scholarly journals Endangered Uyghur Medicinal PlantFerulaIdentification through the Second Internal Transcribed Spacer

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Congzhao Fan ◽  
Xiaojin Li ◽  
Jun Zhu ◽  
Jingyuan Song ◽  
Hui Yao
Keyword(s):  
Medicinal Plant ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its2 Sequence ◽  
Sequence Length ◽  
Local Alignment ◽  
Accurate Identification ◽  
Distance Method ◽  
Closely Related Species

The medicinal plantFerulahas been widely used in Asian medicine, especially in Uyghur medicine in Xinjiang, China. Given that various substitutes and closely related species have similar morphological characteristics,Ferulais difficult to distinguish based on morphology alone, thereby causing confusion and threatening the safe use ofFerula. In this study, internal transcribed spacer 2 (ITS2) sequences were analyzed and assessed for the accurate identification of two salableFerulaspecies (Ferula sinkiangensisandFerula fukangensis) and eight substitutes or closely related species. Results showed that the sequence length of ITS2 ranged from 451 bp to 45 bp, whereas guanine and cytosine contents (GC) were from 53.6% to 56.2%. A total of 77 variation sites were detected, including 63 base mutations and 14 insertion/deletion mutations. The ITS2 sequence correctly identified 100% of the samples at the species level using the basic local alignment search tool 1 and nearest-distance method. Furthermore, neighbor-joining tree successfully identified the genuine plantsF. sinkiangensisandF. fukangensisfrom their succedaneum and closely related species. These results indicated that ITS2 sequence could be used as a valuable barcode to distinguish Uyghur medicineFerulafrom counterfeits and closely related species. This study may broaden DNA barcoding application in the Uyghur medicinal plant field.

scholarly journals The new Internal Transcribed Spacer 2 diagnostic tool clarifies the taxonomic position and geographic distribution of the North American malaria vector Anopheles punctipennis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
James M. Hodge ◽  
Andrey A. Yurchenko ◽  
Dmitriy A. Karagodin ◽  
Reem A. Masri ◽  
Ryan C. Smith ◽  
...  
Keyword(s):  
Malaria Vector ◽  
Internal Transcribed Spacer ◽  
Single Species ◽  
Its2 Sequence ◽  
Pathogen Transmission ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Sequence Length ◽  
Phylogenetic Position ◽  
Internal Transcribed Spacer 2

Abstract Background The malaria mosquito Anopheles punctipennis, a widely distributed species in North America, is capable of transmitting human malaria and is actively involved in the transmission of the ungulate malaria parasite Plasmodium odocoilei. However, molecular diagnostic tools based on Internal Transcribed Spacer 2 (ITS2) of ribosomal DNA are lacking for this species. Anopheles punctipennis is a former member of the Anopheles maculipennis complex but its systematic position remains unclear. Methods In this study, ITS2 sequences were obtained from 276 An. punctipennis specimens collected in the eastern and midwestern United States and a simple and robust Restriction Fragment Length Polymorphism approach for species identification was developed. The maximum-likelihood phylogenetic tree was constructed based on ITS2 sequences available through this study and from GenBank for 20 species of Anopheles. Results The analysis demonstrated a consistent ITS2 sequence length and showed no indications of intragenomic variation among the samples based on ITS2, suggesting that An. punctipennis represents a single species in the studied geographic locations. In this study, An. punctipennis was found in urban, rural, and forest settings, suggesting its potential broad role in pathogen transmission. Phylogeny based on ITS2 sequence comparison demonstrated the close relationship of this species with other members of the Maculipennis group. Conclusions This study developed molecular tools based on ITS2 sequences for the malaria vector An. punctipennis and clarified the phylogenetic position of the species within the Maculipennis group.

Trogia benghalensis (Marasmiaceae, Basidiomycota), a new species from India

Phytotaxa ◽  
2017 ◽  
Vol 331 (2) ◽  
pp. 273 ◽  
Author(s):  
ARUN KUMAR DUTTA ◽  
SUDESHNA NANDI ◽  
ENTAJ TARAFDER ◽  
RIMPA SIKDER ◽  
ANIRBAN ROY ◽  
...  
Keyword(s):  
New Species ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
West Bengal ◽  
Internal Transcribed Spacer Region ◽  
Comprehensive Description ◽  
Closely Related Species ◽  
Molecular Sequence ◽  
Region Data ◽  
A New Species

A new species of Trogia (Marasmiaceae, Basidiomycota) is described from West Bengal, India. Analysis of the molecular sequence (nuclear ribosomal internal transcribed spacer region) data suggests that T. benghalesis is phylogenetically distinct from its closely related species. Comprehensive description based on macro- and microscopic characters, photographs and comparisons with morphologically similar and phylogenetically related species are provided.

