Genetic Structure of Field Populations of Begomoviruses and of Their Vector Bemisia tabaci in Pakistan

The genetic structure of field populations of begomoviruses and their whitefly vector Bemisia tabaci in Pakistan was analyzed. Begomoviruses and B. tabaci populations were sampled from different crops and weeds in different locations in Punjab and Sindh provinces, in areas where cotton leaf curl disease (CLCuD) occurs or does not occur. Phylogenetic analysis based on nucleotide sequences of the intergenic region in the viral DNA-A provided evidence of two clusters of isolates: viruses isolated from species in the family Malvaceae, and viruses isolated from other dicotyledon families. Analysis of the capsid protein (CP) open reading frame grouped isolates into three geographical clusters, corresponding to isolates collected in Punjab, Sindh, or both provinces. Random amplified polymorphic DNA analyses of the B. tabaci population showed that intrapopulation diversity was high at both the local and regional scales. Sequence analysis of the mitocondrial cytochrome oxydase I (mt COI) gene showed that the B. tabaci population was structured into at least three genetic lineages corresponding to the previously described Indian, Southeast Asian, and Mediterranean-African clades. The Indian clade was present only in Punjab, the Mediterranean-African only in Sindh, and the Southeast Asian in both provinces. B. tabaci haplotypes of the Indian clade were found only in the Punjab, where CLCuD occurs. Hence, the geographical distribution of virus and vector genotypes may be correlated, because similar phylogenetic relationships were detected for the viral CP and the vector mt COI genes.

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Cotton leaf curl Gezira virus (African cotton leaf curl Begomovirus).

10.1079/cpc.13816.20210102491 ◽

2021 ◽

Author(s):

Judith K Brown

Keyword(s):

Bemisia Tabaci ◽

Yield Loss ◽

Growing Season ◽

Cotton Leaf ◽

Cotton Production ◽

Natural Spread ◽

Sahel Region ◽

Whitefly Vector ◽

African Sahel ◽

Leaf Curl

Abstract Cotton leaf curl Gezira virus (CLCuGV) is endemic to the African Sahel region (Idris et al., 2000). It is an economically important cotton-infecting begomovirus, and poses a serious threat to cotton production. It causes yield loss in all affected cotton-growing areas in Africa. Losses are difficult to assess, but estimates range up to 20% when infection occurs early in the growing season and/or with highly susceptible cultivars. Natural spread is mainly by the whitefly vector, Bemisia tabaci, which transmits the virus in a persistent, circulative manner. Viruliferous whiteflies on infested/infected plants harbouring CLCuGV imported to other countries are of concern for preventing introduction.

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Bemisia tabaci Vesicle-Associated Membrane Protein 2 Interacts with Begomoviruses and Plays a Role in Virus Acquisition

Cells ◽

10.3390/cells10071700 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1700

Author(s):

Yun-Yun Fan ◽

Yu-Wei Zhong ◽

Jing Zhao ◽

Yao Chi ◽

Sophie Bouvaine ◽

...

Keyword(s):

Membrane Protein ◽

Bemisia Tabaci ◽

Species Complex ◽

Molecular Mechanisms ◽

Whole Body ◽

Sri Lankan ◽

Tomato Production ◽

Virus Acquisition ◽

Leaf Curl Virus ◽

Whitefly Vector

Begomoviruses cause substantial losses to agricultural production, especially in tropical and subtropical regions, and are exclusively transmitted by members of the whitefly Bemisia tabaci species complex. However, the molecular mechanisms underlying the transmission of begomoviruses by their whitefly vector are not clear. In this study, we found that B. tabaci vesicle-associated membrane protein 2 (BtVAMP2) interacts with the coat protein (CP) of tomato yellow leaf curl virus (TYLCV), an emergent begomovirus that seriously impacts tomato production globally. After infection with TYLCV, the transcription of BtVAMP2 was increased. When the BtVAMP2 protein was blocked by feeding with a specific BtVAMP2 antibody, the quantity of TYLCV in B. tabaci whole body was significantly reduced. BtVAMP2 was found to be conserved among the B. tabaci species complex and also interacts with the CP of Sri Lankan cassava mosaic virus (SLCMV). When feeding with BtVAMP2 antibody, the acquisition quantity of SLCMV in whitefly whole body was also decreased significantly. Overall, our results demonstrate that BtVAMP2 interacts with the CP of begomoviruses and promotes their acquisition by whitefly.

