scholarly journals Variability in ITS1 and ITS2 sequences of historic herbaria and extant (fresh) Phalaris species (Poaceae)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Allison L. Graper ◽  
Andrzej K. Noyszewski ◽  
Neil O. Anderson ◽  
Alan G. Smith
Keyword(s):  
Species Identification ◽  
North American ◽  
Geographic Origin ◽  
Phalaris Arundinacea ◽  
Control Measures ◽  
Dna Concentration ◽  
Its Regions ◽  
Species Specific ◽  
Its1 And Its2 ◽  
Diagnostic Snps

Abstract Background Phalaris species (Poaceae) occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The nuclear ribosomal internal transcribed spacer (ITS) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic herbaria (1882–2001) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs) and compare ITS regions of historic Phalaris specimens with known, extant Phalaris species. Results We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other USA and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin. Conclusions While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 year range) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need to exercise stringent quality control measures on newly generated sequence data and to approach public sequence databases in a critical way.

scholarly journals Variability in ITS1 and ITS2 Sequences of Historic (herbaria) and Extant (fresh) Phalaris Species

2020 ◽  
Author(s):  
Allison Graper ◽  
Andrzej Noyszewski ◽  
Neil Anderson ◽  
Alan Smith
Keyword(s):  
Species Identification ◽  
North American ◽  
Geographic Origin ◽  
Phalaris Arundinacea ◽  
Internal Transcribed Spacer Region ◽  
Dna Concentration ◽  
Its Regions ◽  
Species Specific ◽  
Its1 And Its2 ◽  
Diagnostic Snps

Abstract Background: Phalaris species occupy diverse environments throughout all continents except Antarctica. Phalaris arundinacea is an important forage, ornamental, wetland restoration and biofuel crop grown globally as well as being a wetland invasive. The ITS (internal transcribed spacer) region has been used for Phalaris barcoding as a DNA region with high nucleotide diversity for Phalaris species identification. Recent findings that P. arundinacea populations in Minnesota USA are most likely native and not European prompted this analysis to determine whether Eurasian vs. native North American P. arundinacea differed in ITS regions. Our objectives were to amplify and compare ITS regions (ITS1 and ITS2) of historic (herbaria) and extant (fresh) Phalaris specimens; analyze ITS regions for species-specific polymorphisms (diagnostic SNPs); compare ITS regions of historic Phalaris specimens with known, extant Phalaris species.Results: We obtained complete ITS1 and ITS2 sequences from 31 Phalaris historic (herbaria samples, 1908 to 2001) and five extant (fresh) specimens. Herbaria Phalaris specimens did not produce new SNPs (single nucleotide polymorphisms) not present in extant specimens. Diagnostic SNPs were identified in 8/12 (66.6%) Phalaris species. This study demonstrates the use of herbaria tissue for barcoding as a means for improved species identification of Phalaris herbaria type specimens. No significant correlation between specimen age and genomic DNA concentration was found. Phalaris arundinacea showed high SNP variation within its clade, with the North American being distinctly different than other U.S. and most Eurasian types, potentially allowing for future identification of specific SNPs to geographic origin.Conclusions: While not as efficient as extant specimens to obtain DNA, Phalaris herbaria specimens can produce high quality ITS sequences to evaluate historic genetic resources and facilitate identification of new species-specific barcodes. No correlation between DNA concentration and age of historic samples (119 years) occurred. Considerable polymorphism was exhibited in the P. arundinacea clade with several N. American accessions being distinct from Eurasian types. Further development of within species- and genus-specific barcodes could contribute to designing PCR primers for efficient and accurate identification of N. American P. arundinacea. Our finding of misidentified Phalaris species indicates the need for DNA sequence database curation for proper specimen identification.

scholarly journals A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia

2011 ◽  
Vol 80 (3) ◽  
pp. 185-192 ◽  
Author(s):  
Jakub Sawicki ◽  
Monika Szczecińska
Keyword(s):  
Species Identification ◽  
Molecular Identification ◽  
Restriction Analysis ◽  
Genetic Relationships ◽  
Restriction Enzymes ◽  
Number Of Species ◽  
Highly Effective ◽  
Species Specific ◽  
Its1 And Its2

RAPDs, ISJs, ISSRs, ITS and <em>kat</em>Gs were applied to determine genetic relationships between common <em>Sphagnum </em>species of the section <em>Acutifolia</em>. Twenty populations were genotyped using ten ISJ primers, 12 pairs of <em>kat</em>G primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and <em>kat</em>G markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.

scholarly journals A Forensic Detection Method for Hallucinogenic Mushrooms via High-Resolution Melting (HRM) Analysis

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 199
Author(s):  
Xiaochun Zhang ◽  
Huan Yu ◽  
Qi Yang ◽  
Ziwei Wang ◽  
Ruocheng Xia ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Barcoding ◽  
High Resolution Melting ◽  
Its Region ◽  
Its Sequencing ◽  
Melting Temperatures ◽  
Hrm Analysis ◽  
National Drug ◽  
Species Specific ◽  
Its1 And Its2

