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Journal articles on the topic 'ITS2 sequence'

Author: Grafiati

Published: 5 June 2025

Last updated: 2 August 2025

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1

Hsueh, John Y. C., Rudolf P. Bohm, Peter J. Didier, et al. "Internal Transcribed Spacer Regions of rRNA Genes of Pneumocystis carinii from Monkeys." Clinical Diagnostic Laboratory Immunology 8, no. 3 (2001): 503–8. http://dx.doi.org/10.1128/cdli.8.3.503-508.2001.

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ABSTRACT Analysis of sequence variations among isolates ofPneumocystis carinii f. sp. macacae from 14 Indian rhesus monkeys (Macaca mulatta) at the internal transcribed spacer (ITS) regions of the nuclear rRNA gene was undertaken. Like those from P. carinii f. sp.hominis, the ITS sequences from various P. carinii f. sp. macacae isolates were not identical. Two major types of sequences were found. One type of sequence was shared by 13 isolates. These 13 sequences were homologous but not identical. Variations were found at 13 of the 180 positions in the ITS1 region and 28 of the 221 positions in

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2

Gong, Li, Wei Shi, Min Yang, and Xiaoyu Kong. "Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae)." Animal Biology 68, no. 4 (2018): 353–65. http://dx.doi.org/10.1163/15707563-17000134.

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Abstract The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence

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3

Qiu, J. H., Y. Lou, Y. Zhang, et al. "Sequence variability in internal transcribed spacers of nuclear ribosomal DNA among isolates of the oxyurid nematodes Syphacia obvelata and Aspiculuris tetraptera from mice reared in laboratories in China." Journal of Helminthology 90, no. 1 (2015): 81–85. http://dx.doi.org/10.1017/s0022149x1400087x.

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AbstractThis study examined sequence variability in internal transcribed spacers (ITS) of nuclear ribosomal DNA among Syphacia obvelata and Aspiculuris tetraptera isolates from laboratory mice from different geographical locations in China. ITS1, 5.8S and ITS2 rDNA were amplified separately from adult S. obvelata and A. tetraptera individuals by polymerase chain reaction (PCR), and the amplicons were subjected to sequencing from both directions. The lengths of the sequences of ITS1, 5.8S and ITS2 rDNA from both nematodes were 314 bp and 456 bp, 157 bp, and 273 bp and 419 bp, respectively. The

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4

Lee, Taebum, Hee Young Na, Sun-ju Byeon, et al. "Mycobiome analysis in fungal infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: a pilot study." F1000Research 9 (July 22, 2020): 758. http://dx.doi.org/10.12688/f1000research.25126.1.

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Background: Fungal organisms are frequently observed in surgical pathological diagnosis. In order to more accurately identify fungi in formalin-fixed and paraffin-embedded (FFPE) tissues, it is necessary to use genomic information. The purpose of our pilot study is to identify the factors to be considered for the identification of pathogenic fungi using mycobiome analysis in FFPE tissues. Methods: We selected 49 cases in five hospitals. In each case, FFPE tissue was cut into 50 µm and DNA was extracted. Multiplex PCR with four primers (ITS1, ITS2, ITS3 and ITS4) was performed. Multiplex sequen

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5

Fenille, Roseli C., Maísa B. Ciampi, Eiko E. Kuramae, and Nilton L. Souza. "Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences." Fitopatologia Brasileira 28, no. 4 (2003): 413–19. http://dx.doi.org/10.1590/s0100-41582003000400011.

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The aim of this study was to identify isolates of Rhizoctonia solani causing hypocotyl rot and foliar blight in soybean (Glycine max) in Brazil by the nucleotide sequences of ITS-5.8S regions of rDNA. The 5.8S rDNA gene sequence (155 bp) was highly conserved among all isolates but differences in length and nucleotide sequence of the ITS1 and ITS2 regions were observed between soybean isolates and AG testers. The similarity of the nucleotide sequence among AG-1 IA isolates, causing foliar blight, was 95.1-100% and 98.5-100% in the ITS1 and ITS2 regions, respectively. The nucleotide sequence sim

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Nazlić, Marija, Dario Kremer, Željana Fredotović, Željka Trumbić, Valerija Dunkić, and Jasna Puizina. "Free Volatile Compounds as Chemophenetic Markers—Comparison with ITS2 and ITS1-5.8S-ITS2 Sequence Data for 18 Species of the Genus Veronica." Horticulturae 9, no. 5 (2023): 524. http://dx.doi.org/10.3390/horticulturae9050524.

