scholarly journals DNA Barcoding Mushroom Spawn Using EF-1α Barcodes: A Case Study in Oyster Mushrooms (Pleurotus)

2021 ◽  
Vol 12 ◽  
Author(s):  
Peng Zhao ◽  
Sen-Peng Ji ◽  
Xian-Hao Cheng ◽  
Tolgor Bau ◽  
Hong-Xin Dong ◽  
...  
Keyword(s):  
Species Identification ◽  
Dna Barcode ◽  
Elongation Factor ◽  
Pcr Amplification ◽  
Interspecific Variation ◽  
28S Rdna ◽  
Oyster Mushroom ◽  
Success Rates ◽  
Mushroom Species ◽  
Oyster Mushrooms

Oyster mushrooms (genus Pleurotus) are widespread and comprise the most commonly cultivated edible mushrooms in the world. Species identification of oyster mushroom spawn based on cultural, morphological, and cultivated characteristics is time consuming and can be extraordinarily difficult, which has impeded mushroom breeding and caused economic loss for mushroom growers. To explore a precise and concise approach for species identification, the nuclear ribosomal internal transcribed spacer (ITS), 28S rDNA, and the widely used protein-coding marker translation elongation factor 1α (EF-1α) gene were evaluated as candidate DNA barcode markers to investigate their feasibility in identifying 13 oyster mushroom species. A total of 160 sequences of the candidate loci were analyzed. Intra- and interspecific divergences and the ease of nucleotide sequence acquisition were the criteria used to evaluate the candidate genes. EF-1α showed the best intra- and interspecific variation among the candidate markers and discriminated 84.6% of the species tested, only being unable to distinguish two closely related species Pleurotus citrinopileatus and Pleurotus cornucopiae. Furthermore, EF-1α was more likely to be acquired than ITS or 28S rDNA, with an 84% success rate of PCR amplification and sequencing. For ITS and 28S rDNA, the intraspecific differences of several species were distinctly larger than the interspecific differences, and the species identification efficiency of the two candidate markers was worse (61.5 and 46.2%, respectively). In addition, these markers had some sequencing problems, with 55 and 76% success rates of sequencing, respectively. Hence, we propose EF-1α as a possible DNA barcode marker for oyster mushroom spawn.

scholarly journals DNA Barcoding Analysis and Phylogenetic Relation of Mangroves in Guangdong Province, China

Forests ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 56 ◽  
Author(s):  
Feng Wu ◽  
Mei Li ◽  
Baowen Liao ◽  
Xin Shi ◽  
Yong Xu
Keyword(s):  
Dna Barcoding ◽  
Species Identification ◽  
Dna Barcode ◽  
Phylogenetic Reconstruction ◽  
Pcr Amplification ◽  
Guangdong Province ◽  
Nuclear Ribosomal Dna ◽  
Success Rates ◽  
Mangrove Species ◽  
Identification Rate

Mangroves are distributed in the transition zone between sea and land, mostly in tropical and subtropical areas. They provide important ecosystem services and are therefore economically valuable. DNA barcoding is a useful tool for species identification and phylogenetic reconstruction. To evaluate the effectiveness of DNA barcoding in identifying mangrove species, we sampled 135 individuals representing 23 species, 22 genera, and 17 families from Zhanjiang, Shenzhen, Huizhou, and Shantou in the Guangdong province, China. We tested the universality of four DNA barcodes, namely rbcL, matK, trnH-psbA, and the internal transcribed spacer of nuclear ribosomal DNA (ITS), and examined their efficacy for species identification and the phylogenetic reconstruction of mangroves. The success rates for PCR amplification of rbcL, matK, trnH-psbA, and ITS were 100%, 80.29% ± 8.48%, 99.38% ± 1.25%, and 97.18% ± 3.25%, respectively, and the rates of DNA sequencing were 100%, 75.04% ± 6.26%, 94.57% ± 5.06%, and 83.35% ± 4.05%, respectively. These results suggest that both rbcL and trnH–psbA are universal in mangrove species from the Guangdong province. The highest success rate for species identification was 84.48% ± 12.09% with trnH-psbA, followed by rbcL (82.16% ± 9.68%), ITS (66.48% ± 5.97%), and matK (65.09% ± 6.00%), which increased to 91.25% ± 9.78% with the addition of rbcL. Additionally, the identification rate of mangroves was not significantly different between rbcL + trnH-psbA and other random fragment combinations. In conclusion, rbcL and trnH-psbA were the most suitable DNA barcode fragments for species identification in mangrove plants. When the phylogenetic relationships were constructed with random fragment combinations, the optimal evolutionary tree with high supporting values (86.33% ± 4.16%) was established using the combination of matK + rbcL + trnH-psbA + ITS in mangroves. In total, the 476 newly acquired sequences in this study lay the foundation for a DNA barcode database of mangroves.