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Species-diagnostic and species-specific DNA sequences evenly distributed throughout pine and spruce chromosomes

Genome ◽

10.1139/g10-065 ◽

2010 ◽

Vol 53 (10) ◽

pp. 769-777 ◽

Cited By ~ 1

Author(s):

Melanie Mehes-Smith ◽

Paul Michael ◽

Kabwe Nkongolo

Keyword(s):

Dna Sequences ◽

Random Amplified Polymorphic Dna ◽

Inter Simple Sequence Repeat ◽

Issr Markers ◽

Pinus Monticola ◽

The Family ◽

Species Specific ◽

Rapd And Issr ◽

Specific Sequences

Genome organization in the family Pinaceae is complex and largely unknown. The main purpose of the present study was to develop and physically map species-diagnostic and species-specific molecular markers in pine and spruce. Five RAPD (random amplified polymorphic DNA) and one ISSR (inter-simple sequence repeat) species-diagnostic or species-specific markers for Picea mariana , Picea rubens , Pinus strobus , or Pinus monticola were identified, cloned, and sequenced. In situ hybridization of these sequences to spruce and pine chromosomes showed the sequences to be present in high copy number and evenly distributed throughout the genome. The analysis of centromeric and telomeric regions revealed the absence of significant clustering of species-diagnostic and species-specific sequences in all the chromosomes of the four species studied. Both RAPD and ISSR markers showed similar patterns.

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A new silverleaf-inducing biotype Ms of Bemisia tabaci (Hemiptera: Aleyrodidae) indigenous to the islands of the south-west Indian Ocean

Bulletin of Entomological Research ◽

10.1079/ber2004337 ◽

2005 ◽

Vol 95 (1) ◽

pp. 29-35 ◽

Cited By ~ 79

Author(s):

H. Delatte ◽

B. Reynaud ◽

M. Granier ◽

L. Thornary ◽

J.M. Lett ◽

...

Keyword(s):

Bemisia Tabaci ◽

Distinct Group ◽

Genetic Type ◽

Coi Gene ◽

Vegetable Crops ◽

Sequence Comparisons ◽

Genetic Types ◽

South West Indian Ocean ◽

Biotype B ◽

Q Biotype

AbstractFollowing the first detection of tomato yellow leaf curl virus (TYLCV) from R=union (700 km east of Madagascar) in 1997 and the upsurge of Bemisia tabaci (Gennadius) on vegetable crops, two genetic types of B. tabaci were distinguished using RAPD–PCR and cytochrome oxidase I (COI) gene sequence comparisons. One type was assigned to biotype B and the other was genetically dissimilar to the populations described elsewhere and was named Ms, after the Mascarenes Archipelago. This new genetic type forms a distinct group that is sister to two other groups, one to which the B biotype is a member and one to which the Q biotype belongs. The Ms biotype is thought to be indigenous to the region as it was also detected in Mauritius, the Seychelles and Madagascar. Both B and Ms populations of B. tabaci induced silverleaf symptoms on Cucurbita sp., and were able to acquire and transmit TYLCV. Taken together these results indicate that the Ms genetic type should be considered a new biotype of B. tabaci.

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Complete Genome Sequence of a Novel Ourmia-like Mycovirus Infecting the Phytopathogenic Fungus Botryosphaeria Dothidea

10.21203/rs.3.rs-505029/v1 ◽

2021 ◽

Author(s):

Liying Sun ◽

Ziqian Lian ◽

Subha Das ◽

Jingxian Luo ◽

Ida Bagus Andika

Keyword(s):

Amino Acid ◽

Genome Sequence ◽

Amino Acid Sequences ◽

Shanxi Province ◽

Phytopathogenic Fungus ◽

Botryosphaeria Dothidea ◽

Reading Frame ◽

Ring Rot ◽

Ssrna Virus ◽

The Family

Abstract In this study, we describe the full-length genome sequence of a novel ourmia-like mycovirus, tentatively designated Botryosphaeria dothidea ourmia-like virus 1 (BdOLV1), isolated from the phytopathogenic fungus, Botryosphaeria dothidea strain P8, associated with apple ring rot in Shanxi province, China. The complete BdOLV1 genome is comprised of 2797 nucleotides, a positive-sense (+) single-stranded RNA (ssRNA) with a single open reading frame (ORF). The ORF putatively encodes a 642-amino acid polypeptide with conserved RNA-dependent RNA polymerase (RdRp) motifs, related to viruses of the family Botourmiaviridae. Phylogenetic analysis based on the RdRp amino acid sequences showed that BdOLV1 is grouped with oomycete-infecting unclassified viruses closely related to the genus Botoulivirus in Botourmiaviridae. This is the first report of a novel (+)ssRNA virus in B. dothidea related to the genus Botoulivirus in the family Botourmiaviridae.