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(1) Background: The purpose of this study was to compare the free volatile compounds of 18 Veronica species (Plantaginaceae), as previously analyzed by gas chromatography coupled with mass spectrometry, with their DNA sequences for internal transcribed spacers ITS2 and ITS1-5.8S-ITS2 of the nuclear ribosomal DNA. (2) Methods: Two sets of DNA sequence data were generated and used for phylogenetic analysis: ITS2 sequences (~360 bp) obtained by next-generation sequencing and ITS1-5.8S-ITS2 sequences (~580 bp) sequenced by the Sanger sequencing method. Clustering from previously analyzed free vola

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Insua, Ana, María J. López-Piñón, Ruth Freire, and Josefina Méndez. "Sequence analysis of the ribosomal DNA internal transcribed spacer region in some scallop species (Mollusca: Bivalvia: Pectinidae)." Genome 46, no. 4 (2003): 595–604. http://dx.doi.org/10.1139/g03-045.

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The internal transcribed spacer (ITS) region of the ribosomal DNA from the European scallops Aequipecten opercularis, Mimachlamys varia, Hinnites distortus, and Pecten maximus was PCR amplified and sequenced. For each species, three or five clones were examined. The size ranged between 636 and 713 bp (ITS1, 209276 bp; 5.8S rRNA gene, 157 bp; ITS2, 270294 bp) and GC content ranged between 47 and 50% (ITS1, 4349%; 5.8S rRNA gene, 5657%; ITS2, 4449%). Variation within repeats was minimal; only clones from M. varia and P. maximus displayed a few variable sites in ITS2. Among scallops, includi

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8

Lee, Chao-Hung, Jannik Helweg-Larsen, Xing Tang, et al. "Update on Pneumocystis carinii f. sp.hominis Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes." Journal of Clinical Microbiology 36, no. 3 (1998): 734–41. http://dx.doi.org/10.1128/jcm.36.3.734-741.1998.

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Pneumocystis carinii f. sp. hominisisolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 typ

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9

Bhinder, Preety, Asha Chaudhry, and Aditi Soni. "Nimbecidine induced gene mutations in internal transcribed spacers 1 and 2 of Anopheles stephensi." Journal of Applied and Natural Science 4, no. 1 (2012): 23–29. http://dx.doi.org/10.31018/jans.v4i1.216.

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The genotoxic effects of nimbecidine, a commercial botanical pesticide derived from the neem tree were assessed by PCR assay on a mosquito Anopheles stephensi taken as an experimental model. After treatment with LC20 of the nimbecidine, the sequence variations in the internal transcribed spacers 1 and 2 (ITS1 and ITS2) of control and treated individuals were studied from their sequence alignment data and the mutations in the form of insertions, deletions, and substitutions were analyzed. Nimbecidine treatment induced 16 deletions, 13 insertions, 93 transitions and 140 transversions in the ITS1

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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Gábor Gyulai, and Arun K. Pandey. "Application of internal transcribed spacer of nuclear ribosomal DNA for identification of Echinops mandavillei Kit Tan." Bangladesh Journal of Plant Taxonomy 21, no. 1 (2014): 33–42. http://dx.doi.org/10.3329/bjpt.v21i1.19256.

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The present study explored the use of internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA) for identification of Echinops mandavillei Kit Tan, an endemic species to Saudi Arabia. The sequence similarity search using Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses of the ITS sequence of E. mandavillei Kit Tan showed high level of sequence similarity (98%) with E. glaberrimus DC. (section Ritropsis). The novel primary sequence and the secondary structure of ITS2 of E. mandavillei could have a potential use for molecular genotyping.DOI

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Bobrek, K., J. Urbanowicz, P. Chorbiński, and A. Gaweł. "Molecular analysis of Trichomonas gallinae in racing pigeons from Upper Silesia, Poland." Polish Journal of Veterinary Sciences 20, no. 1 (2017): 185–87. http://dx.doi.org/10.1515/pjvs-2017-0023.

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Abstract The aim of the study was the molecular analysis of ITS1/5.8S rRNA/ITS2 region of Trichomonas gallinae isolates from racing pigeon lofts in Upper Silesia, Poland. The analysed region is very useful for the taxonomy of the Trichomonadidae family and indicates the possible existence of different genotypes or species within the T. gallinae. A comparison of the complete ITS1-5.8S-ITS2 region of obtained sequences revealed two different sequences. Twenty-three of the isolates (62%) showed the first sequence (KU954106) while fourteen isolates (38%) showed the second sequence type (KU954107),

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Urbanowicz, Joanna, Andrzej Gaweł, and Kamila Bobrek. "Ascaridia galli isolates with ITS1-5.8rRNA-ITS2 fragment homologous to Ascaridia columbae." Acta Parasitologica 63, no. 3 (2018): 640–44. http://dx.doi.org/10.1515/ap-2018-0073.

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Abstract Ascaridia (A.) galli is one of the most commonly occurring nematodes in poultry worldwide, often in hens and broiler chickens. The infection with Ascaridia galli in free-range chickens was even 70%. There is not much information about A. galli genetic features. The present study was conducted to assess the genetic diversity of A. galli isolated from hens in Poland by analyzing the nucleotide sequence of the region ITS1-5.8rRNA-ITS2 and to define its homology within the family Ascaridiidae. Adult A. galli were collected from the intestines of naturally infected hens from two flocks of

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Phillips, Ruth B., Susan A. Manley, and Thomas J. Daniels. "Systematics of the Salmonid Genus Salvelinus Inferred from Ribosomal DNA Sequences." Canadian Journal of Fisheries and Aquatic Sciences 51, S1 (1994): 198–204. http://dx.doi.org/10.1139/f94-305.

