Nucleotide Sequence Of DNA Research Articles

Скрещивались ли неандертальцы массово с кроманьонцами? (С палеодилетантской точки зрения, но с учетом данных полногеномного секвенирования образцов современной и древней ДНК, а также на основе знаний используемых для этого технологий)

Neanderthals lived on the territory of present-day Western Europe for about 300 thousand years before the arrival of people of modern anatomical type, also called Cro-Magnons, about 50 thousand years ago. After that Neanderthal soon disappeared and what happened to them occupies the minds of many generations of paleoanthropologists, and over the years a large number of different versions have been put forward, according to one of which there was assimilation of Neanderthals by Cro-Magnons, which in fact does not correspond to reality. To the question whether interbreeding of these ancient hominins took place, one can confidently say only one thing – Neanderthal women did not contribute to the populations of modern humans, as can be seen from the differences in the nucleotide DNA sequences of inherited matrilineal mitochondrial genomes in Neanderthals and modern humans. The presence of some allelic variants of individual Neanderthal genes in the form of a number of single-nucleotide substitutions in the genomes of modern humans, detected by full-genome sequencing of nuclear DNA is still necessary an additional verification, which requires sequencing a larger number of complete genomes of ancient hominins with a large coverage. At the same time, the samples of modern genomes for such an analysis should be thoroughly increased, since only now about 8 billion very different modern unique "genomes" “live” on the Planet, and at least 100 million Neanderthals lived for all the years, also carrying unique genomes, although their polymorphism was somewhat lower. The article focuses on the fact that only diploid variant of genome, which can be designated as 6.0, should be considered a complete genome for human, whereas all currently sequenced genomes of ancient people are essentially quasi-haploid and can be designated as 3.0, based on the numbers of billions of pairs of nitrogenous bases in both double and single a set of chromosomes, respectively. Accordingly, the coverage during genome sequencing should be recalculated for their diploid status but not only for ancient organisms. It is also noted that the sequencing of ancient DNA urgently requires the development of new monomolecular sequencing methods, albeit characterized by lower productivity (speed), but independent of any stage of amplification and any enzymatic treatments, which will allow to establish the sequence of nucleotides as it is, including the recognition of uracils and other modifications of nitrogenous bases, as well as the absence of these in the DNA chains, which will certainly increase the accuracy of this process.

Technological Approaches in the Analysis of Extracellular Vesicle Nucleotide Sequences.

Together with metabolites, proteins, and lipid components, the EV cargo consists of DNA and RNA nucleotide sequence species, which are part of the intracellular communication network regulating specific cellular processes and provoking distinct target cell responses. The extracellular vesicle (EV) nucleotide sequence cargo molecules are often investigated in association with a particular pathology and may provide an insight into the physiological and pathological processes in hard-to-access organs and tissues. The diversity and biological function of EV nucleotide sequences are distinct regarding EV subgroups and differ in tissue- and cell-released EVs. EV DNA is present mainly in apoptotic bodies, while there are different species of EV RNAs in all subgroups of EVs. A limited sample volume of unique human liquid biopsy provides a small amount of EVs with limited isolated DNA and RNA, which can be a challenging factor for EV nucleotide sequence analysis, while the additional difficulty is technical variability of molecular nucleotide detection. Every EV study is challenged with its first step of the EV isolation procedure, which determines the EV’s purity, yield, and diameter range and has an impact on the EV’s downstream analysis with a significant impact on the final result. The gold standard EV isolation procedure with ultracentrifugation provides a low output and not highly pure isolated EVs, while modern techniques increase EV’s yield and purity. Different EV DNA and RNA detection techniques include the PCR procedure for nucleotide sequence replication of the molecules of interest, which can undergo a small-input EV DNA or RNA material. The nucleotide sequence detection approaches with their advantages and disadvantages should be considered to appropriately address the study problem and to extract specific EV nucleotide sequence information with the detection using qPCR or next-generation sequencing. Advanced next-generation sequencing techniques allow the detection of total EV genomic or transcriptomic data even at the single-molecule resolution and thus, offering a sensitive and accurate EV DNA or RNA biomarker detection. Additionally, with the processes where the EV genomic or transcriptomic data profiles are compared to identify characteristic EV differences in specific conditions, novel biomarkers could be discovered. Therefore, a suitable differential expression analysis is crucial to define the EV DNA or RNA differences between conditions under investigation. Further bioinformatics analysis can predict molecular cell targets and identify targeted and affected cellular pathways. The prediction target tools with functional studies are essential to help specify the role of the investigated EV-targeted nucleotide sequences in health and disease and support further development of EV-related therapeutics. This review will discuss the biological diversity of human liquid biopsy–obtained EV nucleotide sequences DNA and RNA species reported as potential biomarkers in health and disease and methodological principles of their detection, from human liquid biopsy EV isolation, EV nucleotide sequence extraction, techniques for their detection, and their cell target prediction.

