scholarly journals Identification and Full Characterisation of Two Novel Crustacean Infecting Members of the Family Nudiviridae Provides Support for Two Subfamilies

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1694
Author(s):  
Kelly S. Bateman ◽  
Rose Kerr ◽  
Grant D. Stentiford ◽  
Tim P. Bean ◽  
Chantelle Hooper ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Carcinus Maenas ◽  
International Committee ◽  
Shore Crab ◽  
Cell Nuclei ◽  
Crangon Crangon ◽  
The Family ◽  
Ultrastructural Characteristics ◽  
Core Genes

Multiple enveloped viruses with rod-shaped nucleocapsids have been described, infecting the epithelial cell nuclei within the hepatopancreas tubules of crustaceans. These bacilliform viruses share the ultrastructural characteristics of nudiviruses, a specific clade of viruses infecting arthropods. Using histology, electron microscopy and high throughput sequencing, we characterise two further bacilliform viruses from aquatic hosts, the brown shrimp (Crangon crangon) and the European shore crab (Carcinus maenas). We assembled the full double stranded, circular DNA genome sequences of these viruses (~113 and 132 kbp, respectively). Comparative genomics and phylogenetic analyses confirm that both belong within the family Nudiviridae but in separate clades representing nudiviruses found in freshwater and marine environments. We show that the three thymidine kinase (tk) genes present in all sequenced nudivirus genomes, thus far, were absent in the Crangon crangon nudivirus, suggesting there are twenty-eight core genes shared by all nudiviruses. Furthermore, the phylogenetic data no longer support the subdivision of the family Nudiviridae into four genera (Alphanudivirus to Deltanudivirus), as recently adopted by the International Committee on Taxonomy of Viruses (ICTV), but rather shows two main branches of the family that are further subdivided. Our data support a recent proposal to create two subfamilies within the family Nudiviridae, each subdivided into several genera.

scholarly journals Rhizobium desertarenae sp. nov., isolated from the Saline Desert Soil from the Rann of Kachchh, India

2020 ◽  
Author(s):  
Mitesh Khairnar ◽  
Ashwini Hagir ◽  
Avinash Narayan ◽  
Kunal Jain ◽  
Datta Madamwar ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Desert Soil ◽  
Rrna Gene ◽  
The Family ◽  
Saline Desert ◽  
Distinct Branch ◽  
Core Genes

AbstractA novel bacterial strain designated ADMK78T was isolated from the saline desert soil. The cells were rod-shaped, Gram-negative, and non-motile. The strain ADMK78T grows best at 28°C and pH 7.0 and can tolerate up to 2% (w/v) NaCl. Based on 16S rRNA gene phylogeny, the strain ADMK78T belongs to the genus Rhizobium, with the highest similarity to Rhizobium wuzhouense W44T (98.7%) and Rhizobium ipomoeae shin9-1T (97.9%). Core-genes based phylogenetic analysis revealed that the strain ADMK78T forms a distinct branch in between Rhizobium ipomoeae shin9-1T and Rhizobium selenitireducens BAA-1503T. The average nucleotide identity of ADMK78T was less than 82%, to members of the family Rhizobiaceae. The genomic DNA G+C content of strain ADMK78T is 58.6 mol%. The major fatty acids of strain ADMK78T were C18:0 and C18:1 ω7c. The strain ADMK78T showed differences in physiological, phenotypic, and protein profiles estimated by MALDI-TOF MS to its closest relatives. Based on the phenotypic, chemotaxonomic properties, and phylogenetic analyses, the strain ADMK78T could be distinguished from the recognized species of the genus Rhizobium. It is suggested to represent a novel species of this genus, for which the name Rhizobium desertarenae sp. nov. is proposed. The type strain is ADMK78T (=MCC 3400T; KACC 21383T; JCM 33657T).

scholarly journals Diagnosis and prevalence of two new species of haplosporidians infecting shore crabs Carcinus maenas: Haplosporidium carcini n. sp., and H. cranc n. sp.

