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The immortelle (Helichrysum italicum (Roth) G. Don) is a typical perennial plant of natural vegetation in the Mediterranean region, and due to secondary metabolites with several biological properties (anti-inflammatory, antioxidant, antimicrobial, and anti-proliferative), it has become an important species for essential oil production, especially in the cosmetic industry. To increase the production of highly priced essential oils, it has been moved to cultivated fields. However, due to the lack of highly characterized planting material, there is a great need for genotype identification, and to provide a link with chemical profiles and geographic origin as a basis for the identification of local superior genotypes. The aims of the study were to characterize the ITS (ribosomal internal transcribed spacer) regions, ITS1 and ITS2, in samples from the East Adriatic region to determine the possibility of using these regions for plant genetic resources identification. Genetic variation was observed when comparing the ITS sequence variants of samples from the North-East Adriatic and the South-East Adriatic. Some rare and unique ITS sequence variants can be helpful for identifying specific populations from different geographical regions. [ABSTRACT FROM AUTHOR]

Microcystis aeruginosa is predicted to interact and coexist with diverse broad- and narrow-host-range viruses within a bloom; however, little is known about their affects on Microcystis population dynamics. Here, we developed a real-time PCR assay for the quantification of these viruses that have different host ranges. During the sampling period, total Microcystis abundance showed two peaks in May and August with a temporary decrease in June. The Microcystis population is largely divided into three phylotypes based on internal transcribed sequences (ITS; ITS types I to III). ITS I was the dominant phylotype (66% to 88%) except in June. Although the ITS II and III phylotypes were mostly less abundant, these phylotypes temporarily increased to approximately equivalent abundances of the ITS I population in June. During the same sampling period, the abundances of the broad-host-range virus MVGF_NODE331 increased from April to May and from July to October with a temporary decrease in June, in which its dynamics were in proportion to the increase of total Microcystis abundances regardless of changes in host ITS population composition. In contrast, the narrow-host-range viruses MVG_NODE620 and Ma-LMM01 were considerably less abundant than the broad-host-range virus and generally did not fluctuate in the environment. Considering that M. aeruginosa could increase the abundance and sustain the bloom under the prevalence of the broad-host-range virus, host abundant and diverse antiviral mechanisms might contribute to coexistence with its viruses. [ABSTRACT FROM AUTHOR]

Green mold disease caused by Trichoderma species is a serious problem for Lingzhi growers. Recently, green mold disease of lingzhi mushroom caused by unknown species of Trichoderma was found in lingzhi farm at Songkhla province, Southern Thailand. Therefore, the aim of this research was to identify the species of the causal agent. Trichoderma species were collected from G. lingzhi spawn to isolate and identify based on morphological characteristics and DNA sequence of the internal transcribed spacer regions (ITS). The phylogenetic tree was constructed by maximum likelihood analysis base on the ITS sequence comparison with sequences of ex-type culture from closely related taxa. A total of three Trichoderma species were identified as T. harzianum, T. pleuroticola and T. reesei. T. pleuroticola and T. reesei are the first report of green mold disease of G. lingzhi in Thailand.

Fusarium oxysporum f. sp. cepae causing basal rot disease of onion is a destructive phytopathogen resulting in 30-50% yield loss and remains as a major constraint in onion productivity. The management of disease through application of fungicide is not feasible and economically viable. Hence, the present study is focused on investigation of effective Trichoderma sp. and identifying the effective volatile organic compounds produced by it against the basal rot pathogen in onion. A total of ten Trichoderma spp. were isolated from rhizospheric soil of healthy onion plants and tested against virulent Fusarium oxysporum f. sp. cepae isolate FCIM1. The Trichoderma isolate (TIM2) showed 77.40% inhibition on mycelial growth of pathogen followed by the isolate (TIV1) with 70.36% inhibition. The molecular identification of effective Trichoderma isolate through the analysis of the rDNA of Internal Transcribed Spacers (ITS) region revealed isolate TIM2 as Trichoderma hamatum. The GC-MS analysis of Trichoderma hamatum unravelled the important volatile organic compounds like Methyl stearate, n-Hexadecanoic, Eicosane, 9-cyclohexy, Heptadecane, Dodecane, 2-cyclohexyl, to 2H-Pyran-2-one, 6-pentyl, 5-Hydroxymethylfurfural, Tetrapentacontane, 1-Dodecanol, 2-Propenoic acid, pentadecyl ester, Benzene, (2-methylbutyl) and 1,2-Dimethyltryptamine with peak area and retention time. These bioactive compounds exert a strong antifungal activity against Fusarium oxysporum f. sp. cepae. The scanning electron micrographs of Fusarium paired with effective Trichoderma (TIM2) showed the swollen hyphae with cell wall damage which is clear evident of antagonistic interaction of volatile compounds produced by Trichoderma hamatum. [ABSTRACT FROM AUTHOR]

Abstract Background Australian marsupials harbour a diverse array of helminth parasites. Despite current attempts to assess the extent of this diversity in macropodid hosts, it has been suggested that unique parasite fauna of Australian wildlife is difficult to document comprehensively due to the common occurrence of cryptic species. This paper assessed genetic variation within Austrostrongylus thylogale Johnston & Mawson, 1940 from the tammar wallaby, Notamacropus eugenii (Gray), and the quokka, Setonix brachyurus (Quoy & Gaimard), from different localities using the molecular characterisation of the internal transcribed spacers (ITS) within the nuclear ribosomal DNA. Methods Thirty-seven specimens of A. thylogale collected from N. eugenii (from Parndana, Kangaroo Island, South Australia, and Perup, Western Australia) and S. brachyurus (from Wellington Dam, Western Australia) were characterised using a molecular-phylogenetic approach utilising the first (ITS1) and second (ITS2) internal transcribed spacers. Results Genetic variation was detected in both ITS1 and ITS2 between specimens of A. thylogale from N. eugenii and S. brachyurus; however, no variation was detected between specimens collected from N. eugenii from Parndana, South Australia, and Perup, Western Australia. Furthermore, the phylogenetic analyses of ITS sequences showed two clades of A. thylogale originating from two hosts, N. eugenii and S. brachyurus, suggesting the presence of cryptic species. Conclusions This study provides evidence of genetic variation within A. thylogale based on collections from two different host species. Morphological studies are required to fully confirm the presence of a new species or cryptic species. Further molecular studies using a larger number of specimens are warranted to explore the genetic variation between A. thylogale from different geographical localities.

