Genetic variation of the greenhouse whitefly, Trialeurodes vaporariorum (Hemiptera: Aleyrodidae), among populations from Serbia and neighbouring countries, as inferred from COI sequence variability

2014 ◽  
Vol 104 (3) ◽  
pp. 357-366 ◽  
Author(s):  
M. Prijović ◽  
M. Škaljac ◽  
T. Drobnjaković ◽  
K. Žanić ◽  
P. Perić ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Sequence Data ◽  
Spatial Genetic Structure ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Trialeurodes Vaporariorum ◽  
Plant Viruses ◽  
Sequence Variability ◽  
Greenhouse Whitefly ◽  
The Usa

AbstractThe greenhouse whitefly Trialeurodes vaporariorum Westwood, 1856 (Hemiptera: Aleyrodidae) is an invasive and highly polyphagous phloem-feeding pest of vegetables and ornamentals. Trialeurodes vaporariorum causes serious damage due to direct feeding and transmits several important plant viruses. Excessive use of insecticides has resulted in significantly reduced levels of susceptibility of various T. vaporariorum populations. To determine the genetic variability within and among populations of T. vaporariorum from Serbia and to explore their genetic relatedness with other T. vaporariorum populations, we analysed the mitochondrial cytochrome c oxidase I (COI) sequences of 16 populations from Serbia and six neighbouring countries: Montenegro (three populations), Macedonia (one population) and Croatia (two populations), for a total of 198 analysed specimens. A low overall level of sequence divergence and only five variable nucleotides and six haplotypes were found. The most frequent haplotype, H1, was identified in all Serbian populations and in all specimens from distant localities in Croatia and Macedonia. The COI sequence data that was retrieved from GenBank and the data from our study indicated that H1 is the most globally widespread T. vaporariorum haplotype. A lack of spatial genetic structure among the studied T. vaporariorum populations, as well as two demographic tests that we performed (Tajima's D value and Fu's Fs statistics), indicate a recent colonisation event and population growth. Phylogenetic analyses of the COI haplotypes in this study and other T. vaporariorum haplotypes that were retrieved from GenBank were performed using Bayesian inference and median-joining (MJ) network analysis. Two major haplogroups with only a single unique nucleotide difference were found: haplogroup 1 (containing the five Serbian haplotypes and those previously identified in India, China, the Netherlands, the United Kingdom, Morocco, Reunion and the USA) and haplogroup 3 (containing the single Serbian haplotype H3 and haplotypes from Costa Rica, the USA and Spanish Canary Islands). Collectively, our data indicate a rather limited value of COI as a genetic marker for discrimination between different T. vaporariorum populations in the investigated area. Possible explanations for the observed lack of COI sequence variability, such as specific genetics of biological invasion and/or the influence of bacterial symbionts that manipulate insect reproduction, are discussed.

scholarly journals Taxonomy of Australian clinical isolates of the genus Photorhabdus and proposal of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. and P. asymbiotica subsp. australis subsp. nov.

2004 ◽  
Vol 54 (4) ◽  
pp. 1301-1310 ◽  
Author(s):  
R. J. Akhurst ◽  
N. E. Boemare ◽  
P. H. Janssen ◽  
M. M. Peel ◽  
D. A. Alfredson ◽  
...  
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Isolates ◽  
Rrna Gene ◽  
Clinical Specimens ◽  
The Usa ◽  
Gene Sequence Data

