Intra-genomic variability and pseudogenes in ribosomal ITS regions of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae)

2020 ◽  
Vol 70 (2) ◽  
pp. 145-158 ◽  
Author(s):  
Li Gong ◽  
Xiaoyu Kong ◽  
Hairong Luo ◽  
Shixi Chen ◽  
Wei Shi ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Minimum Free Energy ◽  
Sequence Type ◽  
Nuclear Ribosomal Dna ◽  
Sequence Length ◽  
Type B ◽  
Genomic Variability ◽  
Future Studies ◽  
Rdna Sequences ◽  
Its Regions

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 structure, and minimum free energy. According to the potential features of pseudogenes, Type B sequences are speculated to be putative pseudogenic ITS regions. Cluster analyses also supported two major clades that corresponded to the sequence type. To the best of our knowledge, this is the first report of the ITS regions of tonguefish, and may therefore provide useful information for future studies of the rDNA of flatfishes as well as the patterns of rDNA evolution in teleostean fishes.

scholarly journals Multiple Origins and nrDNA Internal Transcribed Spacer Homeologue Evolution in the Glycine tomentella (Leguminosae) Allopolyploid Complex

Genetics ◽  
2004 ◽  
Vol 166 (2) ◽  
pp. 987-998 ◽  
Author(s):  
Jason T Rauscher ◽  
Jeff J Doyle ◽  
A H D Brown
Keyword(s):  
Molecular Evolution ◽  
Concerted Evolution ◽  
Internal Transcribed Spacer ◽  
Direct Sequencing ◽  
Nuclear Ribosomal Dna ◽  
Nucleolar Dominance ◽  
Future Studies ◽  
Complex Interactions ◽  
Multiple Origins ◽  
Glycine Tomentella

Abstract Despite the importance of polyploidy in the evolution of plants, patterns of molecular evolution and genomic interactions following polyploidy are not well understood. Nuclear ribosomal DNA is particularly complex with respect to these genomic interactions. The composition of nrDNA tandem arrays is influenced by intra- and interlocus concerted evolution and their expression is characterized by patterns such as nucleolar dominance. To understand these complex interactions it is important to study them in diverse natural polyploid systems. In this study we use direct sequencing to isolate and characterize nrDNA internal transcribed spacer (ITS) homeologues from multiple accessions of six different races in the Glycine tomentella allopolyploid complex. The results indicate that in most allopolyploid accessions both homeologous nrDNA repeats are present, but that there are significant biases in copy number toward one homeologue, possibly resulting from interlocus concerted evolution. The predominant homeologue often differs between races and between accessions within a race. A phylogenetic analysis of ITS sequences provides evidence for multiple origins in several of the polyploid races. This evidence for diverse patterns of nrDNA molecular evolution and multiple origins of polyploid races will provide a useful system for future studies of natural variation in patterns of nrDNA expression.

Allium dönmezii, a new species of Allium sect. Melanocrommyum (Amaryllidaceae) from Turkey: morphological and molecular evidence

Phytotaxa ◽  
2019 ◽  
Vol 411 (3) ◽  
pp. 194-204
Author(s):  
ŞÜKRÜ KARAKUŞ ◽  
BİROL MUTLU
Keyword(s):  
New Species ◽  
Molecular Marker ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Nuclear Ribosomal Dna ◽  
Molecular Evidence ◽  
Its Regions ◽  
First Time ◽  
East Anatolia ◽  
A New Species

Allium dönmezii is described as a new species from east Anatolia, Turkey. The molecular marker ITS (Internal Transcribed Spacer of nuclear ribosomal DNA) confirms that the new species belongs to A. sect. Melanocrommyum. The diagnostic characters of the new species are morphologically compared with the related A. woronowii, A. serpentinicum, and A. moderense, as well as with A. rothii and A. chrysantherum. In addition, the ITS regions of A. purpureoviride and A. chrysantherum were sequenced and uploaded on GenBank for the first time.

