scholarly journals Identification of species in the genus Nitraria L. (Nitrariaceae) based on nucleotide variability of nuclear ribosomal DNA

2020 ◽  
Vol 24 (5) ◽  
pp. 481-488
Author(s):  
T. A. Poliakova ◽  
E. V. Banaev ◽  
M. A. Tomoshevich
Keyword(s):  
Ribosomal Dna ◽  
Gc Content ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Single Nucleotide Deletion ◽  
Nucleotide Variability ◽  
Its1 And Its2

Intragenomic polymorphism of ITS1 and ITS2 of nuclear ribosomal DNA sequences was analysed in 33 samples belonging to the Nitraria species N. schoberi, N. sibirica, and N. komarovii. The nucleotide variability of the ITS region was detected in the Nitraria species as single-nucleotide substitutions (mainly transitions) and single-nucleotide deletion. Information about the nucleotide variability of fragments is given for the first time by us. The ITS1-5.8S-ITS2 region contained 17 phylogenetically informative single-nucleotide polymorphisms. Eleven single-nucleotide substitutions (transitions, C/T) were detected in ITS1. The ITS2 spacer contained 273–274 bp and was more conservative. A total of 5 phylogenetically informative single-nucleotide polymorphisms (4 transitions: C/T, G/A, one transversion: G/C), one single-nucleotide deletion (T/–) were detected in ITS2. The average GC content was 61.5 %. The GC content was lower in N. sibirica (59.2 %) than in N. schoberi and N. komarovii (62.7 %). It has been shown that the shorter ITS2 is a suitable molecular marker separating these species, due to the low interspecific variability and simultaneous available intraspecific variability. Phylogenetic ML and BI trees constructed separately for the ITS1 and ITS2 spacers, as well as separately for the full-size ITS region and the ITS2 spacer, were congruent. The results obtained on the intraspecific differentiation of N. sibirica revealed two main ribotypes among the samples of this species: the main Siberian sibirica-ribotype and the main Kazakh sibiricaribotype. Geographical features of the distribution of N. sibirica ribotypes, as well as the presence of significant differences between the main Siberian and Kazakh sibirica-ribotypes (3 single-nucleotide substitutions) indicated significant inter-population differences and taxonomic heterogeneity of N. sibirica. Most likely, the processes of homogenization of nuclear ribosomal DNA of N. sibirica samples, the origin of which is associated with hybridization and speciation, are currently continuing.

scholarly journals Using the ITS2 transcribed spacer of nuclear ribosomal DNA to identify species of the genus Nitraria

2020 ◽  
Vol 24 ◽  
pp. 00009
Author(s):  
Evgeny V. Banaev ◽  
Tatiana A. Poliakova ◽  
Mariya A. Tomoshevich ◽  
Taigana Ak-Lama
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
High Importance ◽  
Single Nucleotide Deletion ◽  
Nucleotide Variability

Intragenomic polymorphism of ITS2 of nuclear ribosomal DNA sequences was analysed in 30 samples belonging to Nitraria schoberi, N. sibirica. The nucleotide variability of the ITS2 region was detected in the studied Nitraria species as single-nucleotide substitutions (mainly transitions) and single-nucleotide deletion. Five ribotypes of Nitraria were identified in Russia, Kazakhstan and Tajikistan. These ribotypes formed two haplogroups that belong to the species N. schoberi and N. sibirica, respectively. The high importance of the discriminatory role of the ITS2 spacer in identifying species of the genus Nitraria is confirmed.

Phylogenetic and genomic relationships in the genus Glycine Willd. based on sequences from the ITS region of nuclear rDNA

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 57-68 ◽  
Author(s):  
Krishna P. Kollipara ◽  
Ram J. Singh ◽  
Theodore Hymowitz
Keyword(s):  
Sequence Variation ◽  
Glycine Soja ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Its Region ◽  
Nuclear Ribosomal Dna ◽  
Single Nucleotide ◽  
Nucleotide Sequence Variation ◽  
Genomic Relationships ◽  
Its1 And Its2

Phylogenetic relationships among all 18 species of the genus Glycine were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Pairwise sequence divergence values ranged from 0.2% (a single nucleotide) between Glycine max and Glycine soja to 8.6% between Glycine hirticaulis and Glycine falcata. The length of the ITS1 and ITS2 sequences ranged from 215 to 238 nucleotides and from 205 to 222 nucleotides, respectively, and that of 5.8S was 168 nucleotides across all the species. Phylogenetic analyses of the ITS region clearly resolved all the genomic groups that were established previously based on cytogenetic and biochemical studies. Based on this study, we assign new genome symbols: HH to Glycine arenaria, H1H1 to Glycine hirticaulis, H2H2 to Glycine pindanica, II to Glycine albicans, and I1I1 to Glycine lactovirens. Parsimony analysis of the entire ITS region, using subgenus Soja as outgroup, resulted in a trichotomy consisting of the clades: G. falcata (F genome), Glycine cyrtoloba and Glycine curvata (C genome), and all other species (A, B, D, E, H, and I genomes) of the subgenus Glycine.Key words: Glycine spp., soybean, genomes, ITS region, rDNA.