The mastic tree (Pistacia lentiscus var. Chia) is extensively cultivated on the southern part of the Greek island of Chios. Its extensive cultivation is due to the production of a special resin, known as mastic gum, or mastiha, which is widely used in several dietary, pharmaceutical and other products since ancient times. Mastic tree is an evergreen, dioecious (consisting of male and female individuals), woody plant. Furthermore, a number of morphological characteristics suggest the existence of several different plant groups, called here "morphotypes", but it is probable that there exist an unknown number of different, deviating genotypes on the island. Nevertheless, five major morphologically determined morphotypes of mastic tree are mainly cultivated, namely "Votomos", "Maroulitis", "Mavroschinos", "Stenophyllos" and "Fardyphyllos". The morphotypes exhibit mostly, but not always, distinct morphology, on which their taxonomy was initially based. Since it is observed that different plant populations differ in the quantity and quality of the produced resin, it is important to explore if and to what extent these differences have a genetic basis, or are due to other factors, such as agricultural practices, or soil composition. To this end, the genetic diversity among these five morphotypes and within each one of them was investigated in the present study, using initially the determination of their Random Amplified Polymorphic DNA profiles and subsequently the sequence divergence of their Internal Transcribed Spacer regions 1 and 2 (ITS1 and ITS2, respectively). The results confirm the existence of a considerable genotypic diversity among the five morphotypes studied and, furthermore, reveal the existence of genotypic diversity within each one of them, as well as the existence of a number of further deviating genotypes. The possibility that this diversity is partly a result of reticulate evolution events is also discussed. This study provides evidence that the population of cultivated mastic trees on the island of Chios consists mainly of two species, i.e. Pistacia lentiscus and Pistacia x saportae, although it is clear that there also exist genetically deviating mastic trees, as well as individual plants, probably produced through hybridization between the two afore mentioned species. [ABSTRACT FROM AUTHOR]

Green mold disease caused by Trichoderma species is a serious problem for Lingzhi growers. Recently, green mold disease of lingzhi mushroom caused by unknown species of Trichoderma was found in lingzhi farm at Songkhla province, Southern Thailand. Therefore, the aim of this research was to identify the species of the causal agent. Trichoderma species were collected from G. lingzhi spawn to isolate and identify based on morphological characteristics and DNA sequence of the internal transcribed spacer regions (ITS). The phylogenetic tree was constructed by maximum likelihood analysis base on the ITS sequence comparison with sequences of ex-type culture from closely related taxa. A total of three Trichoderma species were identified as T. harzianum, T. pleuroticola and T. reesei. T. pleuroticola and T. reesei are the first report of green mold disease of G. lingzhi in Thailand. [ABSTRACT FROM AUTHOR]

Molecular methods are necessary to diagnose immature life stages of the agricultural pest fruit fly Bactrocera dorsalis (Hendel), and are useful to corroborate identifications based on adults because morphological variation within the species can overlap with congeners. DNA sequencing of the nuclear ribosomal internal transcribed spacer 1 (ITS-1) has been adopted by the International Plant Protection Convention as an internationally accepted method to distinguish between the 2 pestiferous fruit fly species Bactrocera dorsalis and Bactrocera carambolae (Drew & Hancock). Reported ITS-1 sequences also are distinct and diagnostically informative to distinguish several other Bactrocera species related to B. dorsalis. In this study, we applied DNA sequencing of ITS-1 to a collection of 513 adult flies trapped in California, USA, in the yr 2008 to 2018. Internal transcribed spacer 1 sequences were successfully recovered from 504 (98%) of these flies. One fly had an ITS-1 sequence that matched B. occipitalis (Bezzi) records. Re-examination of that fly using cytochrome c oxidase I, elongation factor 1-alpha, and morphology supports it as the second record of B. occipitalis trapped in California. The other 503 flies had ITS-1 sequences consistent with B. dorsalis. Six unique ITS-1 sequences (or DNA types) were observed in the collection of 503 B. dorsalis. Three of the ITS-1 sequences (types A, B, and C) were present in 84% of the 503 flies and match ITS-1 records reported in prior publications on B. dorsalis. The other 3 sequences (types D, E, and F) observed in 4% of the 503 B. dorsalis have not been reported in publications. Ambiguous nucleotides were observed from 12% of the 503 B. dorsalis flies, precluding designation of a sequence type. Including the 3 new types from the current study, a total of 15 unique ITS-1 sequences now are known for B. dorsalis. The study, therefore, documents additional intraspecific variation of ITS-1 that aids in future applications for species identification. [ABSTRACT FROM AUTHOR]

The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora, Edgeworthia chrysantha, and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndhF to the trnL-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia, further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia.

Trichoderma is a genus of soil-borne fungus with an abundance of reports of its economic importance in the agriculture industry. Thus, the correct identification of Trichoderma species is necessary for its commercial purposes. Globally, Trichoderma species are routinely identified from micro-morphological descriptions which can be tedious and prone to errors. Thus, we emphasize that the accurate identification of Trichoderma strains requires a three-pronged approach i.e. based on its morphological characteristics, multilocus gene sequences of the rDNA [internal transcribed spacer (ITS) 1 and 2 regions], translation elongation factor 1-α (TEF-1α), Calmodulin (CAL) and its lignocellulolytic activities. We used this approach to identify a total of 53 Trichoderma strains which were isolated from a wet paddy field located at Tuaran, Sabah, Malaysia. The 53 strains were positively identified as belonging to three Trichoderma species, namely T. asperellum (43 strains), T. harzianum (9 strains), and T. reesei (one strain) on the basis of its morphological characteristics and multilocus gene sequences. Phylogenetic trees constructed based on the UPGMA method of the ITS 1 and 2 regions of the rDNA, TEF-1α and CAL revealed three distinct groups with the T. asperellum, T. harzianum and T. reesei strains placed under the section of Trichoderma, Pachybasium and Longibrachiatum, respectively. In addition, the lignocellulolytic activities of the isolates were measured based on the diameters of the halo zones produced when degrading cellulose, lignin, and starch, respectively. This diagnostic assay can be used to identify Trichoderma as it produces polyphenol oxidase when Tannic Acid Media is used for the lignin test, endoglucanases when Jensen media is used for cellulose, and it hydrolyzes starch to glucose when the modified Melin–Nokrans media is used for the starch test. Accurate identification of Trichoderma species is needed as these strains can potentially be used as a biocontrol agent to prevent diseases and to increase yield in agriculture crops. [ABSTRACT FROM AUTHOR]

The complete chloroplast genomes of three species of Edgeworthia namely, Edgeworthia albiflora , Edgeworthia chrysantha , and Edgeworthia gardneri (Thymelaeaceae), are reported and characterized. The chloroplast genomes displayed a typical quadripartite structure with conserved genome arrangement and specific divergence. The genomes ranged in length from 172,708 to 173,621 bp and displayed similar GC content of 36.5–36.7%. A total of 138–139 genes were predicted, including 92–93 protein-coding, 38 tRNAs and eight rRNAs genes. Variation in the number of short simple repeats and inverted region boundaries of the three cp genomes were observed. A mutational hotspot was detected along the nucleotide sequence from the ndh F to the trn L-UAG genes. The chloroplast genome-based and internal transcribed spacer (ITS)-based phylogenetic analyses using maximum-likelihood (ML) and Bayesian inference (BI) revealed that E. albiflora diverged before E. chrysantha and E. gardneri and placed the Edgeworthia clade at the base of the Eurasian Daphne group with strong bootstrap support. With an effective taxonomic treatment of the species of Edgeworthia , further molecular analyses of their intra- and interspecific genetic variation are inclined to support the treatment of E. albiflora and E. gardneri as two natural groups. The genetic information obtained from this study will provide valuable genomic resources for the identification of additional species and for deducing the phylogenetic evolution of Edgeworthia. [ABSTRACT FROM AUTHOR]

