scholarly journals Quaranfil, Johnston Atoll, and Lake Chad Viruses Are Novel Members of the Family Orthomyxoviridae

2009 ◽  
Vol 83 (22) ◽  
pp. 11599-11606 ◽  
Author(s):  
Rachel M. Presti ◽  
Guoyan Zhao ◽  
Wandy L. Beatty ◽  
Kathie A. Mihindukulasuriya ◽  
Amelia P. A. Travassos da Rosa ◽  
...  
Keyword(s):  
Amino Acid ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Febrile Illness ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Emerging Infections ◽  
Lake Chad ◽  
Acid Identity ◽  
The Family

ABSTRACT Arboviral infections are an important cause of emerging infections due to the movements of humans, animals, and hematophagous arthropods. Quaranfil virus (QRFV) is an unclassified arbovirus originally isolated from children with mild febrile illness in Quaranfil, Egypt, in 1953. It has subsequently been isolated in multiple geographic areas from ticks and birds. We used high-throughput sequencing to classify QRFV as a novel orthomyxovirus. The genome of this virus is comprised of multiple RNA segments; five were completely sequenced. Proteins with limited amino acid similarity to conserved domains in polymerase (PA, PB1, and PB2) and hemagglutinin (HA) genes from known orthomyxoviruses were predicted to be present in four of the segments. The fifth sequenced segment shared no detectable similarity to any protein and is of uncertain function. The end-terminal sequences of QRFV are conserved between segments and are different from those of the known orthomyxovirus genera. QRFV is known to cross-react serologically with two other unclassified viruses, Johnston Atoll virus (JAV) and Lake Chad virus (LKCV). The complete open reading frames of PB1 and HA were sequenced for JAV, while a fragment of PB1 of LKCV was identified by mass sequencing. QRFV and JAV PB1 and HA shared 80% and 70% amino acid identity to each other, respectively; the LKCV PB1 fragment shared 83% amino acid identity with the corresponding region of QRFV PB1. Based on phylogenetic analyses, virion ultrastructural features, and the unique end-terminal sequences identified, we propose that QRFV, JAV, and LKCV comprise a novel genus of the family Orthomyxoviridae.

scholarly journals Triticum mosaic virus: A Distinct Member of the Family Potyviridae with an Unusually Long Leader Sequence

2009 ◽  
Vol 99 (8) ◽  
pp. 943-950 ◽  
Author(s):  
Satyanarayana Tatineni ◽  
Amy D. Ziems ◽  
Stephen N. Wegulo ◽  
Roy French
Keyword(s):  
Amino Acid ◽  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Recent Common Ancestor ◽  
Acid Identity ◽  
Most Recent Common Ancestor ◽  
Nontranslated Region ◽  
The Family ◽  
Distinct Member

The complete genome sequence of Triticum mosaic virus (TriMV), a member in the family Potyviridae, has been determined to be 10,266 nucleotides (nt) excluding the 3′ polyadenylated tail. The genome encodes a large polyprotein of 3,112 amino acids with the “hall-mark proteins” of potyviruses, including a small overlapping gene, PIPO, in the P3 cistron. The genome of TriMV has an unusually long 5′ nontranslated region of 739 nt with 12 translation initiation codons and three small open reading frames, which resemble those of the internal ribosome entry site containing 5′ leader sequences of the members of Picornaviridae. Pairwise comparison of 10 putative mature proteins of TriMV with those of representative members of genera in the family Potyviridae revealed 33 to 44% amino acid identity within the highly conserved NIb protein sequence and 15 to 29% amino acid identity within the least conserved P1 protein, suggesting that TriMV is a distinct member in the family Potyviridae. In contrast, TriMV displayed 47 to 65% amino acid sequence identity with available sequences of mature proteins of Sugarcane streak mosaic virus (SCSMV), an unassigned member of the Potyviridae. Phylogenetic analyses of the complete polyprotein, NIa-Pro, NIb, and coat protein sequences of representative species of six genera and unassigned members of the family Potyviridae suggested that TriMV and SCSMV are sister taxa and share a most recent common ancestor with tritimoviruses or ipomoviruses. These results suggest that TriMV and SCSMV should be classified in a new genus, and we propose the genus Poacevirus in the family Potyviridae, with TriMV as the type member.