scholarly journals Molecular identification of species of Physalis (Solanaceae) using a candidate DNA barcode: the chloroplast psbA–trnH intergenic region

Genome ◽  
2018 ◽  
Vol 61 (1) ◽  
pp. 15-20 ◽  
Author(s):  
Shangguo Feng ◽  
Kaili Jiao ◽  
Yujia Zhu ◽  
Hongfen Wang ◽  
Mengying Jiang ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Morphological Traits ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Genetic Distances ◽  
Success Rates ◽  
Medicinal Species ◽  
Distance Methods ◽  
Identification Of Species ◽  
Related Plant

Physalis L., an important genus of the family Solanaceae, includes many commercially important edible and medicinal species. Traditionally, species identification is based on morphological traits; however, the highly similar morphological traits among species of Physalis make this approach difficult. In this study, we evaluated the feasibility of using a popular DNA barcode, the chloroplast psbA–trnH intergenic region, in the identification of species of Physalis. Thirty-six psbA–trnH regions of species of Physalis and of the closely related plant Nicandra physalodes were analyzed. The success rates of PCR amplification and sequencing of the psbA–trnH region were 100%. MEGA V6.0 was utilized to align the psbA–trnH sequences and to compute genetic distances. The results show an apparent barcoding gap between intra- and interspecific variations. Results of both BLAST1 and nearest-distance methods prove that the psbA–trnH regions can be used to identify all species examined in the present study. In addition, phylogenetic analysis using psbA–trnH data revealed a distinct boundary between species. It also confirmed the relationship between species of Physalis and closely related species, as established by previous studies. In conclusion, the psbA–trnH intergenic region can be used as an efficient DNA barcode for the identification of species of Physalis.

scholarly journals Comparative Analysis of Temperature on Yield of Different Varieties of Oyster Mushroom Production

2021 ◽  
Vol 10 (10) ◽  
pp. 296-301
Author(s):  
K. Chitra K. Dhanalakshmi ◽  
S. Dharani S. Gowshika ◽  
Jagadeesh Kumar C. Lavanya ◽  
V. Ambethgar
Keyword(s):  
Comparative Analysis ◽  
Climatic Conditions ◽  
Edible Mushrooms ◽  
Oyster Mushroom ◽  
Mushroom Cultivation ◽  
Mushroom Species ◽  
Mushroom Production ◽  
Pleurotus Florida ◽  
Pleurotus Eous ◽  
Oyster Mushrooms

Oyster mushrooms are economical and most easily grown of all cultivated edible mushrooms. The crop has a range of varieties, differing in form, colour, texture and odor, which can be cultivated throughout the year under a diverse agro-climatic conditions. Three different oyster mushroom species viz., Hypsizygus ulmarius (var. CO2), Pleurotus eous (var. APK1) and Pleurotus florida (var. PF) along with three cropping rooms of varied temperatures was used for the study. Among the different cropping rooms, thatched shed with a temperature of 23o C recorded a highest yield of 748g, 712 and 673 g per 500 g of substrate by PF, CO 2 and APK 1 respectively than AC room and Concrete room. The temperature of the cropping room is inversely proportional to the yield of oyster mushroom. Hence, the thatched shed was best suited for oyster mushroom cultivation, which was both economic and easy to use.