Abstract Background Pharyngostrongylus kappa Mawson, 1965 is a nematode (Strongyloidea: Cloacininae), endemic to the sacculated forestomachs of Australian macropodid marsupials (kangaroos and wallaroos). A recent study revealed genetic variation within the internal transcribed spacer region of the nuclear ribosomal DNA among P. kappa specimens collected from Macropus giganteus Shaw and Osphranter robustus (Gould). This study aimed to characterise the genetic and morphological diversity within P. kappa from four macropodid host species, including M. giganteus, O. robustus, O. antilopinus (Gould) and O. bernardus (Rothschild). Methods Specimens of P. kappa from M. giganteus and Osphranter spp. from various localities across Australia were examined. The first and second internal transcribed spacers (ITS1 and ITS2, respectively) were amplified using polymerase chain reaction and sequenced. Phylogenetic methods were used to determine the interspecific diversification within P. kappa and its evolutionary relationship with other congeners. Results Morphological examination revealed that P. kappa from M. giganteus, the type-host, can be distinguished from those in Osphranter spp. by the greater length and number of striations on the buccal capsules. DNA sequences showed that P. kappa from M. giganteus was genetically distinct from that in Osphranter spp., thereby supporting the morphological findings. Based on these finding, a new species from Osphranter spp., Pharyngostrongylus patriciae n. sp., is described. Conclusion Pharyngostrongylus patriciae n. sp. from Osphranter spp. is distinguished from P. kappa based on molecular and morphological evidence. The study highlights the importance of combining molecular and morphological techniques for advancing the nematode taxonomy. Although ITS genetic markers have proven to be effective for molecular prospecting as claimed in previous studies, future utilisation of mitochondrial DNA to validate ITS data could further elucidate the extent of speciation among macropodid nematodes.

Southern Australian waters feature remarkably diverse assemblages of the sea spider family Callipallenidae Hilton, 1942. The most speciose of the three Australian-endemic genera currently recognised has been known as Meridionale Staples, 2014, but is here reinstated under the name Pallenella Schimkewitsch, 1909 based on its type species Pallenella laevis (Hoek, 1881). This genus includes several brightly coloured forms that occur in high abundance on arborescent bryozoans. However, considerable similarity of congeners and scarcity of diagnostic characters continue to render species delineation in this genus challenging. Using an integrative taxonomic approach, we combine detailed morphological investigation with analysis of two genetic markers (mitochondrial cytochrome c oxidase subunit I, and nuclear rDNA including internal transcribed spacers 1 and 2) to explore the extraordinary species richness of the genus Pallenella in south-east Tasmania. In agreement with our morphology-based segregation of different species and morphotypes, we recovered well-supported corresponding clades in the genetic analyses. Strong mito-nuclear concordance in the two markers supports the inference of sustained reproductive isolation between the sympatrically occurring forms. Based on these findings, we distinguish a total of 13 Tasmanian congeners, representing the most diverse assemblage of sympatric species in the same microhabitat reported for a single pycnogonid genus. Within this assemblage, we (1) record the type species P. laevis for the first time after almost 150 years, (2) delineate the two Tasmanian morphotypes of the provisional ' variabilis ' complex, and (3) describe two species new to science (P. karenae , sp. nov., P. baroni , sp. nov.). Despite considerable genetic divergences between most congeners, only few and often subtle characters are found to be suitable for morphology-based delineation. Notably, colouration of living specimens is suggested to be informative in some cases. For morphology-based species identification of preserved specimens, a key relying on combinations of characters rather than single diagnostic features is proposed. Australian waters harbour remarkably diverse assemblages of sea spiders (Pycnogonida), including the endemic genus Pallenella Schimkewitsch, 1909 with several colourful but morphologically similar forms. Using an integrative taxonomic approach, we studied the extraordinary diversity of Pallenella in south-east Tasmania. Based on concordance of morphology, live colouration and two molecular markers, we distinguish 13 congeners and describe two new species. To date, this represents the most diverse assemblage of sympatric species in the same microhabitat reported for a single pycnogonid genus. [ABSTRACT FROM AUTHOR]

Background: Australian marsupials harbour a diverse array of helminth parasites. Despite current attempts to assess the extent of this diversity in macropodid hosts, it has been suggested that unique parasite fauna of Australian wildlife is difficult to document comprehensively due to the common occurrence of cryptic species. This paper assessed genetic variation within Austrostrongylus thylogale Johnston & Mawson, 1940 from the tammar wallaby, Notamacropus eugenii (Gray), and the quokka, Setonix brachyurus (Quoy & Gaimard), from different localities using the molecular characterisation of the internal transcribed spacers (ITS) within the nuclear ribosomal DNA. Methods: Thirty-seven specimens of A. thylogale collected from N. eugenii (from Parndana, Kangaroo Island, South Australia, and Perup, Western Australia) and S. brachyurus (from Wellington Dam, Western Australia) were characterised using a molecular-phylogenetic approach utilising the first (ITS1) and second (ITS2) internal transcribed spacers. Results: Genetic variation was detected in both ITS1 and ITS2 between specimens of A. thylogale from N. eugenii and S. brachyurus; however, no variation was detected between specimens collected from N. eugenii from Parndana, South Australia, and Perup, Western Australia. Furthermore, the phylogenetic analyses of ITS sequences showed two clades of A. thylogale originating from two hosts, N. eugenii and S. brachyurus, suggesting the presence of cryptic species. Conclusions: This study provides evidence of genetic variation within A. thylogale based on collections from two different host species. Morphological studies are required to fully confirm the presence of a new species or cryptic species. Further molecular studies using a larger number of specimens are warranted to explore the genetic variation between A. thylogale from different geographical localities. [ABSTRACT FROM AUTHOR]

Abstract Background Nematodes of the family Anisakidae are parasites of many fishes and aquatic invertebrates which act as intermediate or paratenic hosts, while mammals and fish-eating birds are definitive hosts. Infective L3 larvae may be incidentally taken by human through eating raw or undercooked fish meat, causing anisakidosis. The main purpose of this study is to provide a basis for the future investigations to discover the genetic diversity of this widely distributed parasite nematodes of fishes and fish eating animals and their effect on fisheries and public health in Egypt and worldwide. Results One thousand, one hundred and fifteen specimens belong to nine fish species were collected from Lake Nasser, Egypt, and examined for infection with Anisakid larvae. Four fish species (Oreochromis niloticus, Tilapia galilaea, Lates niloticus, and Hydrocynus forskahlii) were found infected with third stage larvae of Contracaecum spp. No other Anisakid nematodes were detected. Larvae were found in the body cavity adhering to mesenteries by a thin membrane, except in Oreochromis niloticus and Tilapia galilaea were found free in branchial chambers. The highest prevalence was recorded in L. niloticus (100%) and H. forskahlii (82%). The mean intensity of infections were 0.17–4.12 and 5.1–10.3 in L. niloticus and H. forskahlii respectively. For further identification, the internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA from isolated larvae (n = 54) were amplified by PCR, followed by single-strand conformation polymorphism (SSCP) analysis which revealed five possible profiles. Conclusion Light and scanning electron microscope studies revealed that all anisakid larvae in the present study showed the most typical features of the genus Contracaecum. The sequencing (n = 28) and sequence and phylogenetic analyses showed that the present nematode larvae are likely belonging to C. multipapillatum.