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DNA sequences of the second internal transcribed spacer (ITS2) of the nuclear ribosomal DNA were determined for six species of the genus Salvelinus: S. alpinus (Arctic char), S. malma (Dolly Varden), S. confluentus (bull trout), S. leucomaenis (Japanese char), S. fontinalis (brook trout), and S. namaycush (lake trout), and for Hucho perryi (huchen). The ITS2 sequence data (approximately 375 base pairs (bp)) were combined with previously determined sequence data for the ITS1 (approximately 575 bp), giving a total of 981 bp of aligned sequence for each species. Phylogenetic analysis of the align

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Thu Hien, Le Thi, and Ha Hong Hanh. "Efficiency of ITS1-5.8S-ITS2 region in identifying Cordyceps species." Vietnam Journal of Biotechnology 16, no. 4 (2020): 705–12. http://dx.doi.org/10.15625/1811-4989/16/4/13220.

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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

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15

Gong, Li, Xiaoyu Kong, Hairong Luo, Shixi Chen, Wei Shi, and Min Yang. "Intra-genomic variability and pseudogenes in ribosomal ITS regions of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae)." Animal Biology 70, no. 2 (2020): 145–58. http://dx.doi.org/10.1163/15707563-20191141.

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Abstract Eukaryotic nuclear ribosomal DNA (rDNA) typically evolves in a concerted manner, in which hundreds of rDNA sequences within species show little or no variations, whereas the sequences of different species diverge. There are few studies of the internal transcribed spacer regions (ITS1-5.8S-ITS2) in teleostean fishes and only one report on flatfishes. Here, we reported the discovery of two types of highly divergent ITS1-5.8S-ITS2 rDNA sequences (Type A and B) in the genome of the Bloch’s tonguesole, Paraplagusia blochii. These sequences mainly differ in sequence length, secondary struct

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Nafisi, Haniyeh, Akram Kaveh, and Shahrokh Kazempour-Osaloo. "Characterizing nrDNA ITS1, 5.8S and ITS2 secondary structures and their phylogenetic utility in the legume tribe Hedysareae with special reference to Hedysarum." PLOS ONE 18, no. 4 (2023): e0283847. http://dx.doi.org/10.1371/journal.pone.0283847.

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This is the first study to systematically evaluate rRNA secondary structures of Hedysareae with an emphasis on Hedysarum. ITS2 and 5.8S regions of the genus shared a common secondary structure with a four-fingered central loop, whereas ITS1 possessed five distinct structures. The secondary structural features of the two regions provided advantageous data for clades, species groups, and closely related species. Hemi-CBCs were mostly observed in the reconstruction of species groups, and Nsts, mostly between closely related species. The investigations showed that ITS1 varied more than ITS2 in len

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17

Wang, D. M., and Y. J. Yao. "Intrastrain internal transcribed spacer heterogeneity inGanodermaspecies." Canadian Journal of Microbiology 51, no. 2 (2005): 113–21. http://dx.doi.org/10.1139/w04-118.

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Intrastrain internal transcribed spacer (ITS) heterogeneity is first reported from Ganoderma, a fungal genus within Basidiomycetes. ITS amplification products from 4 strains, representing 4 Ganoderma species, were cloned and sequenced. Two to five different ITS types were found within a single strain. The clone sequences were analyzed along with other sequences from Ganoderma retrieved from GenBank. The results show that sequence variation within strains varies considerably with species and the heterogeneity may occur in the 3 parts (ITS1, ITS2, and 5.8S) of the ITS region.Key words: intrageno

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Galazzo, Daniel E., Selvadurai Dayanandan, David J. Marcogliese, and J. Daniel McLaughlin. "Molecular systematics of some North American species of Diplostomum (Digenea) based on rDNA-sequence data and comparisons with European congeners." Canadian Journal of Zoology 80, no. 12 (2002): 2207–17. http://dx.doi.org/10.1139/z02-198.

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The systematics of Diplostomum species, common intestinal parasites of piscivorous birds, has long been problematic, owing to phenotypic plasticity and the paucity of morphological features that are often subject to age- and host-induced variation. We sequenced the ITS15.8SITS2 regions of the rDNA from adult Diplostomum huronense, Diplostomum indistinctum, and Diplostomum baeri obtained from experimentally infected ring-bill gulls (Larus delawarensis) and compared them with partial ITS1 sequences from several species of Diplostomum in GenBank. The three North American species were distinguis

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Li, Hsin Chieh, Jean-Philippe Bouchara, Mark Ming-Long Hsu, Richard Barton, Shuli Su, and Tsung Chain Chang. "Identification of dermatophytes by sequence analysis of the rRNA gene internal transcribed spacer regions." Journal of Medical Microbiology 57, no. 5 (2008): 592–600. http://dx.doi.org/10.1099/jmm.0.47607-0.