scholarly journals A Mating-Induced Protein of Phytophthora infestans Is a Member of a Family of Elicitors with Divergent Structures and Stage-Specific Patterns of Expression

2003 ◽  
Vol 16 (10) ◽  
pp. 926-935 ◽  
Author(s):  
Anna-Liisa Fabritius ◽  
Howard S. Judelson
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gene Family ◽  
Phytophthora Infestans ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Terminal Domain ◽  
Defense Reactions ◽  
The Family ◽  
Microbe Interactions

Five members of an elicitor-like gene family from Phytophthora infestans were examined. The family was identified through the analysis of M81, a mating-induced gene. The predicted M81 product resembled a 42-kDa P. sojae glycoprotein known to elicit defense reactions in plants, including a host of P. infestans, potato. M81 was the most structurally and functionally divergent of the P. infestans genes compared with the P. sojae sequence. M81 lacked elicitor activity, had the lowest protein identity (47%), displayed mating-specific transcription, and had a novel C-terminal domain. The latter contained a 30-residue proline- and threonine-rich motif, which, remarkably, was tandemly repeated 24 to 36 times in different alleles. M81C, M81D, and M81E better resembled the P. sojae protein based on amino acid identity (63 to 75%) and conserved elicitor activity. M81C and M81D mRNA accumulated only during zoosporogenesis, while M81E expression was restricted to hyphae. M81B, an apparent pseudogene, was physically linked to M81. The protein products of each gene were predicted to be extracellular transglutaminases ranging in size from 436 to 1,607 amino acids. Genes with an elicitor, proline- and threonine-rich repeat, and both elicitor and repeat domains were widely distributed throughout Phytophthora infestans. These findings help explain the natural functions of elicitors in pathogen biology and plant-microbe interactions.

scholarly journals Comparative Genomics and Environmental Distribution of Large dsDNA viruses in the family Asfarviridae

2021 ◽  
Author(s):  
Sangita Karki ◽  
Mohammad Moniruzzaman ◽  
Frank O. Aylward
Keyword(s):  
Amino Acid ◽  
African Swine Fever Virus ◽  
Phylogenetic Analyses ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Metagenomic Data ◽  
Genome Comparison ◽  
Marker Genes ◽  
Environmental Distribution ◽  
Acid Identity

AbstractThe Asfarviridae is a family of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) of which African swine fever virus (ASFV) is the most well-characterized. Recently the discovery of several Asfarviridae members other than ASFV has suggested that this family represents a diverse and cosmopolitan group of viruses, but the genomics and distribution of this family have not been studied in detail. To this end we analyzed five complete genomes and 35 metagenome-assembled genomes (MAGs) of viruses from this family to shed light on their evolutionary relationships and environmental distribution. The Asfarvirus MAGs derive from diverse marine, freshwater, and terrestrial habitats, underscoring the broad environmental distribution of this family. We present phylogenetic analyses using conserved marker genes and whole-genome comparison of pairwise average amino acid identity values, revealing a high level of genomic divergence across disparate Asfarviruses. Further, we found that Asfarviridae genomes encode genes with diverse predicted metabolic roles and detectable sequence homology to proteins in bacteria, archaea, and different eukaryotes, highlighting the genomic chimerism that is a salient feature of NCLDV. Our read mapping from Tara oceans metagenomic data also revealed that three Asfarviridae MAGs were present in multiple marine samples, indicating that they are widespread in the ocean. In one of these MAGs we identified four marker genes with >95% amino acid identity to genes sequenced from a virus that infects the dinoflagellate Heterocapsa circularisquama (HcDNAV). This suggests a potential host for this MAG, which would thereby represent a near-complete genome of a dinoflagellate-infecting giant virus. Together, these results show that Asfarviridae are ubiquitous, comprise similar sequence divergence as other NCLDV families, and include several members that are widespread in the ocean and potentially infect ecologically important protists.

