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Morphological Identification (morphological + identification)
Selected AbstractsReal-time PCR assay for the identification of Thrips palmi,EPPO BULLETIN, Issue 1 2005L. F. F. Kox Since Thrips palmi became a regulated pest for most European countries, inspections at points of entry into Europe and monitoring in Europe have intensified not only for T. palmi but also for thrips as a whole. Morphological identification of thrips is performed on adults and to a lesser extent on second-stage larvae only, because no adequate identification keys for the separation of species based on the characteristics of eggs, first-stage larvae, pre-pupae or pupae are available. We have developed a real-time PCR assay based on TaqMan. A T. palmi -specific set of primers and probe were selected within the mitochondrial cytochrome oxidase I (COI) gene. The specificity of the assay was assessed using 15 specimens of Thrips palmi and 61 specimens of 23 other thrips species commonly occuring in Europe. All T. palmi specimens were detected, and no cross reactions with other thrips were observed. The method was tested on single larvae and adults and proved to be applicable for both those stages of T. palmi. [source] RAPHIDOPHYCEAE [CHADEFAUD EX SILVA] SYSTEMATICS AND RAPID IDENTIFICATION: SEQUENCE ANALYSES AND REAL-TIME PCR ASSAYS,JOURNAL OF PHYCOLOGY, Issue 6 2006Holly A. Bowers Species within the class Raphidophyceae were associated with fish kill events in Japanese, European, Canadian, and U.S. coastal waters. Fish mortality was attributable to gill damage with exposure to reactive oxygen species (peroxide, superoxide, and hydroxide radicals), neurotoxins, physical clogging, and hemolytic substances. Morphological identification of these organisms in environmental water samples is difficult, particularly when fixatives are used. Because of this difficulty and the continued global emergence of these species in coastal estuarine waters, we initiated the development and validation of a suite of real-time polymerase chain reaction (PCR) assays. Sequencing was used to generate complete data sets for nuclear encoded small-subunit ribosomal RNA (SSU rRNA; 18S); internal transcribed spacers 1 and 2, 5.8S; and plastid encoded SSU rRNA (16S) for confirmed raphidophyte cultures from various geographic locations. Sequences for several Chattonella species (C. antiqua, C. marina, C. ovata, C. subsalsa, and C. verruculosa), Heterosigma akashiwo, and Fibrocapsa japonica were generated and used to design rapid and specific PCR assays for several species including C. verruculosa Hara et Chihara, C. subsalsa Biecheler, the complex comprised of C. marina Hara et Chihara, C. antiqua Ono and C. ovata, H. akashiwo Ono, and F. japonica Toriumi et Takano using appropriate loci. With this comprehensive data set, we were also able to perform phylogenetic analyses to determine the relationship between these species. [source] Identification, distribution and current taxonomy of Botryosphaeriaceae species associated with grapevine decline in New South Wales and South AustraliaAUSTRALIAN JOURNAL OF GRAPE AND WINE RESEARCH, Issue 1 2010W.M. PITT Abstract Background and Aims:, Botryosphaeriaceae species are recognised as important pathogens of grapevines both in Australia and overseas. The identity, prevalence and distribution of Botryosphaeriaceae species in vineyards throughout the major winegrowing regions of New South Wales (NSW) and South Australia (SA) was determined to provide a foundation for improved disease prevention and management. Methods and Results:, Field surveys from 91 vineyards across NSW and SA resulted in the collection of 2239 diseased wood samples and subsequent isolation of 1258 Botryosphaeriaceae isolates. Morphological identification along with phylogenetic analysis of ribosomal DNA internal transcribed spacer regions (ITS1-5.8S-ITS2) and partial sequences of the translation elongation factor 1-, gene (EF1-,) showed that eight Botryosphaeriaceae species from four phylogenetic lineages occur on grapevines in eastern Australia, including Diplodia seriata, Diplodia mutila, Lasiodiplodia theobromae, Neofusicoccum parvum, Neofusicoccum australe, Botryosphaeria dothidea, Dothiorella viticola and Dothiorella iberica. Conclusions:, The prevalence of individual species varied according to geography and climate. Species of Diplodia and Dothiorella, characterised by thick-walled, pigmented conidia were the most prevalent and