Background: Cinnamomum osmophloeum (Co), a member of the Lauraceae, is an indigenous medicinal crop in Taiwan, and it contains higher cinnamaldehyde in essential oil than do other Cinnamomum species. Among these species, Cinnamomum burmannii (Cb) is frequently adulterated as Co because of their similar morphological characteristics or features. Objective: The purpose of this study was to develop a DNA-based molecular method for rapid authentication of the indigenous Co and prevention of its adulteration. Materials and Methods: The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA from various Cinnamomum species were amplified by polymerase chain reaction (PCR), and these obtained sequences were used for sequence analysis. Based on the sequence variants among various Cinnamomum species, restriction fragment length polymorphism (RFLP) was used to differentiate these Cinnamomum plants. Results: Two restriction endonucleases, MylI and EcoRV, were specifically used to digest the PCR-amplified ITS DNA from seven Cinnamomum species. The PCR-RFLP results demonstrated that the different restriction patterns that were produced by these two restriction enzymes clearly distinguished Co from Cb and five other Cinnamomum species simultaneously. Conclusion: The PCR-RFLP analysis developed in this study provides an alternative method for rapidly identifying Cinnamomum plants at the species level using DNA polymorphisms. [ABSTRACT FROM AUTHOR]

The genetic variation and taxonomic status of the four morphologically-defined species of Macropostrongyloides in Australian macropodid and vombatid marsupials were examined using sequence data of the ITS+ region (=first and second internal transcribed spacers, and the 5.8S rRNA gene) of the nuclear ribosomal DNA. The results of the phylogenetic analyses revealed that Ma. baylisi was a species complex consisting of four genetically distinct groups, some of which are host-specific. In addition, Ma. lasiorhini in the common wombat (Vombatus ursinus) did not form a monophyletic clade with Ma. lasiorhini from the southern hairy-nosed wombat (Lasiorhinus latifrons), suggesting the possibility of cryptic (genetically distinct but morphologically similar) species. There was also some genetic divergence between Ma. dissimilis in swamp wallabies (Wallabia bicolor) from different geographical regions. In contrast, there was no genetic divergence among specimens of Ma. yamagutii across its broad geographical range or between host species (i.e. Macropus fuliginosus and M. giganteus). Macropostrongyloides dissimilis represented the sister taxon to Ma. baylisi , Ma. yamagutii and Ma. lasiorhini. Further morphological and molecular studies are required to assess the species complex of Ma. baylisi. [ABSTRACT FROM AUTHOR]

Chromosomes of four Miscanthus (Andersson, 1855) species including M. sinensis (Andersson, 1855), M. floridulus (Schumann & Lauterb, 1901), M. sacchariflorus (Hackel, 1882) and M. lutarioriparius (Chen & Renvoize, 2005) were analyzed using sequentially combined PI and DAPI (CPD) staining and fluorescence in situ hybridization (FISH) with 45S rDNA probe. To elucidate the phylogenetic relationship among the four Miscanthus species, the homology of repetitive sequences among the four species was analyzed by comparative genomic in situ hybridization (cGISH). Subsequently four Miscanthus species were clustered based on the internal transcribed spacer (ITS) of 45S rDNA. Molecular cytogenetic karyotypes of the four Miscanthus species were established for the first time using chromosome measurements, fluorochrome bands and 45S rDNA FISH signals, which will provide a cytogenetic tool for the identification of these four species. All the four have the karyotype formula of Miscanthus species, which is 2n = 2x = 38 = 34m(2SAT) + 4sm, and one pair of 45S rDNA sites. The latter were shown as strong red bands by CPD staining. A non-rDNA CPD band emerged in M. floridulus and some blue DAPI bands appeared in M. sinensis and M. floridulus. The hybridization signals of M. floridulus genomic DNA to the chromosomes of M. sinensis and M. lutarioriparius genomic DNA to the chromosomes of M. sacchariflorus were stronger and more evenly distributed than other combinations. Molecular phylogenetic trees showed that M. sinensis and M. floridulus were closest relatives, and M. sacchariflorus and M. lutarioriparius were also closely related. These findings were consistent with the phylogenetic relationships inferred from the cGISH patterns. [ABSTRACT FROM AUTHOR]

Abstract Gyrodactylus mojarrae n. sp. is described from the gills of the Neotropical cichlids Thorichthys maculipinnis, Rocio octofasciata, Vieja zonata and V. fenestrata from several localities across southern Mexico. The new species is erected on the basis of the morphology of the haptoral elements (anchors, bars and hooks), and its phylogenetic position within the Gyrodactylidae is evaluated based on the analysis of partial sequences of the ITS1, 5.8 rRNA gene and ITS2. Gyrodactylus mojarrae n. sp. differs from other congeneric species by having hooks with a straight shaft and recurved point, pointed toe and convex heel, presence of reduced superficial anchor roots, by the number and disposition of spinelets of the male copulatory organ, and the absence of shield and lateral processes of the superficial bar. Molecular circumscription of isolates of G. mojarrae n. sp. from different host and hydrological basins showed that these isolates are conspecific and represent a distinct lineage from other congeners, including newly sequenced isolates of Gyodactylus sp. A and Gyrodactylus sp. B from Astyanax mexicanus (Characidae) and Gobiomorus dormitor (Eleotridae), respectively. Genetic affinities of Gyodactylus sp. A and B indicate that they might represent undescribed species infecting freshwater fish from the Americas. Graphical abstract Unlabelled Image Highlights • Gyrodactylus mojarrae n. sp. is characterized based on its haptoral elements and molecular circumscription. • Gyrodactylus mojarrae n. sp. represents a distinct lineage from other congeners parasitizing freshwater and marine fishes. • The newly erected species is genetically distant from other Gyrodactylus spp. infecting perciform fish. • The diversity of species of Gyrodactylus in tropical freshwater fish is still underestimated. [ABSTRACT FROM AUTHOR]

In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian.How to CiteFibriana, F., & Hadiyanti, L. N. (2016). Phylogenetic Relationships of Local Durian Species based on Morphological Characteristics and PCR-RFLP Analysis of the Ribosomal Internal Transcribed Spacer (ITS) DNA. Biosaintifika: Journal of Biology & Biology Education, 8(3), 362-370.