Two new rock-inhabiting species of Cyphellophora from karst habitats in China

Phytotaxa ◽  
2019 ◽  
Vol 397 (1) ◽  
pp. 23
Author(s):  
WEI SUN ◽  
BINGJIE LIU ◽  
RONG FU ◽  
XINGZHONG LIU ◽  
MEICHUN XIANG
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Internal Transcribed Spacer ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Its Region ◽  
Closely Related Species ◽  
Two New Species ◽  
Rock Inhabiting Fungi ◽  
Karst Habitats

During survey on rock-inhabiting fungi from karst habitats in Guizhou, China, two new species in Cyphellophora were discovered and identified. Phylogenetic analysis based on combined sequences of the nuclear large subunit (nucLSU) and internal transcribed spacer (ITS) region of ribosomal DNA revealed that the tested isolates, clustered into two clades that well affiliated in the genus of Cyphellophora. Morphological characteristics were also supported the estabolishment of the new species. Herewith Cyphellophora botryose sp. nov. and Cyphellophora guizhouensis sp. nov. were described and their differences from closely related species were discussed.

scholarly journals Identification of Internal Transcribed Spacer Sequence Motifs in Truffles: a First Step toward Their DNA Bar Coding

2007 ◽  
Vol 73 (16) ◽  
pp. 5320-5330 ◽  
Author(s):  
Khalid El Karkouri ◽  
Claude Murat ◽  
Elisa Zampieri ◽  
Paola Bonfante
Keyword(s):  
Internal Transcribed Spacer ◽  
Repeat Unit ◽  
Blot Hybridization ◽  
Morphological Characteristics ◽  
Its2 Sequence ◽  
Sequence Motifs ◽  
Dot Blot ◽  
Blind Test ◽  
Bar Code ◽  
Close Relatives

ABSTRACT This work presents DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat unit which are useful for the identification of five European and Asiatic truffles (Tuber magnatum, T. melanosporum, T. indicum, T. aestivum, and T. mesentericum). Truffles are edible mycorrhizal ascomycetes that show similar morphological characteristics but that have distinct organoleptic and economic values. A total of 36 out of 46 ITS1 or ITS2 sequence motifs have allowed an accurate in silico distinction of the five truffles to be made (i.e., by pattern matching and/or BLAST analysis on downloaded GenBank sequences and directly against GenBank databases). The motifs considered the intraspecific genetic variability of each species, including rare haplotypes, and assigned their respective species from either the ascocarps or ectomycorrhizas. The data indicate that short ITS1 or ITS2 motifs (≤50 bp in size) can be considered promising tools for truffle species identification. A dot blot hybridization analysis of T. magnatum and T. melanosporum compared with other close relatives or distant lineages allowed at least one highly specific motif to be identified for each species. These results were confirmed in a blind test which included new field isolates. The current work has provided a reliable new tool for a truffle oligonucleotide bar code and identification in ecological and evolutionary studies.

scholarly journals Phallus haitangensis, a new species of stinkhorn from Yunnan Province, China

Phytotaxa ◽  
2016 ◽  
Vol 280 (2) ◽  
pp. 116 ◽  
Author(s):  
HUILI LI ◽  
XUELAN MA ◽  
PETER E. MORTIMER ◽  
SAMANTHA C. KARUNARATHNA ◽  
JIANCHU XU ◽  
...  
Keyword(s):  
New Species ◽  
Related Species ◽  
Internal Transcribed Spacer ◽  
Yunnan Province ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequence ◽  
Closely Related Species ◽  
Line Drawings ◽  
A New Species

Four specimens of Phallus were collected during surveys in a Pinus armandii forest in Baoshan, Yunnan Province, China. Macro- and micro-characteristics, together with Internal Transcribed Spacer (ITS) sequence data, showed that the four specimens belong to a new species, here named Phallus haitangensis. The ITS phylogenetic analyses, morphological descriptions, color photographs, and line drawings are provided, and compared with closely related species in the genus.

Morphological and molecular evidence for a new species of Russula (Russulaceae) from southern China

Phytotaxa ◽  
2015 ◽  
Vol 202 (2) ◽  
pp. 94 ◽  
Author(s):  
Yang Kun Li ◽  
Xin Zhang ◽  
Ye Yuan ◽  
Zheng Cao ◽  
Jun Feng Liang
Keyword(s):  
New Species ◽  
Related Species ◽  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Southern China ◽  
Its Region ◽  
Molecular Evidence ◽  
Closely Related Species ◽  
A New Species

Russula subrutilans sp. nov., a new species of Russula is described from southern China. It is unique for having buff pink to light congo-pink pileus, distant ventricose to subventricose lamellae with rare lamellulae, globose to broadly ellipsoid spores with bluntly conical warts forming a partial reticulum, and narrowly clavate to clavate cheilocystidia and pleurocysitidia with variable tips. Phylogenetic relationships among the new species and other closely related species in the genus are inferred based on the internal transcribed spacer (ITS) region.

scholarly journals SPERGULARIA IRAQENSIS (CARYOPHYLLACEAE), A NEW SPECIES FROM IRAQ

2021 ◽  
Vol 16 (3) ◽  
pp. 291-299
Author(s):  
Ali Haloob ◽  
Ali H. E. Al-Musawi ◽  
Harb Adeel
Keyword(s):  
New Species ◽  
Related Species ◽  
Morphological Characteristics ◽  
Identification Key ◽  
Similar Species ◽  
Closely Related Species ◽  
A New Species