Characterization of the complete nuclear ribosomal DNA sequences of Eurytrema pancreaticum

2017 ◽  
Vol 92 (4) ◽  
pp. 484-490 ◽  
Author(s):  
X. Su ◽  
Y. Zhang ◽  
X. Zheng ◽  
X.X. Wang ◽  
Y. Li ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Internal Transcribed Spacer ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Economic Losses ◽  
Length Variation ◽  
5.8S Rdna ◽  
Rdna Sequences

AbstractEurytrema pancreaticum is one of the most common trematodes of cattle and sheep, and also infects humans occasionally, causing great economic losses and medical costs. In this study, the sequences of the complete nuclear ribosomal DNA (rDNA) repeat units of five E. pancreaticum individuals were determined for the first time. They were 8306–8310 bp in length, including the small subunit (18S) rDNA, internal transcribed spacer 1 (ITS1), 5.8S rDNA, internal transcribed spacer 2 (ITS2), large subunit (28S) rDNA and intergenic spacer (IGS). There were no length variations in any of the investigated 18S (1996 bp), ITS1 (1103 bp), 5.8S (160 bp), ITS2 (231 bp) or 28S (3669 bp) rDNA sequences, whereas the IGS rDNA sequences of E. pancreaticum had a 4-bp length variation, ranging from 1147 to 1151 bp. The intraspecific variations within E. pancreaticum were 0–0.2% for 18S rDNA, 0–0.5% for ITS1, 0% for 5.8S rDNA and ITS2, 0–0.2% for 28S rDNA and 2.9–20.2% for IGS. There were nine types of repeat sequences in ITS1, two types in 28S rDNA, but none in IGS. A phylogenetic analysis based on the 18S rDNA sequences classified E. pancreaticum in the family Dicrocoeliidae of Plagiorchiata, closely related to the suborder Opisthorchiata. These results provide useful information for the further study of Dicrocoeliidae trematodes.

scholarly journals Morphological and molecular characterization of Pisolithus in soil under eucalyptus plantations in Brazil

2010 ◽  
Vol 34 (6) ◽  
pp. 1891-1898 ◽  
Author(s):  
Maria Catarina Megumi Kasuya ◽  
Irene da Silva Coelho ◽  
Daniela Tiago da Silva Campos ◽  
Elza Fernandes de Araújo ◽  
Yutaka Tamai ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Spore Ornamentation ◽  
Eucalyptus Plantations ◽  
Its Regions ◽  
Morphological And Molecular Characterization ◽  
Hypogeous Fungus

Eighteen Pisolithus basidiomes were collected from Eucalyptus plantations in the state of Minas Gerais, Brazil. These basidiomes were characterized morphologically and molecularly. The basidiomes varied in shape, color and size. One of them was found underground, indicating a hypogeous fungus. The main morphological distinctive characteristic was spore ornamentation, which distinguished two groups. One group with short and erect spines was identified as Pisolithus microcarpus, and the other with long and curved spines as Pisolithus marmoratus, after analyzing the cladogram obtained by phylogenetic relationship based on internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA of these isolates.

Sequence variation in two mitochondrial DNA regions and internal transcribed spacer among isolates of the nematode Oesophagostomum asperum originating from goats in Hunan Province, China

2014 ◽  
Vol 90 (1) ◽  
pp. 1-6 ◽  
Author(s):  
F. Li ◽  
T. Hu ◽  
N.C. Duan ◽  
W.Y. Li ◽  
Q. Teng ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Its Rdna ◽  
Hunan Province ◽  
Nuclear Ribosomal Dna ◽  
Specific Sequence ◽  
5.8S Rdna ◽  
Rdna Sequences ◽  
Specific Variation