Phylogenetic position of Phlojodicarpus villosus (Apiaceae) based on ITS and trnH-psbA nucleotide sequences

The aim of our work was to obtain chloroplast (trnH-psbA) and nuclear (ITS1-ITS2) DNA nucleotide sequences and identify the phylogenetic position of Phlojodicarpus villosus (Apiaceae). This species of vascular plants is represented in the Urals by isolated relic populations and is included in the regional Red Data Books. There is no data on P. villosus nucleotide sequences in the international open genetic databases. We studied two herbarium specimens of P. villosus, one collected from the Ural part of its range in the Komi Republic (Northern Urals) and the second collected from the main part of its range in the Magadan Region (Kolyma Highlands). Combining nuclear and chloroplast markers made it possible to reliably determine phylogenetic position of P. villosus within the tribe Selineae (subfamily Apioideae, family Apiaceae). We found ITS1-ITS2 and trnH-psbA nucleotide sequences to be sufficiently informative to identify specimens of this genus. High polymorphism of P. villosus sequences obtained from different parts of its range (Northern Urals and Kolyma Highlands) and the presence of evolutionary events (deletions) require more detail study of P. villosus and other Phlojodicarpus taxa by DNA barcoding methods.

On the Application of the Critical Chromatography Concept for Investigation of the Nucleotide Sequence of Single-Stranded DNA

On the Application of the Critical Chromatography Concept for Investigation of the Nucleotide Sequence of Single-Stranded DNA

New Method for Sequence Similarity Analysis Based on the Position and Frequency of Statistically Significant Repeats

Background: The analysis of DNA nucleotide sequence similarity among different species is crucial in identifying their functional, structural or evolutionary relationships. The number of bioinformatics tools designed to perform the similarity analysis of nucleotide sequences has been growing rapidly. According to the current literature, alignment-free methods have not been performed on repetitive nucleotide sequence of different lengths. Objective: To develop a new algorithm for determining sequence characteristics and similarity based on statistically significant repetitive elements of different lengths, which are located in analyzed sequences. Methods: This paper presents Repeats-Position/Frequency method (R-P/F method), for determining nucleotide sequence similarity which takes into consideration statistically significant repetitive parts of analyzed sequences. It is based on information theory and the fact that both position and frequency of repeated sequences are not expected to occur with the identical presence in a random sequence of the same length. Nucleotide sequences are presented in rn-dimensional vector space and their hierarchy is constructed by applying hierarchical clustering algorithm. Results: R-P/F method has been validated on multiple data sets of nucleotide sequences and compared with results obtained from alignment-based algorithms BLAST and Clustal Omega, and multiple wellestablished alignment-free dissimilarity measures. Presented method provides results comparable with other commonly used methods focused on resolving the same problem, with the novel view on the used repetitive parts of sequences in these calculations. Conclusion: The presented, novel algorithm for calculating sequence similarity measure is effective in discovering relationships among the sequences and makes a powerful and complementary addition to existing sequence similarity methods.

Epigenetics is Promising Direction in Modern Science

Abstract Epigenetics studies the inherited changes in a phenotype or in expression of genes caused by other mechanisms, without changing the nucleotide sequence of DNA. The most distinguished epigenetic tools are: modifications of histones, enzymatic DNA methylation, and gene silencing mediated by small RNAs (miRNA, siRNA). The resulting m5C residues in DNA substantially affect the cooperation of proteins with DNA. It is organized by hormones and aging-related alterations, one of the mechanisms controlling sex and cellular differentiation. DNA methylation regulates all genetic functions: repair, recombination, DNA replication, as well as transcription. Distortions in DNA methylation and other epigenetic signals lead to diabetes, premature aging, mental dysfunctions, and cancer.

