scholarly journals Sequence analysis of the internal transcribed spacer 2 (ITS2) region of rDNA for identifying Trichogramma species and evaluating genetic diversity

2020 ◽  
Author(s):  
J. B. V. Viana ◽  
R. B. Querino ◽  
L. C. B. Carvalho ◽  
P. S. C. Lima
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Its2 Region ◽  
Its2 Rdna ◽  
Multiple Sequence ◽  
Trichogramma Species ◽  
Rdna Sequences ◽  
Group I

Abstract Species of Trichogramma Westwood, 1833 (Hymenoptera: Trichogrammtidae) are frequently used as biological control agents against Lepidoptera, but practical application of these egg endoparasitoids are complicated because of their complex taxonomy. This study aimed to compare sequences of internal transcribed spacer regions of ribosomal DNA (ITS2-rDNA) of Trichogramma accessions with those deposited in GenBank in order to access the reliability of the ITS2 as a barcode for discriminating species and evaluating the genetic diversity. ITS2-rDNA sequences obtained from seventeen specimens of Trichogramma confirmed previous identifications based on morphological characteristics. Multiple sequence alignment revealed the existence of highly conserved regions in ITS2 sequences while the neighbour-joining dendrogram indicated that the specimens formed three clusters comprising T. manicobai and T. marandobai (group I), T. galloi (group II) and T. pretiosum (group III). The ITS2 marker was shown to be a powerful DNA barcode for discriminating Trichogramma species and could be used to complement the morphological approach.

scholarly journals Phylogenetic analysis of 23 accessions of Indonesian banana cultivars based on Internal Transcribed Spacer 2 (ITS2) region

2020 ◽  
Vol 25 (1) ◽  
pp. 1
Author(s):  
Karlia Meitha ◽  
Intan Fatmawati ◽  
Fenny Martha Dwivany ◽  
Agus Sutanto ◽  
Sigit Nur Pratama ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Internal Transcribed Spacer ◽  
Molecular Breeding ◽  
Future Research ◽  
Its2 Region ◽  
Phylogenetic Tree Analysis ◽  
Multiple Sequence ◽  
B Genome ◽  
A Genome

Pisang Kepok (Musa spp. [ABB ’Saba’ subgroup]) has several unique characteristics, such as tolerance to drought and Fusarium Foc (TR4) disease. Currently, the genetic diversity of Pisang Kepok in Indonesia is not well identified, although it is widely cultivated. Information on genetic diversity is essential for developing breeding strategies to achieve efficient cultivar improvement in the future. Aims of this research were to analyze the genetic variation of Pisang Kepok from some islands in Indonesia and to determine the genetic relationship between Pisang Kepok and other accessions banana cultivars based on ITS2 region, as a basis for future research in improving banana quality through molecular breeding. We have conducted the multiple sequence alignment and built the phylogenetic tree analysis using the Bayesian Inference Phylogeny method of one million generations (ngen = 1,000,000). The ITS2 region showed two clade ingroups: first clade consists of banana with B genome (balbisiana), while the second clade consists of banana with only A genome (acuminata). In general, all accessions of Pisang Kepok cultivars were clustered in the B genome of bananas cultivars. In addition, the ITS2 sequences and secondary structures among Pisang Kepok from various regions are identical, suggesting that there was no genetic variation in the ITS2 region of Pisang Kepok from multiple areas in Indonesia.

scholarly journals Genetic diversity and biogeography in Chaetomorpha melagonium (Ulvophyceae, Cladophorales) based on internal transcribed spacer (ITS rDNA) sequences

2017 ◽  
Vol 60 (3) ◽  
Author(s):  
Christian Boedeker ◽  
Frederik Leliaert ◽  
Giuseppe C. Zuccarello
Keyword(s):  
Genetic Diversity ◽  
North Atlantic ◽  
North Pacific ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
The Arctic ◽  
The North ◽  
Rdna Sequences ◽  
The North Atlantic ◽  
The North Pacific