In recent years, trafficking and abuse of hallucinogenic mushrooms have become a serious social problem. It is therefore imperative to identify hallucinogenic mushrooms of the genus Psilocybe for national drug control legislation. An internal transcribed spacer (ITS) is a DNA barcoding tool utilized for species identification. Many methods have been used to discriminate the ITS region, but they are often limited by having a low resolution. In this study, we sought to analyze the ITS and its fragments, ITS1 and ITS2, by using high-resolution melting (HRM) analysis, which is a rapid and sensitive method for evaluating sequence variation within PCR amplicons. The ITS HRM assay was tested for specificity, reproducibility, sensitivity, and the capacity to analyze mixture samples. It was shown that the melting temperatures of the ITS, ITS1, and ITS2 of Psilocybe cubensis were 83.72 ± 0.01, 80.98 ± 0.06, and 83.46 ± 0.08 °C, and for other species, we also obtained species-specific results. Finally, we performed ITS sequencing to validate the presumptive taxonomic identity of our samples, and the sequencing output significantly supported our HRM data. Taken together, these results indicate that the HRM method can quickly distinguish the DNA barcoding of Psilocybe cubensis and other fungi, which can be utilized for drug trafficking cases and forensic science.

scholarly journals Rapid Species Identification of Cooked Poisonous Mushrooms by Using Real-Time PCR

2008 ◽  
Vol 74 (10) ◽  
pp. 3306-3309 ◽  
Author(s):  
Kazuhiko Maeta ◽  
Tomoya Ochi ◽  
Keisuke Tokimoto ◽  
Norihiro Shimomura ◽  
Nitaro Maekawa ◽  
...  
Keyword(s):  
Real Time ◽  
Species Identification ◽  
Real Time Pcr ◽  
Specific Test ◽  
Specific Identification ◽  
Specific Fluorescence ◽  
Species Specific ◽  
Poisonous Mushrooms

ABSTRACT Species-specific identification of the major cooked and fresh poisonous mushrooms in Japan was performed using a real-time PCR system. Specific fluorescence signals were detected, and no nonspecific signals were detected. Therefore, we succeeded in developing a species-specific test for the identification of poisonous mushrooms within 1.5 h.

scholarly journals Wing Morphology and Flight Behavior of Some North American Hummingbird Species

The Auk ◽  
2005 ◽  
Vol 122 (3) ◽  
pp. 872-886 ◽  
Author(s):  
F. Gary Stiles ◽  
Douglas L. Altshuler ◽  
Robert Dudley
Keyword(s):  
Breeding Season ◽  
North American ◽  
Theoretical Models ◽  
Wing Disc ◽  
Territorial Behavior ◽  
Flight Behavior ◽  
Adult Males ◽  
Wing Morphology ◽  
Reversed Sexual Size Dimorphism ◽  
Species Specific

Abstract We explored the relationship between wing morphology and flight behavior with respect to sex and age in five species of North American hummingbirds. We first measured the length, chord or “width,“ and area of entire hummingbird wing planforms. We then calculated additional parameters of wing shape and size, including aspect and shape ratios, degree of taper or “pointedness,“ wing loading, and wing disc loading (WDL). Wings of adult males are not only shorter but also more narrow and tapered than those of adult or immature females; immature males have larger wings and lower WDL, more like those of females. A proposed relationship between WDL and territorial behavior and dominance is not supported, given that adult and immature males show similar feeding territoriality outside the breeding season but females rarely do. The more extreme and divergent wings of adult males probably reflect sexual selection in connection with aerial displays that include species-specific sound effects given during the breeding season. North American species are unusual among hummingbirds in showing reversed sexual size-dimorphism (males smaller, with relatively shorter wings), a feature shared with some other small hummingbirds, notably the “Pygmornis“ hermits. Attempts to explain hummingbird foraging and territorial behavior on the basis of differences in WDL have failed because many aspects of wing morphology, physiology, and flight behavior were not taken into account. Several wing parameters appear more related to other modes of flight than to strategies of nectar exploitation, and the morphology of any given wing represents a compromise between the often conflicting aerodynamic demands of different flight modes. Understanding hummingbird flight will require broad comparative studies of wing morphology and wingbeat kinematics in relation to flight behavior, and new theoretical models and experimental data will be needed to elucidate physiological and aerodynamic mechanisms underlying forward flight and maneuvering. Morfología Alar y Comportamiento de Vuelo de Unas Especies de Colibríes de Norteamérica

Rapid Fish Species Identification by Agarose Gel Isoelectric Focusing of Sarcoplasmic Proteins

1981 ◽  
Vol 64 (1) ◽  
pp. 38-43
Author(s):  
Ronald C Lundstrom
Keyword(s):  
Species Identification ◽  
Isoelectric Focusing ◽  
Fish Species ◽  
Protein Pattern ◽  
Agarose Gel ◽  
Tissue Fluid ◽  
Protein Patterns ◽  
Fish Species Identification ◽  
Species Specific ◽  
Gel Isoelectric Focusing