First molecular detection of Anaplasma species in cattle from Kyrgyzstan; molecular identification of human pathogenic novel genotype Anaplasma capra and Anaplasma phagocytophilum related strain

Anaplasmosis is a rickettsial infection with significant effects on human and animal health, and the discovery of new species or genotypes with zoonotic potential in recent years has increased this importance. The aim of this study was to provide the first assessment of the molecular etiology and prevalence of bovine anaplasmosis in Kyrgyzstan (specifically in the Chuy, Talas, Djalal-Abad, Naryn, and Issyk-Kul regions). The prevalence of bovine anaplasmosis was determined as 1.7% (6/358). PCR and partial DNA sequencing results of the 16S ribosomal RNA (rRNA) gene revealed that Anaplasma centrale, A. phagocytophilum like-1, and the human pathogenic novel genotype A. capra are circulating in cattle herds in Kyrgyzstan. Six DNA nucleotide sequences obtained in this study were deposited in GenBank under the following accession numbers: A. centrale (MW672117, MW672118, MW672119, MW672120), A. phagocytophilum (MW672121), and A. capra (MW672115).

DNA sequence and methylation prescribe the inside-out conformational dynamics and bending energetics of DNA minicircles.

Eukaryotic genome and methylome encode DNA fragments’ propensity to form nucleosome particles. Although the mechanical properties of DNA possibly orchestrate such encoding, the definite link between ‘omics’ and DNA energetics has remained elusive. Here, we bridge the divide by examining the sequence-dependent energetics of highly bent DNA. Molecular dynamics simulations of 42 intact DNA minicircles reveal that each DNA minicircle undergoes inside-out conformational transitions with the most likely configuration uniquely prescribed by the nucleotide sequence and methylation of DNA. The minicircles’ local geometry consists of straight segments connected by sharp bends compressing the DNA’s inward-facing major groove. Such an uneven distribution of the bending stress favors minimum free energy configurations that avoid stiff base pair sequences at inward-facing major grooves. Analysis of the minicircles’ inside-out free energy landscapes yields a discrete worm-like chain model of bent DNA energetics that accurately account for its nucleotide sequence and methylation. Experimentally measuring the dependence of the DNA looping time on the DNA sequence validates the model. When applied to a nucleosome-like DNA configuration, the model quantitatively reproduces yeast and human genomes’ nucleosome occupancy. Further analyses of the genome-wide chromatin structure data suggest that DNA bending energetics is a fundamental determinant of genome architecture.

Paraharmotrema karinganiense n. gen., n. sp. (Digenea: Liolopidae) infecting the intestine of serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger), and South African helmeted turtle (Pelomedusa galeata) and a phylogenetic hypothesis for liolopid genera.

We herein describe Paraharmotrema karinganiense n. gen., n. sp. Dutton & Bullard (Liolopidae Dollfus, 1934) from specimens infecting the intestine of the serrated hinged terrapin (Pelusios sinuatus), east African black mud turtle (Pelusios subniger) (both Nwanedzi River, Mozambique), and South African helmeted terrapin (Pelomedusa galeata) (North-western Zululand, KwaZulu-Natal Province, South Africa). The new genus can be easily differentiated from the other accepted liolopid genera (Liolope Cohn, 1902; Helicotrema Odhner, 1912; Harmotrema Nicoll, 1914; Dracovermis Brooks & Overstreet, 1978) by the combination of having a linguliform body approximately 6–9 × longer than wide, tegumental spines/scales, a minute ventral sucker located in the anterior 1/7−1/8 of the body, deeply lobed testes that are transverse and abut the caeca (spanning the intercaecal space), a uterus that is lateral to the anterior testis (not ventral to the anterior testis), a lobed ovary that is dextral and nearest the posterior testis, and a vitellarium that does not extend anteriad to the level of the ventral sucker and that does not fill the intercaecal space. Nucleotide sequences of large subunit ribosomal DNA (28S) and internal transcribed space region (ITS2) from all analyzed specimens of the new species were identical, respectively; the 28S sequences differed from that of Liolope copulans Cohn, 1902 and from that of Harmotrema laticaudae Yamaguti, 1933 by 103 (8%) and 105 (8%) nucleotides, respectively. The 28S phylogenetic analysis recovered the new genus sister to a clade comprising L. copulans and H. laticaudae. A key to liolopid genera is provided herein. The present study comprises the first nucleotide-based phylogenetic placement of Harmotrema and first record of a liolopid from South Africa or Mozambique. It is the first proposal of a new liolopid genus in 43 yrs, and it documents a second liolopid genus from P. subniger while tripling the number of liolopid turtle hosts reported from the continent of Africa.