Abstractis a morphologically distinct species of green algae that occurs throughout the North Atlantic, the North Pacific and the Arctic Ocean. In this study, we analyzed the intraspecific genetic diversity among 14 samples of

New record of Chaetomium grande Asgari & Zare (Chaetomiaceae) for the Egyptian and African mycobiota

Phytotaxa ◽  
2018 ◽  
Vol 343 (3) ◽  
pp. 283 ◽  
Author(s):  
AHMED M. ABDEL-AZEEM ◽  
ROBERT A. BLANCHETTE ◽  
BENJAMIN W. HELD
Keyword(s):  
Internal Transcribed Spacer ◽  
New Record ◽  
First Record ◽  
Full Description ◽  
Its2 Rdna ◽  
Accession Number ◽  
Rdna Sequences ◽  
Development Technology

The first record of Chaetomium grande (Ascomycota, Chaetomiaceae) for the Egyptian and African fungi is reported here. The species was found during an extensive taxonomic and ecological revision of the genus Chaetomium supported by Science and Development Technology Fund in Egypt. Ch. grande identified phenotypically and was subjected to sequencing for confirmation. The internal transcribed spacer (ITS) 1–5.8 s – ITS2 rDNA sequences obtained were compared with those deposited in the GenBank Database and registered with accession number MF787599 in the NCBI Database. We provide an updated full description and illustration of the species.

scholarly journals Efficiency of ITS1-5.8S-ITS2 region in identifying Cordyceps species

2020 ◽  
Vol 16 (4) ◽  
pp. 705-712
Author(s):  
Le Thi Thu Hien ◽  
Ha Hong Hanh
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Nearest Neighbor ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Pcr Amplification ◽  
Cordyceps Sinensis ◽  
Its2 Region ◽  
Dna Barcodes ◽  
Plastid Genomes

Cordyceps genus is a well-known traditional medicine worldwide. It contains abundant physiological active compounds that were demonstrated to perform benefit in reducing progression of cancer as well as protecting human health. Accurately classifying species in this genus is essential in order to prevent commercial counterfeit medicines. Nowadays, a taxonomic classification of species based on DNA sequences can overcome the existed limitation in identifying by using only morphological characteristics of this genus. DNA barcodes are standard short genomic regions that are universally present in target lineages and has sufficient sequence variation to discriminate species in the genus. A variety of loci has been suggested as DNA barcodes for plants, including genes and non-coding regions in the nuclear and plastid genomes such as psbA-trnH, matK, rbcL, and ITS. Thus, the objective of this study was to identify selected species of Cordyceps genus using DNA barcodes. Seven strains of Cordyceps were collected. Total DNA extraction and purification, PCR amplification and DNA sequencing were performed with standard chemicals and kits. The candidate ITS1-5.8S-ITS2 region was amplified and sequenced. Data were analyzed using Bioedit 7.2.6 and MEGA 7 softwares. Analysis of seven obtained DNA barcode sequences of collected samples revealed that the ITS1-5.8S-ITS2 region provided high species discriminating power for Cordyceps genus. Accordingly, phylogenetic trees based on this DNA barcode exhibited six samples had closed relationship to Cordyceps militaris, while another specimen was the nearest neighbor to Cordyceps sinensis with average similarities at 99.82% and 99.81%, respectively. Our results support the identification of valuable medicinal plant species within Cordyceps genus.

Molecular approaches to differentiate three species of Nematodirus in sheep and goats from China based on internal transcribed spacer rDNA sequences

2013 ◽  
Vol 89 (3) ◽  
pp. 259-266 ◽  
Author(s):  
G.H. Zhao ◽  
Y.Q. Jia ◽  
Q.Q. Bian ◽  
A.J. Nisbet ◽  
W.Y. Cheng ◽  
...  
Keyword(s):  
New Zealand ◽  
Internal Transcribed Spacer ◽  
Small Ruminants ◽  
Genetic Variations ◽  
Its2 Rdna ◽  
Accurate Identification ◽  
Specific Pcr ◽  
Molecular Approaches ◽  
Rdna Sequences ◽  
Its1 And Its2