were distributed widely throughout both NSW and SA. Species with hyaline conidia, such as Neofusicoccum and Fusicoccum, were isolated less frequently and displayed more limited geographic ranges, whilst only a single isolate of Lasiodiplodia was recovered, this being from the northern most region of NSW. Significance of the Study:, The identification of eight taxa within the Botryosphaeriaceae, and their distributions throughout south-eastern Australia was established and discussed in context with climate, reported optimum growth temperatures, and more recent taxonomic and nomenclatural revisions. We established a sound base for control strategies based on the prevailing species in Australian viticultural regions. [source] BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversityDIVERSITY AND DISTRIBUTIONS, Issue 5 2010Erik M. Pilgrim Abstract Aim, We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location, Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods, We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results, Phylogenetic inference indicates that inaccurate species-level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north-eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions, Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north-eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera. [source] Genetic divergence and ecological specialisation of seed weevils (Exapion spp.) on gorses (Ulex spp.)ECOLOGICAL ENTOMOLOGY, Issue 3 2008MYRIAM BARAT Abstract 1.,Reproductive isolation of sympatric populations may result from divergent selection of populations in different environments, and lead to ecological specialisation. In Brittany (France), the gorse Ulex europaeus (Fabaceae, Genisteae), may be encountered in sympatry with one of the two other gorse species present: U. gallii and U. minor. A recent study based on morphological identification of seed predators of gorse has shown that two weevil species (Curculionoidea, Apionidae) infest gorse pods at different seasons and have different host ranges: Exapion ulicis infests U. europaeus in spring, whereas E. lemovicinum infests U. gallii and U. minor in autumn. Weevil populations may thus have diverged in sympatry. 2.,As morphological identification of weevils is often difficult and some of the characters used may exhibit individual or environmental variation, mitochondrial and nuclear sequences of weevils collected within pods of the three gorse species in 10 populations of Brittany were used to reconstruct their phylogeny. 3.,The results reveal that species differentiation based on morphological characters is confirmed by the two molecular data sets, showing that E. ulicis and E. lemovicinum are distinct species, and suggesting the absence of host races. Finally, E. ulicis was able to use U. gallii and U. minor pods in spring in some years in some populations, which appeared to depend on the availability of pods present during its reproductive period. 4.,Divergence between E. ulicis and E. lemovicinum may have resulted from temporal isolation of reproductive periods of weevil populations followed by specialisation of insects to host phenology. [source] Molecular link of different stages of the trematode host of Neorickettsia risticii to Acanthatrium oregonenseENVIRONMENTAL MICROBIOLOGY, Issue 8 2008Kathryn E. Gibson Summary Neorickettsia risticii, the obligatory intracellular bacterium that causes Potomac horse fever, has been detected in various developmental stages of digenetic trematodes in the environment. Neorickettsia risticii -infected gravid trematodes were identified as Acanthatrium oregonense, based on morphologic keys. However, whether immature trematodes harbouring N. risticii are also A. oregonense was unknown. The objective of this study was to infer the life cycle of N. risticii -positive trematode hosts and transstadial transmission of the bacterium by molecularly characterizing the relationship among adult and immature stages of trematodes confirmed infected with N. risticii. Sequences of 18S ribosomal RNA genes up to 1922 bp in size were obtained from infected adult gravid trematodes, sporocysts and cercariae, and metacercariae. The sequences from the different immature stages of trematode are closely related to those of adult trematodes, some with 100% sequence identity; thus, they likely are life stages of A. oregonense. Comparisons with known 18S ribosomal RNA gene sequences of other digenetic trematodes indicated that all tested