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Identification of dermatophytes using the traditional method is sometimes problematic because of atypical microscopic or macroscopic morphology. The aim of this study was to evaluate the feasibility of using sequencing of the ribosomal internal transcribed spacer (ITS)1 and ITS2 regions for identification of 17 dermatophyte species. The ITS regions of 188 strains (62 reference strains and 126 clinical isolates) were amplified by PCR and sequenced. Species identification was made by sequence comparison with an in-house database comprising ITS sequences of type or neotype strains or by blast sea

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Mishra, Shobhna, Gunjan Sharma, Manoj K. Das, Veena Pande, and Om P. Singh. "Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vector Anopheles stephensi." PLOS ONE 16, no. 6 (2021): e0253173. http://dx.doi.org/10.1371/journal.pone.0253173.

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Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 of Anopheles stephensi have been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA of An. stephensi and hypothesizes that observed intra-specific differences in this species may have resulted due to ambiguous DNA sequence-chromatogram resulting from

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21

Belair, Marie, Flora Pensec, Jean-Luc Jany, Gaétan Le Floch, and Adeline Picot. "Profiling Walnut Fungal Pathobiome Associated with Walnut Dieback Using Community-Targeted DNA Metabarcoding." Plants 12, no. 12 (2023): 2383. http://dx.doi.org/10.3390/plants12122383.

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Walnut dieback can be caused by several fungal pathogenic species, which are associated with symptoms ranging from branch dieback to fruit necrosis and blight, challenging the one pathogen–one disease concept. Therefore, an accurate and extensive description of the walnut fungal pathobiome is crucial. To this end, DNA metabarcoding represents a powerful approach provided that bioinformatic pipelines are evaluated to avoid misinterpretation. In this context, this study aimed to determine (i) the performance of five primer pairs targeting the ITS region in amplifying genera of interest and estim

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Schnabel, G., E. L. Schnabel, and A. L. Jones. "Characterization of Ribosomal DNA from Venturia inaequalis and Its Phylogenetic Relationship to rDNA from Other Tree-Fruit Venturia Species." Phytopathology® 89, no. 1 (1999): 100–108. http://dx.doi.org/10.1094/phyto.1999.89.1.100.

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A portion of the 18S ribosomal DNA (rDNA) gene, the internal transcribed spacers (ITS1 and ITS2), and the 5.8S rDNA gene were polymerase chain reaction-amplified from strains and field populations of Venturia inaequalis and assessed for genetic variation. A previously reported optional group I intron in the 18S rDNA gene of V. inaequalis was detected in 75.0% of 92 strains collected worldwide and in 61.1 and 71.2% of 54 and 59 strains from two Michigan orchards, respectively. Sequence and restriction analysis of rDNA revealed four intron alleles, three of which were present both in worldwide s

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23

Grünig, Christoph R., Thomas N. Sieber, Scott O. Rogers, and Ottmar Holdenrieder. "Genetic variability among strains of Phialocephala fortinii and phylogenetic analysis of the genus Phialocephala based on rDNA ITS sequence comparisons." Canadian Journal of Botany 80, no. 12 (2002): 1239–49. http://dx.doi.org/10.1139/b02-115.

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Two methods to determine variability among strains of Phialocephala fortinii and sterile DSE (dark septate endophyte) Type 1 were compared: inter-simple sequence repeat polymerase chain reaction analysis (ISSRPCR) and sequence analysis of the two internal transcribed spacers and the 5.8S ribosomal DNA (ITS1-5.8S-ITS2). Both methods showed similar results for some strains, but different results for others. Phylogenetic analysis of various strains of P. fortinii and Type 1 based on ITS1-5.8S-ITS2 sequence information showed that Type 1 strains, with the exception of one Type 1 strain and a stra

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Andreev, I. O., І. І. Konvalyuk, V. M. Mel'nyk, M. V. Humeniuk, and V. A. Kunakh. "Molecular genetic analysis of Rauvolfia serpentina tissue culture strain K-27M using the ITS1-5.8S-ITS2 region of 35S rRNA genes." Visnik ukrains'kogo tovaristva genetikiv i selekcioneriv 22, no. 1-2 (2025): 18–23. https://doi.org/10.7124/visnyk.utgis.22.1-2.1685.

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Hormone-independent strain K-27M of Rauvolfia serpentina tissue culture, which is a valuable source of indoline alkaloids, was created in the Department of genetics of cell populations at the Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine. This strain differs significantly from R. serpentina plants in composition and content of alkaloids. Furthermore, there are no clear data on the plant material used to obtain this tissue culture strain. The aim of this study was to carry out species identification of tissue culture strain K-27M based on molecular g

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ÖZGİŞİ, Kurtuluş. "CHARACTERIZATION OF ITS1 SECONDARY STRUCTURE IN TEN SPECIES OF COLUTEOCARPEAE (BRASSICACEAE) AND ITS TAXONOMICAL UTILITY." Communications Faculty of Science University of Ankara Series C Biology Geological Engineering and Geophysical Engineering 30, no. 1 (2021): 1–12. http://dx.doi.org/10.53447/communc.820287.