The complete mitochondrial genome and phylogenetic analysis of Neorhodomela munita

Neorhodomela munita (Perestenko) Masuda 1982 is distributed in the coastal areas of Shandong and Liaoning in China, and also in Japan. In this study, the complete nucleotide sequence of the circular mitochondrial DNA of the red alga Neorhodomela munita has been determined. The complete mitochondrial DNA sequence of Neorhodomela munita was 25,318 bp in length with an overall GC content of 25.1% and encoded 23 protein-coding genes, two ribosomal RNAs and 24 transfer RNAs. Phylogenetic tree showed that Neorhodomela munita clustered together with Choreocolax polysiphoniae. The phylogenetic analysis may provide a better understanding of the evolution of the Rhodophyta species.

Algebraic harmony and probabilities in genomes. Long-range coherence in quantum code biology

According to the founders of quantum mechanics and quantum biology P. Jordan and E. Schrödinger, the main difference between living and inanimate objects is the dictatorial influence of genetic molecules on the whole living organism. Code biology can make a valuable contribution to understanding this dictatorial influence of genetic molecules whose ensemble is endowed with many interconnected alphabets and codes. The paper is devoted to probability rules of nucleotide sequences of single-stranded DNA in eukaryotic and prokaryotic genomes. These rules are connected with n-plets alphabets of DNA whose nucleotide sequences are considered as bunches of many parallel texts written in interconnected n-plets alphabets. The rules draw attention to genomic phenomena of special tetragroupings of n-plets and new genomic symmetries. A generalization of the second Chargaff's rule is described. They show the existence of long-range coherence in genomic DNA sequences and reveal new connections of structural features of genomic sequences with formalisms of quantum mechanics and quantum informatics. The author supposes that the received results are related to the known vibration-resonance theory of G. Frohlich about long-range coherence in biological systems, that is, about collective quantum effects there. The possible influence of the described genetiс probability phenomena on the genetically inherited physiological structures is noted and discussed.

A revised circumscription and clarification of the taxonomic position of Miconia tetrazygioides (Melastomataceae: miconieae): an endemic to the Massif de la Hotte, Haiti

An investigation of the type material of Miconia tetrazygioides indicates that this species, only known from the type gathering (Ekman H10684), is conspecific with the recently described M. cineana. The two differ vegetatively in no significant characters, showing only a slight difference in the range in variation of leaf width, shape, apex, and margin. The species has been poorly collected, with only a total of five gatherings known, and flowers have yet to be collected; it is endemic to the Massif de la Hotte, of Haiti, occurring in rak bwa from 930 to 1300 m. DNA nucleotide sequences indicate that the species is related to those of the M. decorticans clade, which have moderate-sized to large flowers with more or less constricted hypanthia/calyces. Traditionally, most species of the M. decorticans clade were included within Tetrazygia or Pachyanthus. In contrast the reproductive parts, e.g., calyx, hypanthium, ovary, and fruit, of M. tetrazygioides (incl. M. cineana) are quite small, and its hypanthia/calyces are not constricted, which is why it was originally circumscribed under Miconia rather than the other two mentioned genera.

Existence of genetic lineages within Asian genotype of Taenia solium-Genetic characterization based on mitochondrial and ribosomal DNA markers.

Taenia solium cysticercosis is a potentially eradicable neglected zoonotic disease with public health importance. The genetic lineages of T.solium in Asia and Africa/America are distinct and the genetic composition of the parasite was found to influence the clinical symptoms in patients with cysticercosis. In the present study, the Cysticerci collected from pigs of two southern states of India (Karnataka and Andhra Pradesh) were genetically characterized based on mitochondrial (COX 1 and Cyt b) and ribosomal (ITS-1 and TBR) DNA markers. The study confirms the existence of two mitochondrial lineages of the parasite as Asian and African/American. Cytochrome oxidase 1 (COX 1) based analysis revealed the existence of two sub-lineages of the parasite within the Asian lineage based on the polymorphism at 994 position as 994A/G. In India, both the sub-lineages were identified and genetic divergence among different Indian isolates was evident. Further, the sequence analysis of Cytochrome B (Cyt b) revealed the existence of six sub-lineages of T.solium in India as 69T/69G, 97A/97G as well as 264T/264C. The analysis of nucleotide sequence of large subunit ribosomal DNA (TBR) revealed the existence of two sub-lineages in India based on the deletion of a nucleotide at 624th position. The cysts collected in the present study were more closely related to those of China and Indonesia than with other Indian isolates. Further, the sequence analysis did not indicate the presence of Taenia asiatica in the examined pigs and African/American lineages of T.solium. The results of the present study help to better understand the genetic diversity of T.solium in India.