Shankhpushpi is a reputed drug from an Indian system of medicine for treating mental disorders and enhancing memory. Two herbs, namely Convolvulus prostratus Forssk. and Evolvulus alsinoides (L.) L., are commonly known as Shankhpushpi. Ambiguous vernacular identity can affect the scientific validity of the Shankpushpi-based herbal drug therapy. In the present investigation, a novel and sensitive multiplex PCR method based on polymorphism in the internal transcribed spacer (ITS) region was developed to establish the molecular identity of C. prostratus and E. alsinoides. DNA was isolated and the ITS region was amplified, sequenced and assembled. Sequences were aligned to identify variable nucleotides in order to develop plant-specific primers. Primers were validated in singleplex reactions and eventually a multiplex assay was developed. This assay was tested for sensitivity and validated by amplifying DNA isolated from the simulated blended powdered plant material. Primers developed for C. prostratus resulted into a 200 bp amplicon and 596 bp for E. alsinoides. The assay was found to be sensitive enough for amplification of low quantities of DNA. The method can detect 10% of the mixing of plants with each other in blended material. This PCR assay can be used for rapid botanical identification of Shankhpushpi plant materials and will improve evidence-based herbal drug therapy.

The strongyloid nematode subfamily Phascolostrongylinae comprises parasites of the large intestine and stomach of Australian macropods and wombats. In this study, we tested the phylogenetic relationships among the genera of the Phascolostrongylinae using the first and second internal transcribed spacers of the nuclear ribosomal DNA. Monophyly was encountered in the tribe Phascolostrongylinea comprising two genera, Phascolostrongylus and Oesophagostomoides, found exclusively in the large intestine of wombats. The tribe Hypodontinea, represented by the genera Hypodontus and Macropicola from the ileum and large intestine of macropods, was also found to be monophyletic. The tribe Macropostrongyloidinea, comprising the genera Macropostrongyloides and Paramacropostrongylus, was paraphyletic with the species occurring in the stomach grouping separately from those found in the large intestines of their hosts. However, Macropostrongyloidesdissimilis from the stomach of the swamp wallaby and Paramacropostrongylus toraliformis from the large intestine of the eastern grey kangaroo were distinct from their respective congeners. This study provided strong support for the generic composition of the tribe Phascolostrongylinea. The unexpected finding of M. dissimilis and P. toraliformis being distantly related to their respective congeners suggests a requirement for future taxonomic revision that may warrant separation of these species at the generic level.

Heterakis gallinarum is one of the most recurrently diagnosed nematodes within the gastrointestinal tract of galliform birds. In the present study, we investigated the genetic diversity of 96 H. gallinarum collected from free-range chickens from different localities in Tunisia. We assessed phylogeny and genetic variability using the internal transcribed spacers (ITS) of the nuclear ribosomal DNA and the mitochondrial cytochrome c oxidase subunit I gene. Haplotype and nucleotide diversities indicate that H. gallinarum is a species with extremely low genetic diversity. Based on the networks and phylogenetic trees, there was strong support for the absence of significant geographical structuring among the H. gallinarum populations in different localities in Tunisia. Mismatch distributions and neutrality tests of both genetic markers suggest that at least one expansion event occurred in the population demographic history of H. gallinarum. Our data showed a lack of population structure using the pairwise fixation index (FST) and an extensive gene flow. It indicated that the most likely major contributor to the low genetic diversity and gene flow is the movement of the parasitized birds; in other words, the frequency of the poultry trade considerably affects patterns of worm gene flow. [ABSTRACT FROM AUTHOR]

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Abstract Background The purpose of this study was to assess the genetic variation and differentiation of Blastocystis subtypes (STs) recovered from symptomatic children by analysing partial sequences of the small subunit rDNA gene region (SSUrDNA) and internal transcribed spacers (1 and 2) plus the 5.8S region (ITS, ITS1 + 5.8S + ITS2) and comparing with isolates from other countries. Findings Faecal samples from 47 Blastocystis-infected children with gastrointestinal symptoms and negative for pathogenic enterobacteria were analysed. PCR was performed on DNA from all the samples to identify Blastocystis STs, amplifying a fragment of SSUrDNA and the ITS region. The amplicons were purified and sequenced, and consensus sequences were submitted to GenBank; afterwards, SSUrDNA sequences were analysed for genetic diversity according to geographic area. Regarding the Blastocystis STs found, 51% were ST1, 23% ST2, 19% ST3 and 2% ST7. For ITS, a haplotype network tree and Bayesian inference revealed the presence of two novel variants of ST1, clustering some sequences into ST1A and ST1B. The values of nucleotide diversity (π) and haplotype polymorphism (θ) for ST1, ST2 and ST3 ranged from 0 to 1, whereas the ratio of genetic differentiation (FST)/migration index (Nm) showed the highest differentiation between Libya and Thailand-Philippines for ST2 (0.282/0.63). In contrast, a high flow gene was observed between Czech Republic-Denmark-Holland-Spain and USA-Mexico-Colombia for ST1 (0.003/84). Conclusion Our data on genetic differentiation and gene flow might explain the differences for the prevalence of Blastocystis STs. Moreover, the ITS region could be used as a genetic marker to assess genetic variation in this parasite.

Background: Nematodes of the family Anisakidae are parasites of many fishes and aquatic invertebrates which act as intermediate or paratenic hosts, while mammals and fish-eating birds are definitive hosts. Infective L3 larvae may be incidentally taken by human through eating raw or undercooked fish meat, causing anisakidosis. The main purpose of this study is to provide a basis for the future investigations to discover the genetic diversity of this widely distributed parasite nematodes of fishes and fish eating animals and their effect on fisheries and public health in Egypt and worldwide. Results: One thousand, one hundred and fifteen specimens belong to nine fish species were collected from Lake Nasser, Egypt, and examined for infection with Anisakid larvae. Four fish species ( Oreochromis niloticus, Tilapia galilaea, Lates niloticus, and Hydrocynus forskahlii) were found infected with third stage larvae of Contracaecum spp. No other Anisakid nematodes were detected. Larvae were found in the body cavity adhering to mesenteries by a thin membrane, except in Oreochromis niloticus and Tilapia galilaea were found free in branchial chambers. The highest prevalence was recorded in L. niloticus (100%) and H. forskahlii (82%). The mean intensity of infections were 0.17-4.12 and 5.1-10.3 in L. niloticus and H. forskahlii respectively. For further identification, the internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA from isolated larvae ( n = 54) were amplified by PCR, followed by single-strand conformation polymorphism (SSCP) analysis which revealed five possible profiles. Conclusion: Light and scanning electron microscope studies revealed that all anisakid larvae in the present study showed the most typical features of the genus Contracaecum. The sequencing ( n = 28) and sequence and phylogenetic analyses showed that the present nematode larvae are likely belonging to C. multipapillatum. [ABSTRACT FROM AUTHOR]