scholarly journals A Novel Test System for Genotyping rs43703016 Single-nucleotide Substitutions in the Bovine CSN3 Gene

2019 ◽  
pp. 1-5
Author(s):  
Svetlana Kovalchuk ◽  
Arina Tagmazyan ◽  
Eugene Klimov
Keyword(s):  
Nucleotide Substitution ◽  
Milk Proteins ◽  
Test System ◽  
Nucleotide Polymorphisms ◽  
Dna Testing ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Allele Specific ◽  
Selection Of

Aims: Caseins are among the main milk proteins that determine many of its properties. Bovine kappa-casein (CSN3) is associated with the qualitative composition of milk, as well as with the quality of cheese obtained from this milk. The rs43703016 single-nucleotide substitution (g.88532332A>C; Asp148Ala) in exon 4 of the bovine CSN3 gene plays an important role in the production of quality hard cheeses. Various methods for the DNA testing of this substitution have been developed in the last three decades. Emergent DNA technologies provide an opportunity to modernize methods of genotyping single-nucleotide polymorphisms. Results: We have developed and verified a method to differentiate A/C alleles of the rs43703016 substitution in the bovine CSN3 gene by real-time PCR using allele-specific fluorescent probes. Conclusion: Our new method allows fast genotyping of animals, and may be used for selection of cows carrying the CC genotype, which determines good cheese-making properties of milk.

Peucedanum huangshanense (Apiaceae), a new species from Anhui, China

Phytotaxa ◽  
2020 ◽  
Vol 430 (1) ◽  
pp. 17-24
Author(s):  
SHAN-SHAN CHU ◽  
DE-QUN WANG ◽  
HUA-SHENG PENG ◽  
LU-QI HUANG
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Position ◽  
A New Species

Peucedanum huangshanense, a new species discovered in Anhui, China, is illustrated and described. Detailed morphological comparisons have showed that it is similar to P. praeruptorum but differs from the latter by having larger compound umbels (5–14 cm across), rays up to 25, and long-ovoid mericarps with lateral ribs narrowly winged. To explore the phylogenetic position of this species, nuclear ribosomal DNA internal transcribed spacer (ITS) region was sequenced for P. huangshanense and P. praeruptorum collected in different places. The morphological and molecular evidences support the hypothesis that P. huangshanense is a new distinct species.

scholarly journals POLYMORPHISMS IN THE GENES OF REPARATIONS AMONG EMPLOYEES OF THE ATOMIC INDUSTRY OF KAZAKHSTAN

2020 ◽  
Vol 1 (337) ◽  
pp. 5-10
Author(s):  
D. M. Botbаeyev ◽  
А. M. Belkozhаev ◽  
A. K. Khanseitova ◽  
A. Zh. Borbayeva ◽  
N. А. Аitkhozhinа
Keyword(s):  
Nuclear Industry ◽  
Repair System ◽  
Nucleotide Polymorphisms ◽  
Low Dose Radiation ◽  
Nucleotide Substitutions ◽  
Single Nucleotide ◽  
Variable Regions ◽  
And Control ◽  
Dose Radiation

Single nucleotide polymorphisms (SNPs) are the most convenient marker and the widespread subject of polymorphism testing. To identify the presence or absence of the effects of chronic low-dose radiation on nuclear industry personnel, the occurrence of single-nucleotide substitutions at the polymorphic sites of the genes of the repair system 3 and 6 of the introns of the APC gene P53.11 gene, in positions -2549 of the VEGF gene, XPD gene rs313181 ( Lys751Gln) and rs25487 of the XRCC gene (Аrg399Gln) were compared. Analysis of allele frequencies and distribution of genotypes in the variable regions of the tested genes was performed by the method of polymerase chain reaction (PCR), followed by determination of restriction fragment length polymorphism (RFLP). When com-paring the frequencies of alleles and the distribution of genotypes between the second group of miners (11–20 years’ experience) and control, differences in the distribution of genotypes in the rs25487 XRCC plot (χ2 = 7.11, p = 0.028) were revealed. These differences satisfy the criterion p <0.05 and, accordingly, are statistically significant. Key words: polymorphism, genes, a nuclear industry.

scholarly journals Whole-Genome Sequencing of a Year-Round Fruiting Jackfruit Variety Reveals Very High Single Nucleotide Polymorphisms in Inter-Genic Regions

2021 ◽  
Author(s):  
Tofazzal Islam ◽  
Nadia Afroz ◽  
ChuShin Koh ◽  
M. Nazmul Haque ◽  
Md. Jillur Rahman ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genome Sequence ◽  
De Novo ◽  
Agricultural Research ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tropical Fruit