Testing three proposed DNA barcodes for the wood identification of Dalbergia odorifera T. Chen and Dalbergia tonkinensis Prain

Holzforschung ◽  
2016 ◽  
Vol 70 (2) ◽  
pp. 127-136 ◽  
Author(s):  
Min Yu ◽  
Kai Liu ◽  
Liang Zhou ◽  
Lei Zhao ◽  
Shengquan Liu
Keyword(s):  
Economic Value ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
First Grade ◽  
Wood Identification ◽  
Dna Barcodes ◽  
Success Rates ◽  
Interspecific Differences ◽  
Dalbergia Odorifera ◽  
Dalbergia Tonkinensis

Abstract Dalbergia odorifera T. Chen is a first-grade state protected plant in China. However, it is difficult to distinguish it from the closely related species Dalbergia tonkinensis Prain, which is less important in economic value, by wood anatomical features. In this study, three potential DNA barcode sequences, namely rpoC1, trnH-psbA and internal transcribed spacer (ITS), were used to differentiate wood of D. odorifera from D. tonkinensis. The average quantities of DNA extracts from twigs, sapwood and heartwood were 16.3, 11.5 and 6.0 ng mg-1, respectively. The success rates for polymerase chain reaction (PCR) amplification for three loci, namely ITS, trnH-psbA and rpoC1, were 62.5, 100 and 81.25%, respectively. The success rate for bidirectional sequencing of amplified products was 100% for all the three loci. The identification power of the three proposed DNA barcodes has been calculated by the BLAST, tree-based method and the TAXONDNA method. The interspecific differences of the trnH-psbA region were greater than intraspecific variations. Moreover, the identification power of trnH-psbA was higher than that of ITS and rpoC1 regions at the species level. Finally, the trnH-psbA region is proposed as a DNA barcode for wood identification between D. odorifera and D. tonkinensis.

Extraction and amplification of DNA from aged and archaeological Populus euphratica wood for species identification

Holzforschung ◽  
2015 ◽  
Vol 69 (8) ◽  
pp. 925-931 ◽  
Author(s):  
Lichao Jiao ◽  
Xiaoli Liu ◽  
Xiaomei Jiang ◽  
Yafang Yin
Keyword(s):  
Species Identification ◽  
Arid Regions ◽  
Wood Specimen ◽  
Dna Barcode ◽  
Populus Euphratica ◽  
Pcr Amplification ◽  
The Other ◽  
Western China ◽  
Archaeological Wood ◽  
Plant Remains

Abstract The wood samples of Populus euphratica Oliv. (Salicaceae) are common archaeological plant remains in the hot and arid regions of western China. However, it is difficult to identify P. euphratica wood based on traditional wood anatomical methods alone. DNA barcoding might provide a higher security for species identification. In this study, aged wood specimens stored for approximately 30, 60, and 80 years and archaeological wood up to 3600 years old were in focus to explore the potential of DNA extraction and PCR amplification for different-sized fragments, ranging between 100 and 800 bp, taken from wood stored for different periods. The results indicated that DNA fragments of more than 100 bp could be successfully retrieved from a wood specimen stored for about 80 years based on a modified Qiagen kit protocol. However, it was impossible to obtain DNA segments from the 3600-year-old wood according to the current extraction protocol. Moreover, it was deduced that two-stage PCR amplification could play a significant role in the analysis of DNA retrieved from aged wood materials. With the aid of phylogenetic analysis, based on the short DNA barcode rbcL-2 of 202 bp in length, it was possible to differentiate P. euphratica from the other species of the Populus genus.