Molecular identification of Haemaphysalis sulcata (Acari: Ixodidae) larval stages collected using the Berlese funnel in Northern Iran

Molecular detection techniques based on conventional PCR and sequencing of the partial genome of living organisms are considered an important tool for identification. BLASTn and comparison of evolutionary relationships between taxa are the next analysis steps on sequences. The construction of a phylogenetic tree is done using genetic distance difference; nucleotide substitution models and comparison with the outgroup. In the present study, two samples of tick larvae were collected in Mirafzal forest area (36°07'39.0N 53°35'45.0E) located in Mazandaran province, northern Iran using the Berlese funnel. Tick samples were initially identified using a generic identification key (Bregetova et al. 1955) and in order to determine specific identification of species, PCR of partial internal transcribed spacer 2 (ITS2) gene and Sanger sequencing were performed. Morphological results showed that tick samples belonged to Haemaphysalis genus because they had a relatively short capitulum, no eyes with festoons. DNA extraction, PCR amplification and sequencing of a partial fragment (ca. 1400-bp) ITS2 gene of tick sample were done, successfully. The results of BLASTn showed that the larvae belonged to the species Haemaphysalis sulcata. A nucleotide DNA sequence of ITS2 was submitted to GenBank under the accession number MW929218. The molecular technique of this study is recommended to identify immature and dead tick samples that cannot be reared until the adult stage. The present study was the first report on the identification of H. sulcata larvae isolated from the Berlese funnel. The result of this study will help to better understand the biology of this tick and the presence of immature larval stages with questing behaviour in the soil environment.

REDESCRIPTION OF CATHARIOTREMA SELACHII (MACCALLUM, 1916) JOHNSTON AND TIEGS, 1922 (MONOGENOIDEA: MONOCOTYLIDAE), EMENDATION OF MONOTYPIC CATHARIOTREMA JOHNSTON AND TIEGS, 1922, AND PROPOSAL OF CATHARIOTREMATINAE N. SUBFAM. BASED ON MORPHOLOGICAL AND NUCLEOTIDE EVIDENCE.

We herein redescribe the enigmatic Cathariotrema selachii (MacCallum, 1916) Johnston and Tiegs, 1922 based on the holotype, paratypes, and newly collected specimens infecting the olfactory organ of 5 shark species from the Gulf of Mexico (all new host records): scalloped hammerhead shark, Sphyrna lewini (Griffith and Smith, 1834) (Carcharhiniformes: Sphyrnidae); great hammerhead shark, Sphyrna mokarran (Rüppell, 1837); blacktip shark, Carcharhinus limbatus (Müller and Henle, 1839) (Carcharhiniformes: Carcharhinidae); spinner shark, Carcharhinus brevipinna (Müller and Henle, 1839); and Atlantic sharpnose shark, Rhizoprionodon terraenovae (Richardson, 1836) (Carcharhinidae). These specimens were morphologically indistinguishable from each other and from MacCallum's holotype and paratypes. Those sequenced had identical first internal transcribed spacer (ITS1) and large subunit ribosomal DNA (28S) nucleotide sequences. As such, C. selachii infects sharks of 2 orders (Carcharhiniformes, Lamniformes) and 3 families (Carcharhinidae, Sphyrnidae, Lamnidae) in the Northwestern Atlantic Ocean (type locality) and Gulf of Mexico (new records herein). This report is the first of new specimens of C. selachii in the Atlantic Ocean Basin in 95 yr and corrects long-standing error cascades and ambiguities concerning the morphology and systematic placement of C. selachii. Considering morphology and nucleotide-based phylogenetic evidence (28S, Bayesian analysis), we herein emend monotypic CathariotremaJohnston and Tiegs, 1922 and propose Cathariotrematinae Bullard n. subfam. for it and 4 other genera (all formerly assigned to Merizocotylinae Johnston and Tiegs, 1922). These genera comprise species infecting only the nose of sharks (monotypic Cathariotrema, SqualotremaKearn and Green, 1983 and SeptitremaKheddam, Chisholm, and Tazerouti, 2020 plus 3 species of TriloculotremaKearn, 1993) and nose of a chimaera (monotypic HolocephalocotyleDerouiche, Neifar, Gey, Justine, and Tazerouti, 2019). Cathariotrematinae differs from Merizocotylinae by having a 3-part attachment organ and by lacking open loculi that symmetrically encircle a cluster of >2 loculi in the center of the haptor. Monophyletic Cathariotrematinae (with sequences representing species of Cathariotrema, Triloculotrema, and Holocephalocotyle only) was sister to monophyletic Merizocotylinae, which together were sister to monophyletic Calicotylinae Monticelli, 1903. These subfamilies comprise a monophyletic group of monocotylids that have a double vagina and infect extrabranchial, enclosed niches (urogenital system, body cavity, olfactory chamber/nose) on their shark, ray, and chimaera hosts (all other monocotylids have a single vagina and infect the gill or body surfaces of rays only). Monocotylinae Taschenberg, 1879 and Decacotylinae Chisholm, Wheeler, and Beverley-Burton, 1995 were recovered as monophyletic. Heterocotylinae Chisholm, Wheeler, and Beverley-Burton, 1995 remained paraphyletic. We accept ParacalicotyleSzidat, 1970.