AbstractInternal transcribed spacer (ITS) rDNA sequences of three Nematodirus species from naturally infected goats or sheep in two endemic provinces of China were analysed to establish an effective molecular approach to differentiate Nematodirus species in small ruminants. The respective intra-specific genetic variations in ITS1 and ITS2 rDNA regions were 0.3–1.8% and 0–0.4% in N. spathiger, 0–6.5% and 0–5.4% in N. helvetianus, and 0–4.4% and 0–6.1% in N. oiratianus from China. The respective intra-specific variations of ITS1 and ITS2 were 1.8–4.4% and 1.6–6.1% between N. oiratianus isolates from China and Iran, 5.7–7.1% and 6.3–8.3% between N. helvetianus samples from China and America. For N. spathiger, compared with samples from China, sequence differences in ITS1 rDNA were 0.3–2.4% in isolates from America, 0.3–2.9% in New Zealand and 2.1–2.4% in Australia. Genetic variations in ITS2 rDNA of N. spathiger were 0–0.4% between samples from China and America, and 0–0.8% between samples from China and New Zealand. Using mutation sites, polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) and specific PCR techniques were developed to differentiate these three Nematodirus species. The specific PCR assay allowed the accurate identification of N. oiratianus from other common nematodes with a sensitivity of 0.69 pg and further examination of Nematodirus samples demonstrated the reliability of these two molecular methods.

Cunninghamella binariae, Mucor ardhlaengiktus, Mucor gigasporus and Umbelopsis changbaiensis, newly recorded species from amphibian feces and soil in Korea

Phytotaxa ◽  
2019 ◽  
Vol 425 (1) ◽  
pp. 19-34
Author(s):  
THUONG T.T. NGUYEN ◽  
KEVIN D. HYDE ◽  
HYANG BURM LEE
Keyword(s):  
Sequence Analysis ◽  
Internal Transcribed Spacer ◽  
Morphological Characteristics ◽  
Its Region ◽  
Soil Samples ◽  
28S Rdna ◽  
Rdna Sequences ◽  
28S Rdna Sequences

Four strains, CNUFC SKT18002, CNUFC FKT18033, CNUFC SKT19001, and CNUFC SKT18228 were isolated during an investigation of fungi belonging to the orders Mucorales and Umbelopsidales from amphibian feces and soil samples in Korea. Based on morphological characteristics and the sequence analysis of the internal transcribed spacer (ITS) region and 28S rDNA sequences, the strains CNUFC SKT18002, CNUFC FKT18033, CNUFC SKT19001, and CNUFC SKT18228 were identified as Cunninghamella binariae, Mucor ardhlaengiktus, Mucor gigasporus, and Umbelopsis changbaiensis, respectively. To the best of our knowledge, the species C. binariae, M. ardhlaengiktus, M. gigasporus, and U. changbaiensis have not been previously reported in Korea.

scholarly journals CLASSIFICATION OF SOME COMMERCIAL LINGZHI (Ganoderma spp.) ACCESSIONS IN VIETNAM BY USING ITS DNA BARCODE

2019 ◽  
Vol 128 (1E) ◽  
pp. 163-171
Author(s):  
Hồ Viết Thế ◽  
Võ Thị Ngọc Hà ◽  
Lê Ngọc Giàu
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Genetic Relationship ◽  
Dna Barcode ◽  
Morphological Characteristics ◽  
Market Value ◽  
High Potential ◽  
Genetic Composition ◽  
Breeding Programs

In Vietnam, lingzhi is mainly used for medicinal purposes with high market value leading to the increasing production in recent years. However, the identification and classification of this fungus is inaccurate due mainly to morphological characteristics. In this study, ITS-DNA barcode was used to analyze genetic composition of 10 commercial lingzhi genotypes collected from different regions across the country. The results showed that there is genetic diversity of 10 lingzhi samples. The genetic distance among studies accesson range from 0.000 to 0.047. Seven of ten accessions consisting of TG1, TG2, LD, DN, CC, DLk, and HN were reclassified as G. lingzhi and three accessions were identified as G. lucidum. In addition, 19 nucleotide sites differed among fungal samples were also reported. The results of this study show the high potential of ITS-DNA barcode for identification and classification as well as providing information on the genetic relationship between lingzhi varieties which could be applied as a basis for lingzhi breeding programs.