Parasitology ◽  
2020 ◽  
Vol 147 (11) ◽  
pp. 1229-1237 ◽  
Author(s):  
Charlotte E. Davies ◽  
David Bass ◽  
Georgia M. Ward ◽  
Frederico M. Batista ◽  
Sophie H. Malkin ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Carcinus Maenas ◽  
Small Subunit ◽  
Shore Crab ◽  
Phylogenetic Characterization ◽  
South Wales ◽  
Two New Species ◽  
Shore Crabs ◽  
Swansea Bay

AbstractThis study provides a morphological and phylogenetic characterization of two novel species of the order Haplosporida (Haplosporidium carcini n. sp., and H. cranc n. sp.) infecting the common shore crab Carcinus maenas collected at one location in Swansea Bay, South Wales, UK. Both parasites were observed in the haemolymph, gills and hepatopancreas. The prevalence of clinical infections (i.e. parasites seen directly in fresh haemolymph preparations) was low, at ~1%, whereas subclinical levels, detected by polymerase chain reaction, were slightly higher at ~2%. Although no spores were found in any of the infected crabs examined histologically (n = 334), the morphology of monokaryotic and dikaryotic unicellular stages of the parasites enabled differentiation between the two new species. Phylogenetic analyses of the new species based on the small subunit (SSU) rDNA gene placed H. cranc in a clade of otherwise uncharacterized environmental sequences from marine samples, and H. carcini in a clade with other crustacean-associated lineages.

scholarly journals Characterization of the Mycovirome of the Phytopathogenic Fungus, Neofusicoccum parvum

Viruses ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 375
Author(s):  
Armelle Marais ◽  
Chantal Faure ◽  
Gwenaëlle Comont ◽  
Thierry Candresse ◽  
Elodie Stempien ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Phytopathogenic Fungus ◽  
Sequencing Analysis ◽  
Single Strain ◽  
Neofusicoccum Parvum ◽  
The Family ◽  
Pcr Products ◽  
Botryosphaeria Dieback

Neofusicoccum parvum is a fungal plant-pathogen belonging to the family Botryosphaeriaceae, and is considered one of the most aggressive causal agents of the grapevine trunk disease (GTD) Botryosphaeria dieback. In this study, the mycovirome of a single strain of N. parvum (COLB) was characterized by high throughput sequencing analysis of total RNA and subsequent bioinformatic analyses. Contig annotations, genome completions, and phylogenetic analyses allowed us to describe six novel mycoviruses belonging to four different viral families. The virome is composed of two victoriviruses in the family Totiviridae, one alphaendornavirus in the family Endornaviridae, two mitoviruses in the family Mitoviridae, and one narnavirus belonging to the family Narnaviridae. The presence of the co-infecting viruses was confirmed by sequencing the RT-PCR products generated from total nucleic acids extracted from COLB. This study shows that the mycovirome of a single N. parvum strain is highly diverse and distinct from that previously described in N. parvum strains isolated from grapevines.

scholarly journals The (non) accuracy of mitochondrial genomes for family level phylogenetics: the case of erebid moths (Lepidoptera; Erebidae)

2021 ◽  
Author(s):  
Hamid Reza Ghanavi ◽  
Victoria Twort ◽  
Tobias Joannes Hartman ◽  
Reza Zahiri ◽  
Niklas Wahlberg
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
The Family ◽  
History Of ◽  
Genomic Scale

The use of molecular data to study evolutionary history of different organisms, revolutionized the field of systematics. Now with the appearance of high throughput sequencing (HTS) technologies more and more genetic sequence data is available. One of the important sources of genetic data for phylogenetic analyses has been mitochondrial DNA. The limitations of mitochondrial DNA for the study of phylogenetic relationships have been thoroughly explored in the age of single locus phylogenies. Now with the appearance of genomic scale data, more and more mitochondrial genomes are available. Here we assemble 47 mitochondrial genomes using whole genome Illumina short reads of representatives of the family Erebidae (Lepidoptera), in order to evaluate the accuracy of mitochondrial genome application in resolving deep phylogenetic relationships. We find that mitogenomes are inadequate for resolving subfamily level relationships in Erebidae, but given good taxon sampling, we see its potential in resolving lower level phylogenetic relationships.