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Utility of the internal transcribed spacers (ITSs) of ribosomal RNA sequences to infer phylogenetic relationships among organisms have been proven. Although ITS1 and ITS2 are highly variable in sequence, they have conserved structures that have a key function in the processing of rRNA gene transcripts. Determining of such a conserved motif can help to identify relationships between organisms. Since ITS2 has much more conserved secondary structure, structural properties of ITS1 are generally neglected by researchers. In this study, ITS1 secondary structures of ten representative species, which

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Tynkevich, Y., K. Nord, Ya Ivanovych, I. Moysiyenko, and I. Panchuk. "ANALYSIS OF THE TAXONOMIC STATUS OF LIMONIUM CASPIUM (WILLD.) P. FOURN. USING THE ITS1-5.8S-ITS2 REGION." Biolohichni systemy 15, no. 2 (2023): 165–70. http://dx.doi.org/10.31861/biosystems2023.02.165.

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There are 15 representatives of the genus Limonium Mill in Ukraine. The taxonomic status of some of them requires clarification. In particular, some taxonomists consider L. caspium (Willd.) P. Fourn. to be a separate species, while others tend to consider this name as a synonym for L. bellidifolium Dumort. Until now, only one sample of L. caspium from eastern Iran has been analyzed using molecular genetic approaches: for this accession, the ITS1-5.8S-ITS2 of 35S rDNA region was sequenced. For both species, L. caspium and L. bellidifolium, samples from the territory of Ukraine have not yet been

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H. Hajia Hasan, Amal, Dhia A. Al-Bader, Akira F. Peters, and Frithjof C. Küpper. "Revision of the family Sargassaceae (Fucales, Phaeophyceae) from Kuwait (Arabian / Persian Gulf, NW Indian Ocean) based on analysis of morphology and ITS2 sequences." Ukrainian Botanical Journal 80, no. 1 (2023): 3–20. http://dx.doi.org/10.15407/ukrbotj80.01.003.

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This article investigates the species of the family Sargassaceae present in Kuwait, analyzing nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences of 67 individuals collected in 2018–2020. Morphological characterization and DNA barcoding confirmed the presence of eight taxa that belong to Sargassaceae. Five species belong to the genus Sargassum, while three other taxa, namely Sirophysalis trinodis, Hormophysa cuneiformis, and Polycladia myrica, belong to other genera. For the latter species, there was no ITS2 sequence available so far. As for Sargassum species, previous records bas

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Albo, Jonathan Eric, Jean-Philippe Marelli, and Alina Sandra Puig. "Rapid Molecular Identification of Scolytinae (Coleoptera: Curculionidae)." International Journal of Molecular Sciences 20, no. 23 (2019): 5944. http://dx.doi.org/10.3390/ijms20235944.

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Routine identification of bark and ambrosia beetles is done using morphology. For people lacking the necessary taxonomic knowledge, proper identification of a novel specimen can be challenging and time consuming. This study compares the usefulness of four genetic markers (28S, EF-1a, ITS2, and COI) and five primer pairs (D2F1/D3R2, eflafor1/eflarev1, ets149/efa754, ITS2F/ITS2R, and LCO1490/HCO2198) to identify Scolytinae beetles, and outlines a molecular identification strategy, with results possible in two days. Markers COI and EF-1a were selected based on the ability of the respective primer

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Jomhe, Farsangi Forough, Avinash Shivaji Thorat, and Rachayya Mallikarjun Devarumath. "Assessment of genetic diversity among different sugarcane genotypes using internal transcribed spacer (ITS) region of the ribosomal DNA (rDNA)." GSC Biological and Pharmaceutical Sciences 5, no. 2 (2018): 017–25. https://doi.org/10.5281/zenodo.4305351.

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Internal transcribed spacer or ITS region of nuclear ribosomal DNA (rDNA) has been used to evaluate genetic assortment and phylogenetic relationship in nine sugarcane genotypes including <em>Saccharum</em> species and another related genus as <em>Erianthus</em><em>,</em> Narenga and hybrid. DNA was extracted from selected genotypes and ITS (ITS-1 and ITS-2) regions were amplified using specific primers. The sequence lengths ITS-1 showed 205- 207 bp, while ITS2 was ranged from 211- 218 bp. However, G+C content (%) 65.2% - 67% in ITS-1 and in ITS-2 68.4% - 99.7%. The sequence

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Sun, Ping, John C. Clamp, Dapeng Xu, Yasushi Kusuoka, and Manabu Hori. "Molecular phylogeny of the family Vorticellidae (Ciliophora, Peritrichia) using combined datasets with a special emphasis on the three morphologically similar genera Carchesium, Epicarchesium and Apocarchesium." International Journal of Systematic and Evolutionary Microbiology 61, no. 4 (2011): 1001–10. http://dx.doi.org/10.1099/ijs.0.020255-0.