The relationship of Photorhabdus isolates that were cultured from human clinical specimens in Australia to Photorhabdus asymbiotica isolates from human clinical specimens in the USA and to species of the genus Photorhabdus that are associated symbiotically with entomopathogenic nematodes was evaluated. A polyphasic approach that involved DNA–DNA hybridization, phylogenetic analyses of 16S rRNA and gyrB gene sequences and phenotypic characterization was adopted. These investigations showed that gyrB gene sequence data correlated well with DNA–DNA hybridization and phenotypic data, but that 16S rRNA gene sequence data were not suitable for defining species within the genus Photorhabdus. Australian clinical isolates proved to be related most closely to clinical isolates from the USA, but the two groups were distinct. A novel subspecies, Photorhabdus asymbiotica subsp. australis subsp. nov. (type strain, 9802892T=CIP 108025T=ACM 5210T), is proposed, with the concomitant creation of Photorhabdus asymbiotica subsp. asymbiotica subsp. nov. Analysis of gyrB sequences, coupled with previously published data on DNA–DNA hybridization and PCR-RFLP analysis of the 16S rRNA gene, indicated that there are more than the three subspecies of Photorhabdus luminescens that have been described and confirmed the validity of the previously proposed subdivision of Photorhabdus temperata. Although a non-luminescent, symbiotic isolate clustered consistently with P. asymbiotica in gyrB phylogenetic analyses, DNA–DNA hybridization indicated that this isolate does not belong to the species P. asymbiotica and that there is a clear distinction between symbiotic and clinical species of Photorhabdus.

Sequence variability in two mitochondrial DNA regions and internal transcribed spacer among three cestodes infecting animals and humans from China

2011 ◽  
Vol 86 (2) ◽  
pp. 245-251 ◽  
Author(s):  
R.S. Dai ◽  
G.H. Liu ◽  
H.Q. Song ◽  
R.Q. Lin ◽  
Z.G. Yuan ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Sequence Variability ◽  
Taenia Hydatigena ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractSequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochromecoxidase subunit 1 (cox1) and NADH dehydrogenase subunit 4 (nad4), and internal transcribed spacer (ITS) of rDNA among and within three cestodes,Spirometra erinaceieuropaei,Taenia multicepsandTaenia hydatigena, from different geographical origins in China was examined. A portion of thecox1 (pcox1),nad4 genes (pnad4) and the ITS (ITS1+5.8S rDNA+ITS2) were amplified separately from individual cestodes by polymerase chain reaction (PCR). Representative amplicons were subjected to sequencing in order to estimate sequence variability. While the intra-specific sequence variations within each of the tapeworm species were 0–0.7% for pcox1, 0–1.7% for pnad4 and 0.1–3.6% for ITS, the inter-specific sequence differences were significantly higher, being 12.1–17.6%, 18.7–26.2% and 31–75.5% for pcox1, pnad4 and ITS, respectively. Phylogenetic analyses based on the pcox1 sequence data revealed thatT. multicepsandT. hydatigenawere more closely related to the other members of theTaeniagenus, andS. erinaceieuropaeiwas more closely related to the other members of theSpirometragenus. These findings demonstrated clearly the usefulness of mtDNA and rDNA sequences for population genetic studies of these cestodes of socio-economic importance.

scholarly journals 98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray

2010 ◽  
Vol 365 (1548) ◽  
pp. 1891-1897 ◽  
Author(s):  
Siobain Duffy ◽  
Yee Mey Seah
Keyword(s):  
Plant Pathogens ◽  
Sequence Data ◽  
Short Form ◽  
Sequence Divergence ◽  
Standard Technique ◽  
Plant Viruses ◽  
Nucleotide Identity ◽  
Virus Species ◽  
Multiple Introductions ◽  
Established Plant

Short-form publications such as Plant Disease reports serve essential functions: the rapid dissemination of information on the geography of established plant pathogens, incidence and symptomology of pathogens in new hosts, and the discovery of novel pathogens. Many of these sentinel publications include viral sequence data, but most use that information only to confirm the virus' species. When researchers use the standard technique of per cent nucleotide identity to determine that the new sequence is closely related to another sequence, potentially erroneous conclusions can be drawn from the results. Multiple introductions of the same pathogen into a country are being ignored because researchers know fast-evolving plant viruses can accumulate substantial sequence divergence over time, even from a single introduction. An increased use of phylogenetic methods in short-form publications could speed our understanding of these cryptic second introductions and aid in control of epidemics.