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.

Occurrence and distribution of Actinidia viruses in Shaanxi Province of China

Plant Disease ◽  
2020 ◽  
Author(s):  
Zhao Lei ◽  
Mengji Cao ◽  
Qianru Huang ◽  
Yicheng Wang ◽  
Jiaxiu Sun ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Virus Detection ◽  
International Committee ◽  
Shaanxi Province ◽  
Transmission Electron ◽  
Viral Particles ◽  
The Family ◽  
Novel Virus ◽  
Actinidia Spp ◽  
Yellowing Virus

Kiwifruit (Actinidia spp.) is an economically important fruit crop globally. China is the largest kiwifruit-growing country in the world, and Shaanxi Province is the major kiwifruit-growing region in China. A systematic survey detected various symptoms in kiwifruit plants grown in a commercial kiwifruit field in Shaanxi Province. Samples were collected from kiwifruit plants showing symptoms and used for virus detection by high-throughput sequencing. In addition to ten known kiwifruit viruses, three new viruses were detected and tentatively named Actinidia yellowing ringspot virus (AYRSpV), Actinidia yellowing virus 1 (AcYV1) and Actinidia yellowing virus 2 (AcYV2). The genome sequences of the three new viruses and four known viruses were determined. Based on the demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV), AYRSpV might be a new member of the genus Ilarvirus in the family Bromoviridae, AcYV1 might be a new virus of the genus Waikavirus in the family Secoviridae, and AcYV2 might be a novel virus in the family Tombusviridae. Spherical viral particles were found in the samples infected with AYRSpV, AcYV1 and AcYV2 by transmission electron microscopy. Further analysis showed that all thirteen viruses can infect both A. deliciosa and A. chinensis, but the incidences of these infections vary among different kiwifruit cultivars in different regions. These results provide valuable information for understanding the viriome of kiwifruit in China.

Description of Maritrema portucalensis sp. nov. (Digenea, Microphallidae) parasite of Carcinus maenas (Crustacea, Decapoda) from Aveiro estuary, Northern Portugal

2011 ◽  
Vol 56 (4) ◽  
Author(s):  
Susana Pina ◽  
Fernanda Russell-Pinto ◽  
Pedro Rodrigues
Keyword(s):  
New Species ◽  
Carcinus Maenas ◽  
Morphological Characterization ◽  
The Body ◽  
Shore Crab ◽  
Northern Portugal ◽  
The Family ◽  
Its1 Rdna ◽  
Second Intermediate Host ◽  
Gill Lamellae

AbstractMaritrema portucalensis sp. nov. (Digenea, Microphallidae) from Aveiro estuary, northern Portugal, is described on the basis of excysted metacercariae obtained from the gill lamellae of the shore crab Carcinus maenas (L.). M. portucalensis sp. nov. most closely resembles Maritrema subdolum Jägerskiöld, 1909, a species that also frequently uses C. maenas as second intermediate host. The new species differs from M. subdolum in having a narrower body at the level of testes and a smaller ovary and testes. Also, the digestive caeca presented various folds along their length, thickening in the terminal region. Moreover, the body surface was fully covered by tegumental spines provided with several teeth. To complement our morphological characterization and to identify M. portucalensis metacercariae, the ITS1 rDNA region of the cysts isolated from C. maenas was sequenced and compared with the corresponding available sequences of digenean trematodes belonging to the family Microphallidae. Alignments revealed 28 base-pair differences between the query-ITS1 and that of M. subdolum, and more importantly a 100% similarity with the sequence of Microphallidae sp. no. 15 cercaria from the snail Hydrobia ulvae. The last observation allowed us to establish an unequivocal association between cercaria known as Microphallidae sp. no. 15, and the metacercaria of M. portucalensis sp. nov. characterized in this work, contributing decisively to the clarification of its life cycle.

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