Sequences of ribosomal internal transcribed spacers ( ITS s) are of great importance to molecular phylogenetics and DNA barcoding, but remain unstudied in some large taxa of Deuterostomia. We have analyzed complete ITS1 and ITS2 sequences in 62 species from 16 Deuterostomia classes, with ITS sequences in 24 species from 11 classes initially obtained using unannotated contigs and raw read sequences. A general tendency for both ITS length and GC-content increase from interior to superior Deuterostomia taxa, a uniform GC-content in both ITS s within the same species, thymine content decrease in sense DNA sequences of both ITS s are shown. A possible role of GC-based gene conversion in Deuterostomia ITS evolutionary changes is hypothesized. The first example of non-LTR retrotransposon insertion into ITS sequence in Deuterostomia is described in turtle Geochelone nigra . The roles of mobile genetic element insertions in the evolution of ITS sequences in some Sauropsida taxa are discussed as well. [ABSTRACT FROM AUTHOR]

Sequences of the first and second internal transcribed spacers (ITS1 + ITS2) of nuclear ribosomal DNA were employed to determine whether the congeneric assemblages of species of the strongyloid nematode genus Cloacina, found in the forestomachs of individual species of kangaroos and wallabies (Marsupialia: Macropodidae), considered to represent species flocks, were monophyletic. Nematode assemblages examined in the black-striped wallaby, Macropus (Notamacropus) dorsalis, the wallaroos, Macropus (Osphranter) antilopinus/robustus, rock wallabies, Petrogale spp., the quokka, Setonix brachyurus, and the swamp wallaby, Wallabia bicolor, were not monophyletic and appeared to have arisen by host colonization. However, a number of instances of within-host speciation were detected, suggesting that a variety of methods of speciation have contributed to the evolution of the complex assemblages of species present in this genus. [ABSTRACT FROM PUBLISHER]

Copyright of Ecoscience (Ecoscience) is the property of Taylor & Francis Ltd and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Mecistocirrus digitatus and Toxocara vitulorum are common pathogenic nematode parasites of mithun ( Bos frontalis). Species identification by morphological features was confirmed by molecular identification of M. digitatus and T. vitulorum. The internal transcribed spacer-2 (ITS-2) region and beta tubulin gene of M. digitatus were polymerase chain reaction (PCR) amplified and sequenced. ITS-2 sequence analysis showed 100% homology with other isolates of M. digitatus and 83% identity with Haemonchus contortus and H. placei, respectively. Likewise, ITS-1 and ITS-2 sequences of T. vitulorum were PCR amplified and sequenced. Sequence analysis of these internal transcribed spacers from five worms of the parasite from mithun showed no intraspecific variations with T. vitulorum isolates from domestic ruminants. [ABSTRACT FROM AUTHOR]

This study deals with the molecular systematics of Asian collections of Hebeloma theobrominum and H. mesophaeum which have not been previously reported from any Himalayan part of the world, and are new to Pakistan. Both were identified using morpho-anatomical and molecular characterization. The target rDNA of both species was amplified by using universal fungal primers. In phylogenetic analysis, both species distinctly clustered with their respective groups. These both species have been described first time from Asia using ITS-rDNA barcoding. The sequences of both species were compared with those of same European species from the GenBank. These species clustered with European species in phylogenetic tree proving their cosmopolitan distribution. [ABSTRACT FROM AUTHOR]

Avian trichomoniasis caused by Trichomonas gallinae is a serious protozoan disease worldwide. The domestic pigeon (Columba livia domestica) is the main host for T. gallinae and plays an important role in the spread of the disease. Based on the internal transcribed spacers of nuclear ribosomal DNA of this parasite, a pair of primers (TgF2/TgR2) was designed and used to develop a PCR assay for the diagnosis of T. gallinae infection in domestic pigeons. This approach allowed the identification of T. gallinae, and no amplicons were produced when using DNA from other common avian pathogens. The minimum amount of DNA detectable by the specific PCR assay developed in this study was 15 pg. Clinical samples from Guangzhou, China, were examined using this PCR assay and a standard microscopy method, and their molecular characteristics were determined by phylogenetic analysis. All of the T. gallinae-positive samples detected by microscopic examination were also detected as positive by the PCR assay. Most of the samples identified as negative by microscopic examination were detected as T. gallinae positive by the PCR assay and were confirmed by sequencing. The positive samples of T. gallinae collected from Guangzhou, China, were identified as T. gallinae genotype B by sequencing and phylogenetic analyses, providing relevant data for studying the ecology and population genetic structures of trichomonads and for the prevention and control of the diseases they cause. [ABSTRACT FROM AUTHOR]

The Yellow Sea is one of the mega diversity centers of the world and contains vast amount of flora and fauna. The Penicillium species belongs to one of the most common and economically significant group of marine micro-fungi family. The study comprised isolation, microscopic observations and ribotyping, allowed discrimination of the marine fungal isolates as Penicillium viticola F1, Penicillium restrictum F2, Penicillium rubens F8, Penicillium implicatum F10, Penicillium piceum F11, Penicillium oxalicum F12, Penicillium sumatrense F15, and Penicillium vinaceum F16. This study demonstrated that Yellow Sea can be considered as a valuable natural source of Penicillium species, which can be used for the production of medicinally important different secondary metabolites and organic acids. [ABSTRACT FROM AUTHOR]

Intercontinental dislocations between tropical regions harboring two-thirds of the flowering plants have always drawn attention from taxonomists and biogeographers. One such family belonging to angiosperms is Orchidaceae with an herbaceous habit and high species diversity in the tropics. Here, we investigate the evolutionary and biogeographical history of the genus Cymbidium, which represents a monophyletic subfamily (Epidendroideae) of the orchids and comprises 50 odd species that are distinctly distributed in tropical to temperate regions. Much is not known about correlations among the level of CAM activity (one of the photosynthetic pathways often regarded as an adaptation to water stress in land plants), habitat, life forms, and phylogenetic relationships of orchids from an evolutionary perspective. A relatively well-resolved and highly supported phylogeny for Cymbidium orchids is reconstructed based on sequence analysis of ITS2 and matK regions from the chloroplast DNA available in public repositories viz. GenBank at NCBI. This study examines a genus level analysis by integrating different molecular matrices to existing fossil data on orchids in a molecular Bayesian relaxed clock employed in BEAST and assessed divergence times for the genus Cymbidium with a focus on evolutionary history of photosynthetic characters. Our study has enabled age estimations (45Ma) as well as ancestral area reconstruction for the genus Cymbidium using BEAST by addition of previously analyzed two internal calibration points. [ABSTRACT FROM AUTHOR]

In this study, twenty local durian accessions obtained from Central Java in situ collection were characterized using the morphological characteristics and the restriction patterns which generated from the region spanning the internal transcribed spacers ITS LEU and ITS 4. Morphological characteristics of durian leaf, stem, tree, and fruit showed variations for the different accessions, whereas polymerase chain reaction (PCR) products of ribosomal DNA region showed a low length of variation. The size of the PCR products and the restriction analyses with the restriction endonucleases Bsp1431yielded a restriction pattern for each accessions. The results of this study can be utilized by local durian farmers as a preliminary reference for durian propagation. The data obtained need to be supported by further research using the other molecular markers to obtain more accurate data. The clear identity of durian species can help the management of propagation systems by farmers to get superior local durian. [ABSTRACT FROM AUTHOR]