stages of the N. risticii -positive trematodes belong to the family Lecithodendriidae, supporting the morphological identification. [source] Identification of economically important Liriomyza species by PCR-RFLP analysis,EPPO BULLETIN, Issue 1 2005L. F. F. Kox Only adult males of Liriomyza bryoniae, L. huidobrensis, L. sativae and L. trifolii can be identified with certainty on basis of their genitalia. Female adults, pupae and larvae can only be identified on the level of groups of species (L. bryoniae and L. huidobrensis vs. L. sativae and L. trifolii). Species identification in all developmental stages is possible using molecular biological techniques. Our method is a PCR amplification of a 790-bp fragment of mitochondrial cytochrome oxidase II (COII) DNA followed by RFLP analysis. The method was tested on single larvae, pupae and adults and proved to be applicable to these three life stages. The specificity of the assay was assessed by comparing the results of the PCR-RFLP analysis with those of morphological analysis using 60 Liriomyza specimens. Molecular and morphological identification agreed for all specimens analysed. PCR-RFLP is a powerful diagnostic tool for rapid and reliable identification of all life stages of economically important Liriomyza species. [source] Trichoderma biodiversity in China: Evidence for a North to South distribution of species in East AsiaFEMS MICROBIOLOGY LETTERS, Issue 2 2005Chu-long Zhang Abstract Towards assessing the biodiversity and biogeography of Trichoderma, we have analyzed the occurrence of Trichoderma species in soil and litter from four areas in China: North (Hebei province), South-East (Zhejiang province), West (Himalayan, Tibet) and South-West (Yunnan province). One hundred and thirty five isolates were grouped according to tentative morphological identification. A representative 64 isolates were verified at the species level by the oligonucleotide barcode program TrichO Key v.1.0 and the custom BLAST server Tricho BLAST, using sequences of the ITS1 and 2 region of the rRNA cluster and from the longest intron of the tef1 (translation elongation factor 1-,) gene. Eleven known species (Trichoderma asperellum, T. koningii, T. atroviride, T. viride, T. velutinum, T. cerinum, T. virens, T. harzianum, T. sinensis, T. citrinoviride, T. longibrachiatum) and two putative new species (T. sp. C1, and T. sp. C2), distinguished from known species both by morphological characters and phylogenetic analysis, were identified. A significant difference in the occurrence of these species was found between the North (Hebei) and South-West (Yunnan) areas, which correlates with previously reported species distributions in Siberia and South-East Asia, respectively. As in previous studies, T. harzianum accounted for almost half of the biodiversity; although, in this study, it was exclusively found in the North, and was predominantly represented by an ITS1 and 2 haplotype, which has so far been rarely found elsewhere. This study therefore reveals a North,South gradient in species distribution in East Asia, and identifies Northern China as a potential center of origin of a unique haplotype of T. harzianum. [source] Identification of Trichoderma strains by image analysis of HPLC chromatogramsFEMS MICROBIOLOGY LETTERS, Issue 2 2001Ulf Thrane Abstract Forty-four Trichoderma strains from water-damaged building materials or indoor dust were classified with chromatographic image analysis on full chromatographic matrices obtained by high performance liquid chromatography with UV detection of culture extracts. The classes were compared with morphological identification and rDNA sequence data, and for each class all strains were of the same identity. With all three techniques each strain , except one , was identified as the same species. These strains belonged to Trichoderma atroviride (nine strains), Trichoderma viride (three strains), Trichoderma harzianum (10 strains), Trichoderma citrinoviride (12 strains), and Trichoderma longibrachiatum (nine strains). The odd strain was identified as Trichoderma hamatum by morphology and rDNA sequencing, but not by image analysis as no reference strains of this species were included. It is concluded that the secondary metabolite profile contains sufficient information for classification and species identification. [source] Genetic divergence between morphological forms of brown trout Salmo trutta L. in the Balkan region of MacedoniaJOURNAL OF FISH BIOLOGY, Issue 5 2010S. Lo Brutto