scholarly journals Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7307
Author(s):  
Siyu Wang ◽  
Hongbo Guo ◽  
JiaJia Li ◽  
Wei Li ◽  
Qin Wang ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Intergenic Spacer ◽  
Its Region ◽  
Small Subunit ◽  
Dna Barcodes ◽  
Success Rates ◽  
Small Subunit Rdna

Background Distinguishing among species in the genus Lepista is difficult because of their similar morphologies. Methods To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations. Results The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.

scholarly journals Improved direct lysis PCR amplification method of microalgal culture for sequencing and species identification

2021 ◽  
Vol 948 (1) ◽  
pp. 012013
Author(s):  
F Fitriyah ◽  
Y Faramitha ◽  
D A Sari ◽  
I Kresnawaty ◽  
T Panji ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Species Identification ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Extraction Methods ◽  
Rbcl Gene ◽  
Direct Pcr ◽  
Nannochloropsis Gaditana ◽  
Amplification Method ◽  
Microalgal Culture

Abstract Molecular approach plays important role in species identification for microalgae which involves sequencing of specific DNA barcode present in the genome. This approach involved preparation of template DNA for polymerase chain reaction (PCR) which is time consuming and requires large amounts of algal cells. Microalgal direct PCR have been used frequently for species identification, which simplified the DNA isolation procedure. However, the recent attempts to amplify the rbcL gene of microalga using the previously reported protocol led to poor repeatability. In this study, Nannochloropsis gaditana NIES-2587 was cultured in f/2 liquid medium. The culture growth was estimated on optical density value and the lysis process was improved using gradual temperature procedure during the PCR process. The same culture was extracted using manual DNA extraction method for comparison. The DNA obtained from both methods were amplified using RbclN primer pair to amplify 1486 bp partial sequence of Nannochloropsis rbcL gene, followed by the sequencing of the PCR product. Molecular identification based on the sequence result and BLAST analysis indicated that direct PCR and manual DNA extraction methods successfully produced high sequences result and confirmed the identity of microalgae species into N. gaditana strain CCMP527 with a genetic similarity of >99%.

scholarly journals Determination of Antioxidant Parameters of Pleurotus Mushrooms Growing on Different Wood Substrates

2017 ◽  
Vol 61 (4) ◽  
pp. 53-58
Author(s):  
I. Strapáč ◽  
M. Kuruc ◽  
M. Baranová
Keyword(s):  
Oyster Mushroom ◽  
Total Flavonoids ◽  
Total Phenols ◽  
Fruiting Bodies ◽  
Pleurotus Pulmonarius ◽  
Antioxidant Parameters ◽  
Oyster Mushrooms ◽  
Maximum Content ◽  
Β Carotene

AbstractExtracts of the fruiting bodies of the Oyster mushroom (Pleurotus ostreatus) grown on wood substrates (beech, oak, linden, walnut, poplar) and extracts of the fruiting bodies of the Oyster mushroom (Pleurotus pulmonarius) grown in nature on aspen wood were used to determine the total phenols, total flavonoids, lycopene and β-carotene. The content of individual antioxidants varies considerably depending, not only on the substrate, but also on the extracting agents. The highest content of total phenols and total flavonoids was found in methanol and water extracts of the fruiting bodies of the Oyster mushrooms grown on oak and linden substrates. The maximum content of lycopene and β-carotene was determined in acetone and n-hexane (ratio 4 : 6) extracts of the fruiting bodies of the Oyster mushroom grown on an oak block. The results obtained in this study demonstrated that the quantitative and also probably the qualitative composition of the antioxidants in the fruiting bodies of Oyster mushrooms depended considerably on the substrate composition.

scholarly journals Identification of medicinal plant Schisandra chinensis using a potential DNA barcode ITS2