Genetic diversity of Peucedanum japonicum using Internal Transcribed Spacer (ITS) sequence

Planta Medica ◽  
2008 ◽  
Vol 74 (09) ◽  
Author(s):  
YH Kim ◽  
JA Ryuk ◽  
BS Ko ◽  
JW Lee ◽  
SE Oh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Internal Transcribed Spacer ◽  
Its Sequence

scholarly journals Biosystematic Study on Some Egyptian Species of Astragalus L. (Fabaceae)

Agriculture ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 125
Author(s):  
Monier M. Abd El-Ghani ◽  
Ashraf S. A. El-Sayed ◽  
Ahmed Moubarak ◽  
Rabab Rashad ◽  
Hala Nosier ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Dna Barcode ◽  
Plant Morphology ◽  
Its Region ◽  
Its2 Region ◽  
Whole Plant ◽  
Three Samples ◽  
Two Samples ◽  
Region 10 ◽  
Unique Banding Pattern

Astragalus L. is one of the largest angiosperm complex genera that belongs to the family Fabaceae, subfamily Papilionoideae or Faboideae under the subtribe Astragalinae of the tribe Galegeae. The current study includes the whole plant morphology, DNA barcode (ITS2), and molecular marker (SCoT). Ten taxa representing four species of Astragalus were collected from different localities in Egypt during the period from February 2018 to May 2019. Morphologically, identification and classification of collected Astragalus plants occurred by utilizing the light microscope, regarding the taxonomic revisions of the reference collected Astragalus specimens in other Egyptian Herbaria. For molecular validation, ten SCoT primers were used in this study, producing a unique banding pattern to differentiate between ten samples of Astragalus taxa which generated 212 DNA fragments with an average of 12.2 bands per 10 Astragalus samples, with 8 to 37 fragments per primer. The 212 fragments amplified were distributed as 2 monomorphic bands, 27 polymorphic without unique bands, 183 unique bands (210 Polymorphic with unique bands), and ITS2 gene sequence was showed as the optimal barcode for identifying Astragalus L. using BLAST searched on NCBI database, and afterward, analyzing the chromatogram for ITS region, 10 samples have been identified as two samples representing A. hauarensis, four samples representing A. sieberi, three samples representing A. spinosus and one sample representing A. vogelii. Based on the ITS barcode, A. hauarensis RMG1, A. hauarensis RMG2, A. sieberi RMG1, A. sieberi RMG2, A. sieberi RMG3, A. sieberi RMG4, A. spinosus RMG1, A. spinosus RMG2, A. spinosus RMG3, A. vogelii RMG were deposited into GenBank with accession # MT367587.1, MT367591.1, MT367593.1, MT367585.1, MT367586.1, MT367588.1, MT160347.1, MT367590.1, MT367589.1, MT367592.1, respectively. These results indicated the efficiency of SCoT markers and ITS2 region in identifying and determining genetic relationships between Astragalus species.

scholarly journals A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Mohamed Abd. S. El zayat ◽  
Mahmoud El Sayd Ali ◽  
Mohamed Hamdy Amar
Keyword(s):  
Genetic Diversity ◽  
Morphological Characteristics ◽  
Systematic Position ◽  
Diversity Analysis ◽  
Polymorphic Markers ◽  
Ecological Distribution ◽  
Specific Group ◽  
Systematic Revision ◽  
Dna Evidence ◽  
The Family

Abstract Background The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a “trash-basket” family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. Results Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. Conclusion The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.

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