The objective of this study was to characterize the genetic structure of two Balkan brown trout morphotypes, Salmo macedonicus and Salmo pelagonicus, and to test whether molecular traits support the species' status proposed by traditional morphological identification. The mitochondrial DNA 12S-rDNA, cyt b and control region genes were sequenced in 15 specimens collected from three localities in the Former Yugoslav Republic of Macedonia. The results of these markers did not support the taxonomic category of species but confirmed the existence of two morphotypes, Salmo trutta macedonicus and Salmo trutta pelagonicus, in the Aegean,Adriatic lineages of the Salmo trutta species complex. [source] Use of microsatellite DNA and amplified fragment length polymorphism for Cherry salmon (Oncorhynchus masou) complex identificationAQUACULTURE RESEARCH, Issue 9 2010Te-Hua Hsu Abstract Formosa landlocked salmon (Oncorhynchus masou formosanus), an endemic, critically endangered subspecies of Cherry salmon (Oncorhynchus masou) complex, is only found in Taiwan. Because the eyed eggs and ungutted carcasses of Pacific salmons (genus Oncorhynchus) are imported for aquaculture and food to Taiwan from overseas every year, the requirement for preventing illegal trade or accidental commercial imports to avoid unwanted fish from contaminating the gene pool of Formosa landlocked salmon and infect them with diseases is critical for the conservation of Formosa landlocked salmon. Traditional morphology-based species identification is impossible for salmon eggs and larvae that lack clearly defined morphological features. In the present study, the genetic differences among four subspecies (Oncorhynchus masou ishikawae, O. masou subsp., Oncorhynchus masou masou and O. masou formosanus) of Cherry salmon complex were determined from microsatellite DNA and amplified fragment length polymorphism analyses. We successfully generated a genetic marker to aid traditional taxonomy and investigate the integrity of the current taxonomic status among members of Cherry salmon complex. Use of molecular markers, in combination with traditional morphological identification, is a promising tool for identifying four closely related subspecies of Cherry salmon complex. [source] Bayesian analyses of admixture in wild and domestic cats (Felis silvestris) using linked microsatellite lociMOLECULAR ECOLOGY, Issue 1 2006R. LECIS Abstract Methods recently developed to infer population structure and admixture mostly use individual genotypes described by unlinked neutral markers. However, Hardy,Weinberg and linkage disequilibria among independent markers decline rapidly with admixture time, and the admixture signals could be lost in a few generations. In this study, we aimed to describe genetic admixture in 182 European wild and domestic cats (Felis silvestris), which hybridize sporadically in Italy and extensively in Hungary. Cats were genotyped at 27 microsatellites, including 21 linked loci mapping on five distinct feline linkage groups. Genotypes were analysed with structure 2.1, a Bayesian procedure designed to model admixture linkage disequilibrium, which promises to assess efficiently older admixture events using tightly linked markers. Results showed that domestic and wild cats sampled in Italy were split into two distinct clusters with average proportions of membership Q > 0.90, congruent with prior morphological identifications. In contrast, free-living cats sampled in Hungary were assigned partly to the domestic and the wild cat clusters, with Q < 0.50. Admixture analyses of individual genotypes identified, respectively, 5/61 (8%), and 16,20/65 (25,31%) hybrids among the Italian wildcats and Hungarian free-living cats. Similar results were obtained in the past using unlinked loci, although the new linked markers identified additional admixed wildcats in Italy. Linkage analyses confirm that hybridization is limited in Italian, but widespread in Hungarian wildcats, a population that is threatened by cross-breeding with free-ranging domestic cats. The total panel of 27 loci performed better than the linked loci alone in the identification of domestic and known hybrid cats, suggesting that a large number of linked plus unlinked markers can improve the results of admixture analyses. Inferred recombination events led to identify the population of origin of chromosomal segments, suggesting that admixture mapping experiments can be designed also in wild populations. [source] | |||||||||||||