Cloacina johnstoni sp. nov. (Nematoda: Strongyloidea) is described from the sacculated forestomach of the wallaroo, Macropus robustus (Marsupialia: Macropodidae) from Australia. It resembles the synhospitalic species Cloacina macropodis but differs from it principally in the shape of the cephalic papillae. The two species are also distinguishable based on differences in the first and second internal transcribed spacers (ITS) of nuclear ribosomal DNA (rDNA). Cloacina johnstoni commonly co-occurs in the same individual host as C. macropodis but has a more restricted geographical distribution. [ABSTRACT FROM AUTHOR]

A fragment of the mitochondrial COI gene from isolates of several echinoderm species was sequenced. The isolates were from three species of starfish from the Asteriidae family ( Asterias amurensis and Aphelasterias japonica collected in the Sea of Japan and Asterias rubens collected in the White Sea) and from the sea urchin Echinocardium cordatum (family Loveniidae) collected in the Sea of Japan. Additionally, regions including internal transcribed spacers and 5.8S rRNA ( ITS1-5.8S rDNA- ITS2) were sequenced for the three studied starfish species. Phylogenetic analysis of the obtained COI sequences together with earlier determined homologous COI sequences from Ast. forbesii, Ast. rubens, and Echinocardium laevigaster from the North Atlantic and E. cordatum from the Yellow and North Seas (GenBank) placed them into strictly conspecific clusters with high bootstrap support (99% in all cases). Only two exceptions- Ast. rubens DQ077915 sequence placed with the Ast. forbesii cluster and Aph. japonica DQ992560 sequence placed with the Ast. amurensis cluster-were likely results of species misidentification. The intraspecific polymorphism for the COI gene within the Asteriidae family varied within a range of 0.2-0.9% as estimated from the genetic distances. The corresponding intrageneric and intergeneric values were 10.4-12.1 and 21.8-29.8%, respectively. The interspecific divergence for the COI gene in the sea urchin of Echinocardium genus (family Loveniidae) was significantly higher (17.1-17.7%) than in the starfish, while intergeneric divergence (14.6-25.7%) was similar to that in asteroids. The interspecific genetic distances for the nuclear transcribed sequences ( ITS1-5.8S rDNA- ITS2) within the Asteriidae family were lower (3.1-4.5%), and the intergeneric distances were significantly higher (32.8-35.0%), compared to the corresponding distances for the COI gene. These results suggest that the investigated molecular-genetic markers could be used for segregation and identification of echinoderm species. [ABSTRACT FROM AUTHOR]

The genus Erica represents the epitome of plant biodiversity in the South African Cape fynbos with over 700 species. This genus is composed of seeder and resprouter species, but both species diversity and endemism are strongly linked to the seeder habit and concentrated in the southwestern Cape Floristic Region (CFR). Erica coccinea is a relatively abundant and widespread fynbos species whose most remarkable morphological feature is the existence of distinct seeder and resprouter forms, frequently-but not always-in disjunct populations. Both higher within-population genetic diversity and among-population differentiation have been found in seeders, most likely as a consequence of the shorter generation times and faster population turnovers. Resprouters, despite being less diverse, are suspected to be ancestral. However, no solid evidence has yet been provided for the ancestrality of the resprouter form, or for the demographic processes that have determined the current distribution of genetic diversity in both regeneration forms. Here, we used microsatellites and sequences of the nuclear ribosomal internal transcribed spacers to describe the phylogeographic structure of seeder and resprouter E. c occinea populations and provide good evidence for the ancestral status of the resprouter form and the comparatively high rates of molecular evolution in derived seeder populations. We also reveal that mixed populations, where both seeder and resprouter individuals co-occur, were originated by secondary contacts. This study highlights the role of fire in driving accelerated diversification in seeder lineages of highly speciose CFR fynbos taxa. [ABSTRACT FROM AUTHOR]

Aims To phenotypically, physiologically and molecularly characterize the causal agent of olive anthracnose in the northern Tunisia and to study its genetic variability and pathogenicity. Methods and Results A total of 43 isolates were obtained from symptomatic olives collected from four regions in northern Tunisia. A range of morphological and physiological characteristics was recorded; and a phylogenetic study, based on the sequence analysis of both internal transcribed spacers and TUB2 gene regions, was performed. Of the 43 isolates, 41 were identified as Colletotrichum acutatum s.s, and only two were affiliated to Colletotrichum gloeosporioides s.s. Two more representative Spanish isolates, included for comparison, were identified as Colletotrichum godetiae. Using six inter-simple-sequence-repeat markers, homogeneity between isolates from different locations and within the same species was recorded. In pathogenicity and virulence studies, C. gloeosporioides s.s was found to be less virulent, while the Spanish C. godetiae isolate was significantly more virulent than the Tunisian C. acutatum s.s. Conclusions Olive anthracnose in the North of Tunisia is mainly caused by C. acutatum s.s species. Significance and Impact of the Study This is the first study of olive anthracnose in Tunisia, which combines both phenotypic and molecular approaches. Colletotrichum acutatum s.s group was recorded for the first time in the country as the causal agent of olive anthracnose. [ABSTRACT FROM AUTHOR]

Shankhpushpi is a reputed drug from an Indian system of medicine for treating mental disorders and enhancing memory. Two herbs, namely Convolvulus prostratus Forssk. and Evolvulus alsinoides (L.) L., are commonly known as Shankhpushpi. Ambiguous vernacular identity can affect the scientific validity of the Shankpushpi-based herbal drug therapy. In the present investigation, a novel and sensitive multiplex PCR method based on polymorphism in the internal transcribed spacer (ITS) region was developed to establish the molecular identity of C. prostratus and E. alsinoides . DNA was isolated and the ITS region was amplified, sequenced and assembled. Sequences were aligned to identify variable nucleotides in order to develop plant-specific primers. Primers were validated in singleplex reactions and eventually a multiplex assay was developed. This assay was tested for sensitivity and validated by amplifying DNA isolated from the simulated blended powdered plant material. Primers developed for C. prostratus resulted into a 200 bp amplicon and 596 bp for E. alsinoides . The assay was found to be sensitive enough for amplification of low quantities of DNA. The method can detect 10% of the mixing of plants with each other in blended material. This PCR assay can be used for rapid botanical identification of Shankhpushpi plant materials and will improve evidence-based herbal drug therapy. [ABSTRACT FROM AUTHOR]

American trypanosomiasis is a common zoonosis in Colombia and Trypanosoma cruzi presents a wide distribution throughout the country. Although some studies based on enzyme electrophoresis profiles have described the population structure of the parasite, very few molecular analyses of genotipic markers have been conducted using Colombian strains. In this study, we amplified the non-transcribed spacer of the mini-gene by PCR, typing the isolates as T. cruzi I, T. cruzi zymodeme 3 or T. rangeli. In addition, the internal transcribed spacers of the ribosomal gene concomitant with the 5.8S rDNA were amplified and submitted to restriction fragment polymorphism analysis. The profiles were analyzed by a numerical methodology generating a phenetic dendrogram that shows heterogeneity among the T. cruzi isolates. This finding suggests a relationship between the complexity of the sylvatic transmission cycle in Colombia and the diversity of the sylvan parasites.