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The Complete Nucleotide Sequence and Biotype Variability of Papaya leaf distortion mosaic virus

Phytopathology ◽

10.1094/phyto-95-0128 ◽

2005 ◽

Vol 95 (2) ◽

pp. 128-135 ◽

Cited By ~ 20

Author(s):

Tetsuo Maoka ◽

Tatsuji Hataya

Keyword(s):

Amino Acids ◽

Nucleotide Sequence ◽

Mosaic Virus ◽

Complete Nucleotide Sequence ◽

Distinct Species ◽

Cleavage Sites ◽

Reading Frame ◽

The Family ◽

Evolutionary Event ◽

Leaf Distortion

The complete nucleotide sequence of the genome of Papaya leaf distortion mosaic virus (PLDMV) was determined. The viral RNA genome of strain LDM (leaf distortion mosaic) comprised 10,153 nucleotides, excluding the poly(A) tail, and contained one long open reading frame encoding a polyprotein of 3,269 amino acids (molecular weight 373,347). The polyprotein contained nine putative proteolytic cleavage sites and some motifs conserved in other potyviral polyproteins with 44 to 50% identities, indicating that PLDMV is a distinct species in the genus Potyvirus. Like the W biotype of Papaya ringspot virus (PRSV), the non-papaya-infecting biotype of PLDMV (PLDMV-C) was found in plants of the family Cucurbitaceae. The coat protein (CP) sequence of PLDMV-C in naturally infected-Trichosanthes bracteata was compared with those of three strains of the P biotype (PLDMV-P), LDM and two additional strains M (mosaic) and YM (yellow mosaic), which are biologically different from each other. The CP sequences of three strains of PLDMV-P share high identities of 95 to 97%, while they share lower identities of 88 to 89% with that of PLDMV-C. Significant changes in hydrophobicity and a deletion of two amino acids at the N-terminal region of the CP of PLDMV-C were observed. The finding of two biotypes of PLDMV implies the possibility that the papaya-infecting biotype evolved from the cucurbitaceae-infecting potyvirus, as has been previously suggested for PRSV. In addition, a similar evolutionary event acquiring infectivity to papaya may arise frequently in viruses in the family Cucurbitaceae.

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Characterization of beta-lactamase gene blaPER-2, which encodes an extended-spectrum class A beta-lactamase.

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.40.3.616 ◽

1996 ◽

Vol 40 (3) ◽

pp. 616-620 ◽

Cited By ~ 82

Author(s):

A Bauernfeind ◽

I Stemplinger ◽

R Jungwirth ◽

P Mangold ◽

S Amann ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Beta Lactamase ◽

Reading Frame ◽

Beta Lactamases ◽

Class A ◽

Extended Spectrum ◽

The Family ◽

Extended Spectrum Beta Lactamases ◽

Lactamase Gene

Plasmidic extended-spectrum beta-lactamases of Ambler class A are mostly inactive against ceftibuten. Salmonella typhimurium JMC isolated in Argentina harbors a bla gene located on a plasmid (pMVP-5) which confers transferable resistance to oxyiminocephalosporins, aztreonam, and ceftibuten. The beta-lactamase PER-2 (formerly ceftibutenase-1; CTI-1) is highly susceptible to inhibition by clavulanate and is located at a pI of 5.4 after isoelectric focusing. The blaPER-2 gene was cloned and sequenced. The nucleotide sequence of a 2.2-kb insert in vector pBluescript includes an open reading frame of 927 bp. Comparison of the deduced amino acid sequence of PER-2 with those of other beta-lactamases indicates that PER-2 is not closely related to TEM or SHV enzymes (25 to 26% homology). PER-2 is most closely related to PER-1 (86.4% homology), an Ambler class A enzyme first detected in Pseudomonas aeruginosa. An enzyme with an amino acid sequence identical to that of PER-1, meanwhile, was found in various members of the family Enterobacteriaceae isolated from patients in Turkey. Our data indicate that PER-2 and PER-1 represent a new group of Ambler class A extended-spectrum beta-lactamases. PER-2 so far has been detected only in pathogens (S. typhimurium, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis) isolated from patients in South America, while the incidence of PER-1-producing strains so far has been restricted to Turkey, where it occurs both in members of the family Enterobacteriaceae and in P. aeruginosa.