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Little is known about the phylogeny of the family Vorticellidae at the generic level because few comprehensive analyses of molecular phylogenetic relationships between members of this group have, so far, been done. As a result, the phylogenetic positions of some genera that were based originally on morphological analyses remain controversial. In the present study, we performed phylogenetic analyses of vorticellids based on the sequence of the small-subunit (SSU) rRNA gene, including one species of the genus Apocarchesium, for which no sequence has previously been reported. Phylogenetic trees w

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Mbareche, Hamza, Marc Veillette, and Guillaume J. Bilodeau. "In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols." Journal of Fungi 7, no. 2 (2021): 99. http://dx.doi.org/10.3390/jof7020099.

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This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to

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SMOLIK, Milosz, Marcelina KRUPA-MAŁKIEWICZ, Beata SMOLIK, Justyna WIECZOREK, and Katarzyna PREDYGIER. "rDNA Variability Assessed in PCR Reactions of Selected Accessions of Acer." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39, no. 1 (2011): 260. http://dx.doi.org/10.15835/nbha3915760.

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The region of rDNA (SSU, 5.8S, LSU and ITS1, ITS2 spacer sequences) of fourteen Acer accessions was tested in order to determine the possibility to identify genotypic variability within a rDNA sequence. The tests were performed using the PCR technique and a set of combination of several pairs of ‘universal’ primers designed to amplify rDNA sequences. ‘Universal’ primers were selected in such a way as to make the rDNA regions flanking possible in cases where a smaller or larger scope of variability was expected. Thus, within SSU or LSU sequences, monomorphic PCR products were amplified for the

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Al-Hemaid, Fahad M. A., M. Ajmal Ali, Joongku Lee, Soo-Yong Kim, and Md Oliur Rahman. "Molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus inferred from analysis of internal transcribed spacer sequences." Bangladesh Journal of Plant Taxonomy 22, no. 2 (2015): 111–18. http://dx.doi.org/10.3329/bjpt.v22i2.26072.

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The present study explored molecular phylogenetic analysis of 28 species of Euphorbia L. for the identification and establishment of molecular evolutionary relationships of Euphorbia scordifolia Jacq. within the genus based on the internal transcribed spacers (ITS) sequences (ITS1-5.8S-ITS2) of nuclear ribosomal DNA (nrDNA). The sequence similarity search using Basic Local Alignment Search Tool (BLAST) of the ITS sequence of E. scordifolia showed the closest sequence similarity to E. supina Raf. The analysis of ITS sequence data revealed four major clades consistent with subgeneric classificat

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Thanh Hoa, Le, Nguyen Thi Bich Nga, Doan Thi Thanh Huong, Le Thi Kim Xuyen, and Nguyen Thi Khue. "Structure and characterization of the ribosomal transcription units of small liver flukes, Opisthorchis viverrini, O. Felineus and Clonorchis sinensis." Vietnam Journal of Biotechnology 17, no. 3 (2020): 441–47. http://dx.doi.org/10.15625/1811-4989/17/3/13538.

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Opisthorchiasis is a zoonotic parasitic infection caused by small liver fluke species, Opisthorchis viverrini,O. felineus and Clonorchis sinensis, in the family Opisthorchiidae. Vietnam has both species, of which C.sinensis is distributed in the northern and O. viverrini in the central provinces. In addition to the mitochondrialgenomes, the ribosomal DNA sequences (rDNA) of these species are highly needed to obtain for providingmolecular markers in species identification, classification, phylogeny and evolutionary studies. In this study,the near/complete nucleotide sequences of ribosomal trans

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Kalaiventhan, Yuveantheni, Kensuke Seto, and Matthias Wolf. "ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi)." Biology 14, no. 1 (2025): 36. https://doi.org/10.3390/biology14010036.

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To date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been claimed to not be alignable for this group of organisms. Although the ITS2 is a fast-evolving locus, its secondary structure is well conserved. To improve the accuracy and robustness of Chytridiomycota phylogeny, in this study, we attempt, for the first, time to reconstruct an ITS2 sequence–structure ph

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Forin, Niccolò, Alfredo Vizzini, Federico Fainelli, Enrico Ercole, and Barbara Baldan. "Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection." Microorganisms 9, no. 3 (2021): 666. http://dx.doi.org/10.3390/microorganisms9030666.

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In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was re

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Apostolova, Elena, Krasimir Todorov, Ivanka Dimitrova-Dyulgerova, et al. "Analysis of the sequence of ITS1 and ITS2 regions of Three Mentha species." Plant Genetic Resources 15, no. 6 (2016): 563–65. http://dx.doi.org/10.1017/s1479262116000289.