Abstract Background Jackfruit (Artocarpus heterophyllus Lam.) is a tropical and sub-tropical fruit tree distributed in Asia, Africa, and South America. It is the national fruit of Bangladesh and produces fruit in the summer season only. However, a year-round jackfruit variety, BARI Kanthal-3 developed by Bangladesh Agricultural Research Institute (BARI) provides fruits from September to June. This study aimed to evaluate the agronomic performance of BARI Kanthal-3 and to generate a draft whole genome sequence to obtain molecular insights of this important unique variety. Results Number of fruits, average each fruit weight, fruit yield per plant, edible portion in fruit and ß carotene content of BARI Kanthal-3 (n = 5) were 422/plant/year, 5.60 kg, 236.32 kg/year, 53.5% and 3614 mg/100g, respectively. During de novo assembly, 817.7 Mb of the BARI Kanthal-3 genome was scaffolded. However, in the reference-guided genome assembly, almost 843 Mb of the BARI Kanthal-3 genome was scaffolded. Through BUSCO assessment, 97.2% of the core genes were represented in the assembly with 1.3% and 1.5% either fragmented or missing, respectively. By comparing the single copy orthologues (SCOs) in three closely and one distantly related species of BARI Kanthal-3, 706 SCOs were found to be shared across the genomes of the five species. The phylogenetic analysis of the shared SCOs showed that A. heterophyllus is the closest species to BARI Kantal-3. The estimated genome size of BARI Kanthal-3 was 1.04 giga base pairs (Gbp) with a heterozygosity rate of 1.62%. The estimated GC content was 34.10%. Variant analysis revealed that BARI Kanthal-3 includes 5.7 M (35%) and 10.4 M (65%) simple and heterozygous single nucleotide polymorphisms (SNPs), and about 90% of all these polymorphisms are located in inter-genic regions. Conclusion The whole-genome sequence of A. heterophyllus cv. BARI Kanthal-3 reveals extremely high single nucleotide polymorphisms in inter-genic regions. The findings of this study will help better understanding the evolution, domestication, phylogenetic relationships, year-round fruiting and the markers development for molecular breeding of this highly nutritious fruit crop.

scholarly journals DNAbased detection of western gall rust

2004 ◽  
Vol 57 ◽  
pp. 146-150 ◽  
Author(s):  
T.D. Ramsfield ◽  
D.R. Vogler
Keyword(s):  
Ribosomal Dna ◽  
Internal Transcribed Spacer ◽  
Rust Fungus ◽  
Its Region ◽  
Pcr Primers ◽  
Host Tissue ◽  
Nuclear Ribosomal Dna ◽  
Infected Host ◽  
The Novel ◽  
Pcr Product

The internal transcribed spacer (ITS) region of the nuclear ribosomal DNA of the western gall rust fungus (Peridermium harknessii) was amplified using the basidiomycetespecific PCR primers ITS1F and ITS4B The PCR product was then sequenced and aligned with other pine stem rust ITS sequences and a conserved region within P harknessii was targeted with the novel PCR primer Phar1 Our PCR protocol was able to differentiate P harknessii from Cronartium comandrae and C coleosporioides and detected P harknessii within infected host tissue However P harknessii was not distinguishable from C quercuum fsp fusiforme The method provides a rapid and sensitive detection protocol for P harknessii and C quercuum fsp fusiforme within infected host tissue

scholarly journals Functionally Significant Features in the 5′ Untranslated Region of the ABCA1 Gene and Their Comparison in Vertebrates

Cells ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 623 ◽  
Author(s):  
Dvorak ◽  
Leupen ◽  
Soucek
Keyword(s):  
Gene Evolution ◽  
Gc Content ◽  
Point Of View ◽  
Open Reading Frames ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Regulate Gene Expression ◽  
Abca1 Gene ◽  
Atp Binding Cassette Transporter ◽  
Structure Conservation

Single nucleotide polymorphisms located in 5′ untranslated regions (5′UTRs) can regulate gene expression and have clinical impact. Recognition of functionally significant sequences within 5′UTRs is crucial in next-generation sequencing applications. Furthermore, information about the behavior of 5′UTRs during gene evolution is scarce. Using the example of the ATP-binding cassette transporter A1 (ABCA1) gene (Tangier disease), we describe our algorithm for functionally significant sequence finding. 5′UTR features (upstream start and stop codons, open reading frames (ORFs), GC content, motifs, and secondary structures) were studied using freely available bioinformatics tools in 55 vertebrate orthologous genes obtained from Ensembl and UCSC. The most conserved sequences were suggested as hot spots. Exon and intron enhancers and silencers (sc35, ighg2 cgamma2, ctnt, gh-1, and fibronectin eda exon), transcription factors (TFIIA, TATA, NFAT1, NFAT4, and HOXA13), some of them cancer related, and microRNA (hsa-miR-4474-3p) were localized to these regions. An upstream ORF, overlapping with the main ORF in primates and possibly coding for a small bioactive peptide, was also detected. Moreover, we showed several features of 5′UTRs, such as GC content variation, hairpin structure conservation or 5′UTR segmentation, which are interesting from a phylogenetic point of view and can stimulate further evolutionary oriented research.

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