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Integrative taxonomy reveals a rare and new cusk-eel species of Luciobrotula (Teleostei, Ophidiidae) from the Solomon Sea, West Pacific

European Journal of Taxonomy ◽

10.5852/ejt.2021.750.1361 ◽

2021 ◽

Vol 750 ◽

pp. 52-69

Author(s):

Man-Kwan Wong ◽

Mao-Ying Lee ◽

Wei-Jen Chen

Keyword(s):

Lateral Line ◽

Gene Tree ◽

Distinct Species ◽

Integrative Taxonomy ◽

Coi Gene ◽

Valid Species ◽

The West ◽

West Pacific ◽

Fin Ray ◽

The Family

With six valid species, Luciobrotula is a small genus of the family Ophidiidae, commonly known as cusk-eels. They are benthopelagic fishes occurring at depths ranging from 115–2300 m in the Atlantic, Indian, and Pacific Oceans. Among them, Luciobrotula bartschi is the only known species in the West Pacific. Three specimens of Luciobrotula were collected from the Philippine Sea, Bismarck Sea, and Solomon Sea in the West Pacific during the AURORA, PAPUA NIUGINI, and MADEEP expeditions under the Tropical Deep-Sea Benthos program, and all of them were initially identified as L. bartschi. Subsequent examination with integrative taxonomy indicates that they belong to two distinct species, with the specimen collected from the Solomon Sea representing a new species, which is described here. In terms of morphology, Luciobrotula polylepis sp. nov. differs from its congeners by having a relatively longer lateral line (end of the lateral line below the 33rd dorsal-fin ray) and fewer vertebrae (abdominal vertebrae 13, total vertebrae 50). In the inferred COI gene tree, the two western Pacific species of Luciobrotula do not form a monophyletic group. The genetic K2P distance between the two species is 13.8% on average at the COI locus.

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Attenuation of Bunyavirus Replication by Rearrangement of Viral Coding and Noncoding Sequences

Journal of Virology ◽

10.1128/jvi.79.11.6940-6946.2005 ◽

2005 ◽

Vol 79 (11) ◽

pp. 6940-6946 ◽

Cited By ~ 32

Author(s):

Anice C. Lowen ◽

Amanda Boyd ◽

John K. Fazakerley ◽

Richard M. Elliott

Keyword(s):

Mammalian Cells ◽

Reverse Genetics ◽

Viral Rna ◽

Wild Type Virus ◽

Coding Region ◽

Reading Frame ◽

Ribonucleoprotein Complexes ◽

The Family ◽

Prototype Virus ◽

Negative Sense

ABSTRACT Bunyamwera virus (BUN) is the prototype virus of the family Bunyaviridae. BUN has a tripartite negative-sense RNA genome comprising small (S), medium (M), and large (L) segments. Partially complementary untranslated regions (UTRs) flank the coding region of each segment. The terminal 11 nucleotides of these UTRs are conserved between the three segments, while the internal regions are unique. The UTRs direct replication and transcription of viral RNA and are sufficient to allow encapsidation of viral RNA into ribonucleoprotein complexes. To investigate the segment-specific functions of the UTRs, we have used reverse genetics to recover a recombinant virus (called BUN MLM) in which the L segment open reading frame (ORF) is flanked by the M segment UTRs. Compared to wild-type virus, BUN MLM virus shows growth attenuation in cultured mammalian cells and a slower disease progression in mice, produces small plaques, expresses reduced levels of L mRNA and L (RNA polymerase) protein, synthesizes less L genomic and antigenomic RNA, and has an increased particle-to-PFU ratio. Our data suggest that the packaging of BUN RNAs is not segment specific. In addition, the phenotype of BUN MLM virus supports the finding that BUN UTRs differ in their regulation of RNA synthesis but suggests that the interplay between each segment UTR and its cognate ORF may contribute to that regulation. Since BUN MLM virus is attenuated due to an essentially irreversible mutation, the rearrangement of UTRs is a feasible strategy for vaccine design for the more pathogenic members of the Bunyaviridae.

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