scholarly journals Annonaceae substitution rates: a codon model perspective

2014 ◽  
Vol 36 (spe1) ◽  
pp. 108-117 ◽  
Author(s):  
Lars Willem Chatrou ◽  
Michael David Pirie ◽  
Robin Van Velzen ◽  
Freek Theodoor Bakker
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
High Ratio ◽  
Molecular Dating ◽  
Codon Model ◽  
Synonymous Substitutions ◽  
Branch Lengths

The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.

scholarly journals Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly)

2017 ◽  
Vol 108 (1) ◽  
pp. 5-13 ◽  
Author(s):  
J.M. Wainaina ◽  
P. De Barro ◽  
L. Kubatko ◽  
M. A. Kehoe ◽  
J. Harvey ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
The Netherlands ◽  
Phylogenetic Relationships ◽  
Virus Transmission ◽  
Sequence Divergence ◽  
Trialeurodes Vaporariorum ◽  
Greenhouse Whitefly ◽  
Population Structure Analysis ◽  
Clade 1

AbstractTrialeurodes vaporariorum (Westwood, 1856) (Greenhouse whitefly) is an agricultural pest of global importance. It is associated with damage to plants during feeding and subsequent virus transmission. Yet, global phylogenetic relationships, population structure, and estimation of the rates of gene flow within this whitefly species remain largely unexplored. In this study, we obtained and filtered 227 GenBank records of mitochondrial cytochrome c oxidase I (mtCOI) sequences of T. vaporariorum, across various global locations to obtain a final set of 217 GenBank records. We further amplified and sequenced a ~750 bp fragment of mtCOI from an additional 31 samples collected from Kenya in 2014. Based on a total of 248 mtCOI sequences, we identified 16 haplotypes, with extensive overlap across all countries. Population structure analysis did not suggest population differentiation. Phylogenetic analysis indicated the 2014 Kenyan collection of samples clustered with a single sequence from the Netherlands to form a well-supported clade (denoted clade 1a) nested within the total set of sequences (denoted clade 1). Pairwise distances between sequences show greater sequence divergence between clades than within clades. In addition, analysis using migrate-n gave evidence for recent gene flow between the two groups. Overall, we find that T. vaporariorum forms a single large group, with evidence of further diversification consisting primarily of Kenyan sequences and one sequence from the Netherlands forming a well-supported clade.

scholarly journals High Sequence Variability Among Little cherry virus Isolates Occurring in British Columbia

Plant Disease ◽  
2004 ◽  
Vol 88 (10) ◽  
pp. 1092-1098 ◽  
Author(s):  
J. Theilmann ◽  
S. Orban ◽  
D. Rochon
Keyword(s):  
British Columbia ◽  
Nucleotide Sequence ◽  
Sequence Data ◽  
Polyclonal Antibodies ◽  
Severe Disease ◽  
Sequence Divergence ◽  
Bacterial Cells ◽  
Sequence Variability ◽  
Rt Pcr ◽  
High Level

The LC5 isolate of Little cherry virus (LChV-LC5) is one of at least two distinct viruses contributing to a severe disease of cherry (Little cherry disease [LChD]) in British Columbia. A near-complete nucleotide sequence of LChV-LC5 is available as well as polyclonal antibodies against LChV-LC5 coat protein produced in bacterial cells. A survey for LChV-LC5-infected trees in the Okanagan Valley and Kootenay region of British Columbia was carried out using enzyme-linked immunosorbent assays (ELISA) and LChV-LC5 antibodies. Reverse transcriptase polymerase chain reaction (RT-PCR) and sequence analysis of four different regions of the genomes of 31 of these isolates have been conducted. A high level of sequence variability was found: nucleotide sequence divergence between LChV-LC5 and the other sequenced isolates ranged from 0 to 19.7%, and amino acid sequence divergence ranged from 0 to 9.1%. Further examination of RT-PCR and sequence data identified six discrete groups of isolates, including a group identical to LChV-LC5. The high level of divergence in LChV-LC5 isolates occurring in British Columbia suggests that caution should be used in the selection of methods used for diagnosis during surveys for this virus.

scholarly journals Phylogenetic diversity of two common Trypanosoma cruzi lineages in the Southwestern United States