scholarly journals Phylogenetic relationships among haloalkaliphilic archaea of the family Natrialbaceae

2020 ◽  
Author(s):  
Shivakumara Siddaramappa
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Novel Species ◽  
Single Species ◽  
Amino Acid Identity ◽  
Average Nucleotide Identity ◽  
Acid Identity ◽  
Average Amino Acid Identity ◽  
The Family ◽  
Clade 1

ABSTRACTThe family Natrialbaceae is a member of the class Halobacteria of the archaeal phylum Euryarchaeota. Seventeen genera with validly or effectively published names are currently included within this family. In this study, using pairwise average nucleotide identity and average amino acid identity comparisons in conjunction with phylogenetic analysis, it has been shown that the family Natrialbaceae is highly diverse and contains several potentially novel species and genera that are yet to be fully characterized. The deduced proteome sequence-based phylogenetic tree, constructed using the alignment- and parameter-free method CVTree3, contained six major clades, with Salinarchaeum sp. Harcht-Bsk1 being the only representative within clade 1. Furthermore, Haloterrigena daqingensis was found to be closely related to Natronorubrum sediminis, and it is proposed that these archaea together represent a novel genus. Interestingly, Haloterrigena jeotgali, Haloterrigena thermotolerans, and Natrinema pellirubrum were found to be very closely related to each other, and it is proposed that they be merged into a single species. Notably, the type genus Natrialba itself appeared to be heterogenous and contains species that could be broadly classified among two genera. Likewise, the genus Natrinema is also heterogenous and contains species that could be classified among six genera. Altogether, 19 novel genera have been proposed to be created, and four haloalkaliphilic archaea hitherto recognized only using genus names are confirmed to represent novel species.

Sequence and characterization of a novel chromosomal aminoglycoside phosphotransferase gene, aph (3')-IIb, in Pseudomonas aeruginosa.

1996 ◽  
Vol 40 (5) ◽  
pp. 1254-1256 ◽  
Author(s):  
H Hächler ◽  
P Santanam ◽  
F H Kayser
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Acid Identity ◽  
Aminoglycoside Phosphotransferase ◽  
Psti Fragment ◽  
Reading Frames

A novel, probably chromosomally encoded, aminoglycoside phosphotransferase gene was cloned on a 2,996-bp PstI fragment from Pseudomonas aeruginosa and designated aph (3')-IIb. It coded for a protein of 268 amino acids that showed 51.7% amino acid identity with APH (3')-II [APH(3') is aminoglycoside-3' phosphotransferase] from Tn5. Two other open reading frames on the cloned fragment showed homology to a signal-transducing system in P. aeruginosa.

scholarly journals Characterization and Complete Nucleotide Sequence of an Unusual Reptilian Retrovirus Recovered from the Order Crocodylia

2002 ◽  
Vol 76 (9) ◽  
pp. 4651-4654 ◽  
Author(s):  
Joanne Martin ◽  
Peter Kabat ◽  
Elisabeth Herniou ◽  
Michael Tristem
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Complete Nucleotide Sequence ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Acid Identity ◽  
Conserved Regions

ABSTRACT A novel group of retroviruses found within the order Crocodylia are described. Phylogenetic analyses demonstrate that they are probably the most divergent members of the Retroviridae described to date; even the most conserved regions of Pol show an average of only 23% amino acid identity when compared to other retroviruses.

scholarly journals Analysis of the Choristoneura fumiferana nucleopolyhedrovirus genome

2005 ◽  
Vol 86 (4) ◽  
pp. 929-943 ◽  
Author(s):  
Jondavid G. de Jong ◽  
Hilary A. M. Lauzon ◽  
Cliff Dominy ◽  
Arkadi Poloumienko ◽  
Eric B. Carstens ◽  
...  
Keyword(s):  
Amino Acid ◽  
Choristoneura Fumiferana ◽  
Amino Acid Identity ◽  
Open Reading Frames ◽  
Acid Identity ◽  
Orgyia Pseudotsugata ◽  
Double Stranded Dna ◽  
Enhancing Factor ◽  
Group I ◽  
Reading Frames