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AbstractMentha (Nepetoideae, Lamiaceae) is a taxonomically complex genus consisting of 29 species and 11 different hybrids including a number of economically important species among them medical plants used for more than 250 years. Because of its high incidence of polyploidy, diverse morphology, high degree of chromosome number variations and interspecies hybridization, Mentha is considered to be a taxonomical challenge. In this paper, we describe cloning and sequencing of internal transcribed spacers (ITS) 1 and 2 of three mint species: Mentha aquatic L., Mentha longifolia L. (Huds) and Menth

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MORGAN, U. M., P. DEPLAZES, D. A. FORBES, et al. "Sequence and PCR–RFLP analysis of the internal transcribed spacers of the rDNA repeat unit in isolates of Cryptosporidium from different hosts." Parasitology 118, no. 1 (1999): 49–58. http://dx.doi.org/10.1017/s0031182098003412.

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The Cryptosporidium ITS1, 5·8S and ITS2 rDNA regions from a number of Cryptosporidium isolates from different hosts and geographical areas were cloned and sequenced in order to investigate the extent of sequence heterogeneity between human and cattle-derived isolates from different geographical locations and also between isolates of Cryptosporidium from different hosts such as cats, pigs, mice and a koala. Calf-derived isolates from different continents were virtually identical as were human-derived isolates from the UK and Australia. Genetic differences between Cryptosporidium isolates were e

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Gnutikov, A. A., N. N. Nosov, I. G. Loskutov, E. V. Blinova, and A. V. Rodionov. "Molecular phylogenetic study of rare weed-field species of the genus Avena L." Проблемы ботаники южной сибири и монголии 20, no. 1 (2021): 108–11. http://dx.doi.org/10.14258/pbssm.2021022.

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A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those

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Cao, Ruixin, Shuyan Tong, Tianjing Luan, Hanyun Zheng, and Wei Zhang. "Compensatory Base Changes and Varying Phylogenetic Effects on Angiosperm ITS2 Genetic Distances." Plants 11, no. 7 (2022): 929. http://dx.doi.org/10.3390/plants11070929.

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A compensatory base change (CBC) that coevolves in the secondary structure of ribosomal internal transcribed spacer 2 (ITS2) influences the estimation of genetic distance and thus challenges the phylogenetic use of this most popular genetic marker. To date, however, the CBC effect on ITS2 genetic distance is still unclear. Here, ITS2 sequences of 46 more recent angiosperm lineages were screened from 5677 genera and phylogenetically analyzed in sequence-structure format, including secondary structure prediction, structure-based alignment and sequence partition of paired and unpaired regions. IT

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Su'udi, Mukhamad, Fuad Bahrul Ulum, Muhammad Ardiyansah, and Nurfajri Eka Fitri. "Evaluasi Lokus Potensial matK dan ITS2 Untuk DNA Barcoding Anggrek Bulbophyllum lobbii Lindl." Al-Kauniyah: Jurnal Biologi 17, no. 2 (2024): 406–18. http://dx.doi.org/10.15408/kauniyah.v17i2.33897.

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AbstrakBulbophyllum lobbii Lindl. merupakan anggrek dari famili Orchidaceae yang berpotensi sebagai bahan baku obat herbal. Identikasi morfologi anggrek B. lobii memiliki keterbatasan karena kemiripan spesies dengan anggrek lain. Alternatif identifikasi secara molekuler menggunakan sekuen matK dan ITS2 sebagai barcode dalam DNA barcoding diharapkan menjadi salah satu lokus pembeda spesies anggrek B. lobbii secara akurat dan efisien. Penelitian ini bertujuan untuk mengidentifikasi sekuen matK dan ITS2 sebagai penanda molekuler yang efektif untuk anggrek B. lobbii. DNA genom B. lobbii diisolasi

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Zhang, Xinhui, Zhuo Lan, Wei Wei, et al. "Genetic Variation and Population Structure of Clonorchis sinensis: An In Silico Analysis." Pathogens 13, no. 11 (2024): 991. http://dx.doi.org/10.3390/pathogens13110991.

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Clonorchis sinensis is an important zoonotic parasite that is mainly prevalent in China, Korea, Vietnam and the Russian Far East. To explore the genetic variation and population structure of C. sinensis, an in silico analysis was conducted based on mitochondrial cytochrome c oxidase subunit 1 (COX1), ribosomal internal transcribed spacer 1 (ITS1) and ribosomal internal transcribed spacer 2 (ITS2) sequences. The sequences obtained from NCBI were truncated for further analyses, including haplotype network, phylogenetic, gene flow, diversity and neutrality analyses. The results showed that there

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Shimono, Y., S. Taharaguchi, K. Taira, N. Miyoshi, and N. Yasuda. "rDNA ITS sequences of Uncinaria spp. from Tsushima leopard cat (Prionailurus bengalensis euptilura)." Helminthologia 49, no. 3 (2012): 123–27. http://dx.doi.org/10.2478/s11687-012-0026-x.