2021 ◽  
Author(s):  
Carlos A Flores-Lopez ◽  
Elizabeth A Mitchell ◽  
Carolina E Reisenman ◽  
Sahotra Sarkar ◽  
Philip C Williamson ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Copy ◽  
High Genetic Diversity ◽  
Genetic Lineages ◽  
Control Programs ◽  
The Usa

Trypanosoma cruzi is the causative agent of Chagas disease, a devastating parasitic disease endemic to Central and South America, Mexico, and the USA. We characterized the genetic diversity of T. cruzi circulating in five triatomine species (Triatoma gerstaeckeri, T. lecticularia, T. indictiva, T. sanguisuga and T. recurva) collected in Texas and Southern Arizona using nucleotide sequences from four single-copy loci (COII-ND1, MSH2, DHFR-TS, TcCLB.506529.310). All T. cruzi variants fall in two main genetic lineages: 75% of the samples corresponded to T. cruzi Discrete Typing Unit (DTU) I (TcI), and 25% to a North American specific lineage previously labelled TcIV-USA. Phylogenetic and sequence divergence analyses of our new data plus all previously published sequence data from those 4 genes collected in the USA, show that TcIV-USA is significantly different from any other previously defined T. cruzi DTUs. The significant level of genetic divergence between TcIV-USA and other T. cruzi lineages should lead to an increased focus on understanding the epidemiological importance of this lineage, as well as its geographical range and pathogenicity in humans and domestic animals. Our findings further corroborate the fact that there is a high genetic diversity of the parasite in North America and emphasize the need for appropriate surveillance and vector control programs for Chagas disease in southern USA and Mexico.

scholarly journals The English strain of rat cytomegalovirus (CMV) contains a novel captured CD200 (vOX2) gene and a spliced CC chemokine upstream from the major immediate-early region: further evidence for a separate evolutionary lineage from that of rat CMV Maastricht

2005 ◽  
Vol 86 (2) ◽  
pp. 263-274 ◽  
Author(s):  
Sebastian Voigt ◽  
Gordon R. Sandford ◽  
Gary S. Hayward ◽  
William H. Burns
Keyword(s):  
Time Course ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Receptor Gene ◽  
Sequence Divergence ◽  
Northern Blotting ◽  
Immediate Early ◽  
Murine Cytomegalovirus ◽  
Separate Species ◽  
The Right

Sequence data for eight genes, together with time-course Northern blotting and 3′- and 5′-RACE (rapid amplification of cDNA ends) analysis for some mRNAs from a 12 kb region upstream from the major immediate-early (MIE) genes of the English isolate of rat cytomegalovirus (RCMV), are presented. The results identified important differences compared to both murine cytomegalovirus (MCMV) and the Maastricht isolate of RCMV. A striking finding is the presence of a highly conserved, rightwards-oriented homologue of the rat cellular CD200 (OX2) gene immediately to the right of the MIE region, which replaces either the leftwards-oriented AAV REP gene of RCMV (Maastricht) or the upstream spliced portions of the immediate-early 2 gene (ie2) in MCMV. From the presence of other homologues of MCMV- and RCMV-specific genes, such as the β-chemokine MCK-2, SGG1 and an Fcγ receptor gene, as reported here, the basic architecture of the MIE region (reported previously) and the level of IE2 and DNA polymerase (POL) protein conservation in phylogenetic analyses, it is clear that the English strain of RCMV is also a member of the genus Muromegalovirus, but is a β-herpesvirus species that is very distinct from both MCMV and RCMV (Maastricht). Both the lack of a CD200 homologue in the other two rodent viruses and the depth of sequence divergence of the rodent CMV IE2 and POL proteins suggest that these three viruses have evolved as separate species in the genus Muromegalovirus since very early in the host rodent lineage.

scholarly journals Genomic Diversity and Phylogenetic Analysis of SARS-CoV-2 Circulating in Africa and Other Continents: Implications for Diagnosis, Transmission, and Prevention