The double-stranded DNA genome of Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) was sequenced and analysed in the context of other group I nucleopolyhedroviruses (NPVs). The genome consists of 129 593 bp with a G+C content of 50·1 mol%. A total of 146 open reading frames (ORFs) of greater than 150 bp, and with no or minimal overlap were identified. In addition, five homologous regions were identified containing 7–10 repeats of a 36 bp imperfect palindromic core. Comparison with other completely sequenced baculovirus genomes revealed that 139 of the CfMNPV ORFs have homologues in at least one other baculovirus and seven ORFs are unique to CfMNPV. Of the 117 CfMNPV ORFs common to all group I NPVs, 12 are exclusive to group I NPVs. Overall, CfMNPV is most similar to Orgyia pseudotsugata MNPV based on gene content, arrangement and overall amino acid identity. Unlike other group I baculoviruses, however, CfMNPV encodes a viral enhancing factor (vef) and has two copies of p26.

scholarly journals Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

2020 ◽  
Vol 70 (8) ◽  
pp. 4432-4450 ◽  
Author(s):  
Ainsley C. Nicholson ◽  
Christopher A. Gulvik ◽  
Anne M. Whitney ◽  
Ben W. Humrighouse ◽  
Melissa E. Bell ◽  
...  
Keyword(s):  
Amino Acid ◽  
Type Species ◽  
Amino Acid Identity ◽  
The Novel ◽  
Content Type ◽  
Acid Identity ◽  
Link Type ◽  
The Family ◽  
Permian Extinction ◽  
Extinction Events

The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov.

scholarly journals A50 Whole-genome sequencing of African swine fever isolates from Sardinia

2019 ◽  
Vol 5 (Supplement_1) ◽  
Author(s):  
C Torresi ◽  
F Granberg ◽  
L Bertolotti ◽  
A Oggiano ◽  
B Colitti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Temporal Distribution ◽  
African Swine Fever ◽  
Amino Acid Identity ◽  
Genotype I ◽  
Acid Identity ◽  
Wide Range ◽  
Intergenic Sequences ◽  
Genes Encoding

Abstract In order to assess the molecular epidemiology of African swine fever (ASF) in Sardinia, we analyzed a wide range of isolates from wild and domestic pigs over a 31-year period (1978–2009) by genotyping sequence data from the genes encoding the p54 and the p72 proteins and the CVR. On this basis, the analysis of the B602L gene revealed a minor difference, placing the Sardinian isolates into two clusters according to their temporal distribution. As an extension of this study, in order to achieve a higher level of discrimination, three further variable genome regions, namely p30, CD2v, and I73R/I329L, of a large number of isolates collected from outbreaks in the years 2002–14 have been investigated. Sequence analysis of the CD2v region revealed a temporal subdivision of the viruses into two subgroups. These data, together with those from the B602L gene analysis, demonstrated that the viruses circulating in Sardinia belong to p72/genotype I, but since 1990 have undergone minor genetic variations in respect to its ancestor, thus making it impossible to trace isolates, enabling a more accurate assessment of the origin of outbreaks, and extending knowledge of virus evolution. To solve this problem, we have sequenced and annotated the complete genome of nine ASF isolates collected in Sardinia between 1978 and 2012. This was achieved using sequence data determined by next-generation sequencing. The results showed a very high identity with range of nucleotide similarity among isolates of 99.5 per cent to 99.9 per cent. The ASF virus (ASFV) genomes were composed of terminal inverted repeats and conserved and non-conserved ORFs. Among the conserved ORFs, B385R, H339R, and O61R-p12 showed 100 per cent amino acid identity. The same was true for the hypervariable ORFs, with regard to X69R, DP96R, DP60R, EP153R, B407L, I10L, and L60L genes. The EP402R and B602L genes showed, as expected, an amino acid identity range of 98.5 per cent to 100 per cent and 91 per cent to 100 per cent, respectively. In addition, all of the isolates displayed variable intergenic sequences. As a whole, the results from our studies confirmed a remarkable genetic stability of the ASFV/p72 genotype I viruses circulating in Sardinia.

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