AbstractThe present study examined sequence variability in two mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1), and internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA) among Oesophagostomum asperum isolates from goats in Hunan Province, China. A portion of the cox1 (pcox1), nad1 (pnad1) genes and the ITS (ITS1+5.8S rDNA+ITS2) rDNA were amplified by polymerase chain reaction (PCR) separately from adult O. asperum individuals and the representative amplicons were subjected to sequencing from both directions. The lengths of pcox1, pnad1 and ITS rDNA were 366 bp, 681 bp and 785 bp, respectively. The A+T contents of gene sequences were 71.5–72% for pcox1, 73.7–74.2% for pnad1 and 58–58.8% for ITS rDNA. Intra-specific sequence variations within O. asperum were 0–1.6% for pcox1, 0–1.9% for pnad1 and 0–1.7% for ITS rDNA, while inter-specific sequence differences among members of the genus Oesophagostomum were significantly higher, being 11.1–12.5%, 13.3–17.7% and 8.5–18.6% for pcox1, pnad1 and ITS rDNA, respectively. Phylogenetic analyses using combined sequences of pcox1 and pnad1, with three different computational algorithms (Bayesian inference, maximum likelihood and maximum parsimony), revealed distinct groups with high statistical support. These findings demonstrated the existence of intra-specific variation in mtDNA and rDNA sequences among O. asperum isolates from goats in Hunan Province, China, and have implications for studying molecular epidemiology and population genetics of O. asperum.

Inocybe pakistanensis, a new species in section Rimosae s. str. from Pakistan

Phytotaxa ◽  
2018 ◽  
Vol 348 (4) ◽  
pp. 279 ◽  
Author(s):  
ZIA ULLAH ◽  
SANA JABEEN ◽  
HABIB AHMAD ◽  
ABDUL NASIR KHALID
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Molecular Phylogenetic Analysis ◽  
Its Regions ◽  
Molecular Phylogenetic ◽  
A New Species

Inocybe pakistanensis is described and illustrated as a new species based on morphological characters and molecular phylogenetic analysis of nuclear ribosomal DNA including the internal transcribed spacer (ITS) regions along with larger subunit (LSU). The distinctive basidiomata have a highly rimose and fibrillose golden brown pileus with a reddish brown, prominent umbo; ellipsoid to amygdaliform, slightly phasoeliform smooth basidiospores; and clamped septa in all the tissues. Molecular phylogenetic analysis supports the placement of I. pakistanensis in section Rimosae s. str.

scholarly journals Characterization of the Complete Nuclear Ribosomal DNA Sequences ofParamphistomum cervi

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Xu Zheng ◽  
Qiao-Cheng Chang ◽  
Yan Zhang ◽  
Si-Qin Tian ◽  
Yan Lou ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
Internal Transcribed Spacer ◽  
Interspecific Variation ◽  
28S Rdna ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
Rdna Sequences ◽  
Length Range

Sequences of the complete nuclear ribosomal DNA (rDNA) gene from five individualParamphistomum cerviwere determined for the first time. The five complete rDNA sequences, which included the 18S rDNA, the internal transcribed spacer 1 (ITS1), the 5.8S rDNA, the internal transcribed spacer 2 (ITS2), the 28S rDNA, and the intergenic spacer (IGS) regions, had a length range of 8,493–10,221 bp. The lengths of the investigated 18S, ITS1, 5.8S, ITS2, and 28S rDNA sequences, which were 1,994 bp, 1,293 bp, 157 bp, 286 bp, and 4,186 bp, respectively, did not vary. However, the IGS rDNA sequences had a length range of 577–2,305 bp. The 5.8S and ITS-2 rDNA sequences had 100% identity among the five investigated samples, while the identities among the IGS had a range of 53.7–99.8%. A comparative analysis revealed that different types and numbers of repeats were found within each ITS1 and IGS region, which may be related to the length polymorphism of IGS. The phylogenetic position ofP. cerviin Paramphistomatidae was analyzed based on the 18S rDNA sequences. These results will aid in studying the intra- and interspecific variation of the Paramphistomatidae and the systematics and phylogenetics of Digenea.

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.

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.

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