Background: Accurate identification of sheep nematodes is a critical point in epidemiological studies and monitoring of drug resistance in flocks. However, due to a close morphological similarity between the eggs and larval stages of many of these nematodes,such identification is not a trivial task. There are a number of studies showing that molecular targets in ribosomal DNA (Internal transcribed spacer 1, 2 and Intergenic spacer) are suitable for accurate identification of sheep bursate nematodes. The objective of present study was to compare the ITS1, ITS2 and IGS regions of Iranian common bursate nematodes in order to choose best target for specific identification methods. Methods: The first and second internal transcribed spacers (ITS1and ITS2) and intergenic spacer (IGS) of the ribosomal DNA (rDNA) of 5 common Iranian bursate nematodes of sheep were sequenced. The sequences of some non–Iranian isolates were used for comparison in order to evaluate the variation in sequence homology between geographically different nematode populations. Results: Comparison of the ITS1 and ITS2 sequences of Iranian nematodes showed greatest similarity among Teladorsagia circumcincta and Marshallagia marshalli of 94% and 88%, respectively. While Trichostrongylus colubriformis and M. marshalli showed the highest homology (99%) in the IGS sequences. Comparison of the spacer sequences of Iranian with non-Iranian isolates showed significantly higher variation in Haemonchus contortus compared to the other species. Conclusion: Both the ITS1 and ITS2 sequences are convenient targets to have species-specific identification of Iranian bursate nematodes. On the other hand the IGS region may be a less suitable molecular target.

Common cypress (Cupressus sempervirens L.) is an east Mediterranean plant element and one of four native conifers in Iran. During spring and summer of 2012, a field survey was carried out in different areas of Kerman province (south-eastern Iran) to study cypress decline diseases. Samples were collected from crowns, trunks and branches of cypress trees showing yellowing, dieback, canker, wilting of leaves and internal wood discoloration. Isolations were made from symptomatic wood tissues. Based on morphological and molecular characteristics, four species of Phaeoacremonium, namely Phaeoacremonium parasiticum, Pm. aleophilum, Pm. iranianum and Pm. rubrigenum, and two species of the Botryosphaeriaceae, Botryosphaeria dothidea and Neofusicoccum parvum, were isolated and identified. Pathogenicity tests were undertaken to determine the role of these species on 2-year-old potted cypress plants and green shoots of grapevine. Neofusicoccum parvum was more virulent than the other species and caused the largest lesions on both hosts. The fungi were re-isolated from margins of lesions and healthy tissue, thus completing Koch’s postulates. This is the first report of B. dothidea, N. parvum, Pm. aleophilum, Pm. rubrigenum and Pm. iranianum as pathogens on Mediterranean cypress trees.

Nucleotide sequences of internal transcribed spacers (ITS1 and ITS2) of rDNA have been obtained and analyzed in natural populations of Planorbarius corneus snails from the Leningrad and Kaliningrad oblasts. The close similarity between ITS1 and ITS2 of the snails from different areas proves that Planorbarius corneus is a polymorphic but uniform species. [ABSTRACT FROM AUTHOR]

Most plant species harbour a diverse community of endophytic, but their role is still unknown in most cases, including ecologically and economically important tree species. This study describes the culturable fungal endophytic community of Pinus sylvestris L. twigs in northern Spain and its relationship with diametric growth of the host. In all, 360 twig samples were collected from 30 Scots pines in fifteen stands. Isolates were obtained from all twig samples and 43 fungal taxa were identified by morphogrouping and subsequent ITS rDNA sequencing. All isolates were Ascomycetes, being Dothideomycetes and Sordariomycetes the most abundant classes. Half of the species were host generalists while the others were conifer or pine specialists. We found three new endophytic species for the Pinaceae: Biscogniauxia mediterranea , Phaeomoniella effusa and Plectania milleri , and additional six new species for P. sylvestris : Daldinia fissa , Hypocrea viridescens , Nigrospora oryzae , Ophiostoma nigrocarpum , Penicillium melinii and Penicillium polonicum . The endophytic community of fast and slow growing trees showed differences in species composition, abundance and evenness, but not in diversity. Phoma herbarum was associated to fast growing trees and Hypocrea lixii to those growing slow. Our results support the hypothesis that some endophytic species may affect growth of P. sylvestris . [ABSTRACT FROM AUTHOR]

Background. Heavy metals are dangerous industrial pollutants. The development of phytoremediation technologies based on plants having capability to hyperaccumulate heavy metals is a promising approach to detoxify polluted territories. Many such hyperaccumulators belong to the family Brassicaceae and are found mostly within the Alysseae tribe. We analyzed the molecular phylogeny and distribution of the ability to hyperaccumulate Ni within the tribe. Most of the Ni hyperaccumulators are related to the Odontarrhena section. We propose partitioning the tribes into five clades, whose compactness is illustrated by primary and secondary ITS2 structures characteristics. [ABSTRACT FROM AUTHOR]

Aim The evolutionary history of narrow endemic species has received little attention compared with that of more widely distributed species. Small effective population sizes and long-term isolation of many narrow endemic species make research on their genetic make-up important for their future conservation. In this study we investigated the genetic variation and historical distribution of an isolated plant, the monospecific genus Pseudomisopates, as an example of the phylogeographical history of narrow endemics. Location Central Range, Iberian Peninsula, Mediterranean Europe. Methods We used amplified fragment length polymorphisms ( AFLPs), nuclear and plastid DNA sequences and species distribution modelling. Sequence data were analysed using statistical parsimony, molecular dating, and a coalescent-based Bayesian model of isolation with migration. Genetic diversity and differentiation analyses based on AFLP data were performed. We compared the detection of clones using AFLPs with the results of a previous study that used simple sequence repeats ( SSRs). Results AFLP analysis revealed that SSRs underestimate clone number. The coalescent-based Bayesian model of isolation with migration suggested a late Pleistocene divergence between the populations of Pseudomisopates on two mountain massifs (Gredos and La Serrota), despite the presence of a large area suitable for population admixture. Moderate to high levels of genetic diversity and high effective population sizes were inferred. Main conclusions Our results imply that the levels of genetic diversity within narrow endemic species from Mediterranean mountains could primarily be driven by extrinsic historical factors, rather than by intrinsic species-specific factors depending on their own biological characteristics. Narrow endemics are widely believed to harbour low genetic diversity because of small effective population sizes. However, this study and others on narrow endemic angiosperms demonstrate that narrow endemism does not necessarily result in low genetic diversity. [ABSTRACT FROM AUTHOR]