Spergularia iraqensis sp. nov. is described as a new species from Iraq. This species has been collected from Diyala Province in the central east of Iraq; it is closely related to Spergularia rubra (L.) J. Presl & C. Presl, 1819 and Spergularia bocconei (Scheele) Graebn., 1919. The distinguishing of the morphological characteristics of the new species alongside the two similar species are discussed with photographs, and an identification key is given for Spergularia iraqensis and other closely related species.

scholarly journals The larvae of Chinese Hydropsychidae (Insecta: Trichoptera), Part II: Potamyia chinensis and Cheumatopsyche trifascia

Zootaxa ◽  
2021 ◽  
Vol 4926 (4) ◽  
pp. 547-558
Author(s):  
AO ZHANG ◽  
XIN ZHOU
Keyword(s):  
Dna Markers ◽  
Related Species ◽  
Morphological Characteristics ◽  
Species Boundaries ◽  
Closely Related Species ◽  
Molecular Analyses ◽  
Mitochondrial Coi ◽  
Associated Species

The larvae of Chinese caddisflies Potamyia chinensis and Cheumatopsyche trifascia were successfully associated with identifiable adults using independent DNA markers, mitochondrial COI barcodes and nuclear ribosomal 28S D2 genes. A total of 49 specimens collected in China were employed in the molecular analyses. The two markers were congruent on species boundaries for 11 distinctive haplogroups, while D2 failed in differentiating two closely related species. A brief summary for larval studies of both genera is given, followed by an introduction to the generic morphological characteristics, and detailed morphological descriptions and illustrations for the two successfully associated species. The larva of P. chinensis is re-described here based on Chinese materials, following the previous larval description for P. echigoensis, which was recently synonymized with P. chinensis.

scholarly journals Clinical and mycological characteristics of keratitis caused by Colletotrichum gloeosporioides: A case report and review of literature

2021 ◽  
Vol 15 (02) ◽  
pp. 301-305
Author(s):  
Alireza Izadi ◽  
Mohammad Soleimani ◽  
Roshanak Daie Ghazvini ◽  
Seyed Jamal Hashemi ◽  
Mohssen Gramishoar ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Plant Pathogens ◽  
Colletotrichum Gloeosporioides ◽  
Morphological Characteristics ◽  
Fungal Keratitis ◽  
Slit Lamp ◽  
Review Of Literature ◽  
Internal Transcribed Spacer Region ◽  
Accurate Identification ◽  
Case Presentation

Introduction: Colletotrichum species are well-known plant pathogens, which have been increasingly reported as the cause of keratitis or subcutaneous lesions in humans. In this study we reported a rare case of fungal keratitis from Iran and reviewed the literature. Case Presentation: A 69-year-old man whose right eye was injured by herbal material was examined by slit-lamp biomicroscopy and mycology investigation of corneal scrapings was done. The grown filamentous fungal was identified as Colletotrichum gloeosporioides based on morphological characteristics and DNA sequence of the internal transcribed spacer region. The isolated strain was sensitive to amphotericin B, caspofungin, anidolafungin, micafungin, voriconazole, and relatively resistant to fluconazole, and itraconazole. Patient was successfully treated with voriconazole. Conclusions: This report highlights that the early and accurate identification and therapy can helpful to management keratitis caused by C. gloeosporioides.

scholarly journals Differentiation of Taxonomically Closely Related Species of the Genus Acinetobacter Using Raman Spectroscopy and Chemometrics

Molecules ◽  
2019 ◽  
Vol 24 (1) ◽  
pp. 168 ◽  
Author(s):  
A. Margarida Teixeira ◽  
Alexandr Nemec ◽  
Clara Sousa
Keyword(s):  
Raman Spectroscopy ◽  
Related Species ◽  
Low Cost ◽  
Acinetobacter Calcoaceticus ◽  
Species Discrimination ◽  
Accurate Identification ◽  
Closely Related Species ◽  
Acinetobacter Species ◽  
Promising Alternative ◽  
Mortality And Morbidity

In recent years, several efforts have been made to develop quick and low cost bacterial identification methods. Genotypic methods, despite their accuracy, are laborious and time consuming, leaving spectroscopic methods as a potential alternative. Mass and infrared spectroscopy are among the most reconnoitered techniques for this purpose, with Raman having been practically unexplored. Some species of the bacterial genus Acinetobacter are recognized as etiological agents of nosocomial infections associated with high rates of mortality and morbidity, which makes their accurate identification important. The goal of this study was to assess the ability of Raman spectroscopy to discriminate between 16 Acinetobacter species belonging to two phylogroups containing taxonomically closely related species, that is, the Acinetobacter baumannii-Acinetobacter calcoaceticus complex (six species) and haemolytic clade (10 species). Bacterial spectra were acquired without the need for any sample pre-treatment and were further analyzed with multivariate data analysis, namely partial least squares discriminant analysis (PLSDA). Species discrimination was achieved through a series of sequential PLSDA models, with the percentage of correct species assignments ranging from 72.1% to 98.7%. The obtained results suggest that Raman spectroscopy is a promising alternative for identification of Acinetobacter species.

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