the polyphasic evidence presented, strain TTM-71T is considered to represent a novel species of the genus Filimonas , for which the name Filimonas effusa sp. nov. is proposed. The type strain is TTM-71T (=BCRC 81160T=LMG 31017T=KCTC 62871T).

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