2020 ◽  
Vol 4 (3) ◽  
Author(s):  
Idowu A. Taiwo
Keyword(s):  
Genome Sequence ◽  
Genetic Relatedness ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Phase 1 ◽  
Threat Assessment ◽  
Population Based ◽  
Genomic Diversity ◽  
Sequence Length ◽  
Phase 2

Background: COVID-19 pandemic caused by SARS-CoV-2 remains a global health threat. Assessment of the genetic relatedness of the genome sequence is a prerequisite to understanding the dynamics, which is important to improve diagnosis and preventive measures. This study determined genomic diversity and SNP characteristic of genomes of SARS-CoV-2 from Africa and the rest of the world. The study involved molecular and phylogenetic analyses to understand the phylogeny and transmission dynamics of the virus. Methods: The SARS-CoV-2 genome sequence data were mined and retrieved from major databases for one year in two phases: Phase 1; December 2019 to May 2020 and Phase 2; June 2020 to December 2020. A maximum of the four sequences that fulfilled the following predetermined criteria from each country were randomly selected for inclusion in the study: (i) sequence length >29,700 nt, (ii) number of Ns in the sequence not >5%, (iii) inclusion of Poly-A tail in the sequence record to ensure completeness. Results: The similarity of SARS-Cov-2 genomes within and between countries was generally high with an average of 99.9%. Thus, SARS-CoV-2 vary between countries and continents by 0.1% as a result of SNPs in its genome. Phylogenetic data revealed multiple origin of SARS-CoV-2 in Africa and also suggested that the virus spreads by ‘founder’s effect’; whereby few viruses newly introduced into a population multiply rapidly and accumulate mutations as they spread quickly by community transfer to create population-based identity. Tree of continental consensus sequences retrieved in Phase 1 suggested that SARS-CoV-2 virus is of two major clusters: African cluster consisting of Africa, Europe, and North America and Asian cluster made up of Asia, South America, and Oceania. However, this clustering pattern vanished in phase 2. Thus, upholding the view that SARS-CoV-2 is constantly evolving. Conclusion: This dynamism and genetic diversity of SARS-CoV-2 have important implications in diagnosis, transmission, and prevention strategy.

scholarly journals Red yeasts from leaf surfaces and other habitats: three new species and a new combination of Symmetrospora (Pucciniomycotina, Cystobasidiomycetes)

2020 ◽  
Vol 5 (1) ◽  
pp. 187-196
Author(s):  
D. Haelewaters ◽  
M. Toome-Heller ◽  
S. Albu ◽  
M.C. Aime
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
New Combination ◽  
Leaf Surfaces ◽  
Molecular Phylogenetic ◽  
The Usa ◽  
Three New Species ◽  
Decaying Wood ◽  
Yeast Isolation

Our understanding of the systematics of red yeasts has greatly improved with the availability of sequence data and it is now clear that the majority of these fungi belong to three different classes of Pucciniomycotina (Basidiomycota): Agaricostilbomycetes, Cystobasidiomycetes, and Microbotryomycetes. Despite improvements in phylogenetic placement, the taxonomy of these fungi has long been in need of revision and still has not been entirely resolved, partly due to missing taxa. In the present study, we present data of culture-based environmental yeast isolation, revealing several undescribed species of Symmetrospora, which was recently introduced to accommodate six species previously placed in the asexual genera Sporobolomyces and Rhodotorula in the gracilis/marina clade of Cystobasidiomycetes. Based on molecular phylogenetic analyses of three rDNA loci, morphology, and biochemical studies, we formally describe the following new species: Symmetrospora clarorosea sp. nov. from leaf surfaces in Portugal and the USA; S. pseudomarina sp. nov. from leaf surfaces in Brazil, and the USA and decaying wood in the USA; and S. suhii sp. nov. from a beetle gut in the USA, leaf surfaces in Brazil and marine water in the Taiwan and Thailand. Finally, we propose a new combination for Sporobolomyces oryzicola based on our molecular phylogenetic data, Symmetrospora oryzicola comb. nov.

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