Abstract A rapid method is described for fish species identification by agarose gel isoelectric focusing (AGIEF). The AGIEF method can be completed in less than 2 h and gives reproducible species-specific sarcoplasmic protein patterns. Protein patterns are similar using either centrifuged tissue fluid or muscle tissue as the sample. One species, monkfish (Lophius americanus), has a polymorphic protein pattern. A predominant pattern was found in 66.7% of the individuals; 2 variant patterns were equally distributed among the remaining 33.3%. AGIEF offers a more rapid, less expensive alternative to the current AOAC official first action method for fish species identification based on polyacrylamide gel isoelectric focusing.

scholarly journals Characterization of Low-Pathogenicity H5N1 Avian Influenza Viruses from North America

2007 ◽  
Vol 81 (21) ◽  
pp. 11612-11619 ◽  
Author(s):  
Erica Spackman ◽  
David E. Swayne ◽  
David L. Suarez ◽  
Dennis A. Senne ◽  
Janice C. Pedersen ◽  
...  
Keyword(s):  
North America ◽  
Avian Influenza ◽  
North American ◽  
Wild Bird ◽  
Geographic Origin ◽  
Influenza Viruses ◽  
Highly Pathogenic ◽  
Infectious Dose ◽  
Antigenic Relatedness

ABSTRACT Wild-bird surveillance in North America for avian influenza (AI) viruses with a goal of early identification of the Asian H5N1 highly pathogenic AI virus has identified at least six low-pathogenicity H5N1 AI viruses between 2004 and 2006. The hemagglutinin (HA) and neuraminidase (NA) genes from all 6 H5N1 viruses and an additional 38 North American wild-bird-origin H5 subtype and 28 N1 subtype viruses were sequenced and compared with sequences available in GenBank by phylogenetic analysis. Both HA and NA were phylogenetically distinct from those for viruses from outside of North America and from those for viruses recovered from mammals. Four of the H5N1 AI viruses were characterized as low pathogenicity by standard in vivo pathotyping tests. One of the H5N1 viruses, A/MuteSwan/MI/451072-2/06, was shown to replicate to low titers in chickens, turkeys, and ducks. However, transmission of A/MuteSwan/MI/451072-2/06 was more efficient among ducks than among chickens or turkeys based on virus shed. The 50% chicken infectious dose for A/MuteSwan/MI/451072-2/06 and three other wild-waterfowl-origin H5 viruses were also determined and were between 105.3 and 107.5 50% egg infective doses. Finally, seven H5 viruses representing different phylogenetic clades were evaluated for their antigenic relatedness by hemagglutination inhibition assay, showing that the antigenic relatedness was largely associated with geographic origin. Overall, the data support the conclusion that North American H5 wild-bird-origin AI viruses are low-pathogenicity wild-bird-adapted viruses and are antigenically and genetically distinct from the highly pathogenic Asian H5N1 virus lineage.

scholarly journals Genetic Control of Mosquitoes: population suppression strategies

2012 ◽  
Vol 54 (5) ◽  
pp. 287-292 ◽  
Author(s):  
André Barretto Bruno Wilke ◽  
Mauro Toledo Marrelli
Keyword(s):  
Genetic Control ◽  
Mosquito Control ◽  
Public Health Problem ◽  
Mass Rearing ◽  
Control Measures ◽  
Reproductive Capacity ◽  
Lethal Gene ◽  
Control Methods ◽  
Species Specific ◽  
Population Suppression

Over the last two decades, morbidity and mortality from malaria and dengue fever among other pathogens are an increasing Public Health problem. The increase in the geographic distribution of vectors is accompanied by the emergence of viruses and diseases in new areas. There are insufficient specific therapeutic drugs available and there are no reliable vaccines for malaria or dengue, although some progress has been achieved, there is still a long way between its development and actual field use. Most mosquito control measures have failed to achieve their goals, mostly because of the mosquito's great reproductive capacity and genomic flexibility. Chemical control is increasingly restricted due to potential human toxicity, mortality in no target organisms, insecticide resistance, and other environmental impacts. Other strategies for mosquito control are desperately needed. The Sterile Insect Technique (SIT) is a species-specific and environmentally benign method for insect population suppression, it is based on mass rearing, radiation mediated sterilization, and release of a large number of male insects. Releasing of Insects carrying a dominant lethal gene (RIDL) offers a solution to many of the drawbacks of traditional SIT that have limited its application in mosquitoes while maintaining its environmentally friendly and species-specific utility. The self-limiting nature of sterile mosquitoes tends to make the issues related to field use of these somewhat less challenging than for self-spreading systems characteristic of population replacement strategies. They also are closer to field use, so might be appropriate to consider first. The prospect of genetic control methods against mosquito vectored human diseases is rapidly becoming a reality, many decisions will need to be made on a national, regional and international level regarding the biosafety, social, cultural and ethical aspects of the use and deployment of these vector control methods.

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