2013 ◽  
Vol 82 (4) ◽  
pp. 283-288 ◽  
Author(s):  
Xian-kuan Li ◽  
Bing Wang ◽  
Rong-chun Han ◽  
Yan-chao Zheng ◽  
Hai-bo Yin Yin ◽  
...  
Keyword(s):  
Dna Barcode ◽  
Population Level ◽  
Species Level ◽  
Its2 Region ◽  
Schisandra Chinensis ◽  
Success Rates ◽  
Wild Populations ◽  
Efficient Tool ◽  
Different Populations ◽  
Cultivated Populations

To test whether the internal transcribed spacer 2 (ITS2) region is an effective marker for using in authenticating of the <em>Schisandra chinensis</em> at the species and population levels, separately. And the results showed that the wild populations had higher percentage of individuals that had substitution of C→A at site 86-bp than the cultivated populations. At sites 10-bp, 37-bp, 42-bp and 235-bp, these bases of the <em>Schisandra sphenanthera</em> samples differed from that of <em>S. chinensis</em>. Two species showed higher levels of inter-specific divergence than intra-specific divergence within ITS2 sequences. However, 24 populations did not demonstrate much difference as inter-specific and intra-specific divergences were concerned. Both <em>S. chinensis</em> and <em>S. sphenanthera</em> showed monophyly at species level, yet the samples of different populations shown polyphyly at population level. ITS2 performed well when using BLAST1 method. ITS2 obtained 100% identification success rates at the species level for <em>S. chinensis</em>, with no ambiguous identification at the genus level for ITS2 alone. The ITS2 region could be used to identify <em>S. chinensis</em> and <em>S. sphenanthera</em> in the “Chinese Pharmacopoeia”. And it could also correctly distinguish 100% of species and 100% of genera from the 193 sequences of <em>S. chinensis</em>. Hence, the ITS2 is a powerful and efficient tool for species identification of <em>S. chinensis</em>.

Generic classification of some more hyphomycetes with solitary conidia borne on phialides

1998 ◽  
Vol 76 (9) ◽  
pp. 1570-1583 ◽  
Author(s):  
W Gams ◽  
K O'Donnell ◽  
H -J Schroers ◽  
M Christensen
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
28S Rdna ◽  
New Combination ◽  
Rdna Sequences ◽  
28S Rdna Sequences ◽  
Three New Species ◽  
Morphological Species

Unlike most phialide-producing fungi that liberate a multiplicity of conidia from each conidiogenous cell, only single conidia are formed on phialide-like conidiogenous cells in Aphanocladium, Verticimonosporium, and some species of Sibirina. A group of isolates obtained from soil of native Artemisia tridentata (sagebrush) grassland in Wyoming and from desert soil in Iraq is compared with these genera and classified as a fourth genus, Stanjemonium, honouring Stanley J. Hughes. Phylogenetic analyses of partial nuclear small- (18S) and large-subunit (28S) rDNA sequences indicate that Stanjemonium spp. form a monophyletic group with Emericellopsis. Sequences from the nuclear 18S and 28S rDNA were too conserved to resolve morphological species of Stanjemonium; however, phylogenetic analysis of b-tubulin and translation elongation factor 1a gene exons and introns resolved all species distinguished morphologically. Numerous conidiogenous cells or denticles are scattered along the cells of aerial hyphae in Aphanocladium and Stanjemonium spp., very rapidly collapsing into denticles in the former, somewhat more persistent and leaving broad scars in the latter. In Cladobotryum-Sibirina and Verticimonosporium spp., conidiogenous cells are discrete in terminal and intercalary whorls; phialides of the latter taxon are particularly swollen. The taxonomy of Aphanocladium is not yet resolved. Two species are recognized in Verticimonosporium. Three new species of Stanjemonium are described, and one new combination from Aphanocladium is proposed, along with one new species of Cladobotryum.Key words: Aphanocladium, Cladobotryum, conidiogenesis, hyphomycetes, molecular phylogeny, phialide, Stanjemonium, systematics, Verticimonosporium.

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