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AbstractUncinaria spp. parasites were collected from two Tsushima leopard cats found on Tsushima Island, Nagasaki prefecture, Japan. One Uncinaria sp. was observed in the large intestines, and the other was observed in the small intestines. The nematode found in the large intestines was determined to be Uncinaria felidis by morphological identification. The other Uncinaria sp. found in the small intestines was morphologically different from U. felidis in the short-length of prevulvar flap. After isolation of genomic DNA of these worms, a second internal transcribed spacer (ITS2) of ribosomal D

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Zhao, G. H., Y. Q. Jia, Q. Q. Bian, et al. "Molecular approaches to differentiate three species of Nematodirus in sheep and goats from China based on internal transcribed spacer rDNA sequences." Journal of Helminthology 89, no. 3 (2013): 259–66. http://dx.doi.org/10.1017/s0022149x13000825.

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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

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Bobrek, Kamila, Joanna Hildebrand, Joanna Urbanowicz, and Andrzej Gaweł. "Molecular Identification and Phylogenetic Analysis of Heterakis dispar Isolated from Geese." Acta Parasitologica 64, no. 4 (2019): 753–60. http://dx.doi.org/10.2478/s11686-019-00112-1.

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Abstract Purpose Heterakidosis is a common parasitic infection caused in domestic birds by Heterakis species: Heterakis gallinarum, H. isolonche, and H. dispar. Among them, the best described species is H. gallinarum, noted mainly in gallinaceous birds. In waterfowl, H. dispar is the predominant species. The variations in morphology and host specificity qualify H. dispar as a different species, but the phylogenetic relationships between heterakids were unclear for a long time, because of a lack of H. dispar sequences. Methods The authors provided the molecular data for H. dispar and analyzed t

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Zhang, Wei, Wen Tian, Zhipeng Gao, Guoli Wang, and Hong Zhao. "Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint." International Journal of Molecular Sciences 21, no. 17 (2020): 6395. http://dx.doi.org/10.3390/ijms21176395.

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The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of I

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Rogers, S. O., and Z. Kaya. "DNA From Ancient Cedar Wood From King Midas’ Tomb, Turkey, and Al-Aksa Mosque, Israel." Silvae Genetica 55, no. 1-6 (2006): 54–62. http://dx.doi.org/10.1515/sg-2006-0009.

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Abstract Ancient Taurus cedar (Cedrus libani A. Rich) wood samples from the Tumulus of King Midas at the Gordion archaeological site (about 2700 years old), near Ankara, Turkey, and from the Al-Aksa Mosque (about 1500 to 1900 years old), Jerusalem, Israel, were characterized by studying the sequences of ribosomal DNA (rDNA) internal transcribed spacers (ITS1 and ITS2). After extraction of the DNA, the ITS regions were amplified utilizing the polymerase chain reaction, followed by sequencing, BLAST searches for similar sequences, and phylogenetic analyses. Fifty-six sequences were obtained. In

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OKAMOTO, M., T. AGATSUMA, T. KUROSAWA, and A. ITO. "Phylogenetic relationships of three hymenolepidid species inferred from nuclear ribosomal and mitochondrial DNA sequences." Parasitology 115, no. 6 (1997): 661–66. http://dx.doi.org/10.1017/s0031182097001741.

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Three hymenolepidid tapeworms, Hymenolepis diminuta, H. nana and H. microstoma, are commonly maintained in laboratory rodents and used in many experimental model systems of tapeworm infections. We examined partial sequences from the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene and nuclear ribosomal internal transcribed spacer 2 (ITS2) sequences to infer phylogenetic relationships of the 3 hymenolepidid species. Parts of the CO1 gene and ITS2 were amplified by PCR and sequenced directly. The CO1 gene sequence obtained was the same in length (391 bp) among all specimens. In the case o

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Porras-Alfaro, Andrea, Kuan-Liang Liu, Cheryl R. Kuske, and Gary Xie. "From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition." Applied and Environmental Microbiology 80, no. 3 (2013): 829–40. http://dx.doi.org/10.1128/aem.02894-13.

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ABSTRACTWe compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5′ section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Baye

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ULUAR, ONUR, and BATTAL ÇIPLAK. "Evolution, characterization and phylogenetic utility of ITS2 gene in Orthoptera and some Polyneoptera: Highly variable at the order level and highly conserved at the species level." Zootaxa 4780, no. 1 (2020): 54–76. http://dx.doi.org/10.11646/zootaxa.4780.1.2.

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ITS2 is often suggested as a potential marker for evolutionary studies and species barcoding. However, there are many lineages have not been studied. This study focuses on ITS2 in Polyneoptera at the order and species levels. ITS2 sequences representing six polyneopteran orders and 15 species in the genus Anterastes are studied. We arrived at the following conclusions: (i) ITS2 is highly variable and contains little phylogenetic information in Polyneoptera, (ii) the shortest length and the highest GC content of ITS2 is found in Orthoptera among insects, (iii) the secondary structure exhibits g

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