Population genetic structure of hard clam (Meretrix lyrata) along the Southern coast of Thailand

Abstract. Suppapan J, Sangthong P, Songrak A, Supmee V. 2021. Population genetic structure of hard clam (Meretrix lyrata) along the Southern coast of Thailand. Biodiversitas 22: 2489-2496. The hard clam (Meretrix lyrata), which is an economically important fishery item in Southern Thailand, has decreased rapidly due to overexploitation. To construct sustainable management of this species, genetic information is necessary. In our study, the genetic diversity of M. lyrata was investigated based on the variation of the nucleotide sequence (439 bp) of mitochondrial DNA (mtDNA) in the cytochrome oxidase subunit I gene (mtDNA COI). The mtDNA COI sequences of 145 individuals collecting from 6 sampling sites along the Southern coast of Thailand were analyzed. The results revealed that M. lyrata populations showed moderate to low levels of genetic diversity. All of the population genetic structure analysis revealed the genetic differentiation of the hard clam between the Gulf of Thailand and the Andaman Sea populations. Based on these results, a genetic structure of the hard clam M. lyrata in Southern Thailand was possibly caused by a disruptive gene flow from the geographic factors by the Thai-Malay Peninsula. The demographic history test revealed that the hard clam living in Southern Thailand had experienced population expansion. This study provided the first genetic information that could be used for conserving the hard clam M. lyrata in Southern Thailand.

Recurrent sequences and the harmonic progression in genetic biomechanics

The article is devoted to the study of new approaches to the development of mathematical models in genetic biomechanics, which studies the structural relationships of the genetic coding system with genetically inherited biological forms. More specifically, we are talking about models based on the recurrent harmonic progression known in science, the universal connection of which with the information sequences of DNA heredity molecules in the genomes of higher and lower organisms was revealed in the laboratory of biomechanical systems research at the IMASH RAS. This progression is associated with fundamental hyperbolic rules for organizing DNA nucleotide sequences of genomes and is represented on a two-dimensional Cartesian plane by a hyperbolic sequence associated with natural logarithms. The latter have long been used in science to adequately model many inherited biological phenomena. The article describes previously unknown connections of natural logarithms with the structure of the molecular genetic system. The problems of modeling biological phenomena in connection with the revealed structural properties of the molecular genetic system are discussed.

Global phylogeography of a pantropical mangrove genus Rhizophora

Rhizophora is a key genus for revealing the formation process of the pantropical distribution of mangroves. In this study, in order to fully understand the historical scenario of Rhizophora that achieved pantropical distribution, we conducted phylogeographic analyses based on nucleotide sequences of chloroplast and nuclear DNA as well as microsatellites for samples collected worldwide. Phylogenetic trees suggested the monophyly of each AEP and IWP lineages respectively except for R. samoensis and R. × selala. The divergence time between the two lineages was 10.6 million years ago on a dated phylogeny, and biogeographic stochastic mapping analyses supported these lineages separated following a vicariant event. These data suggested that the closure of the Tethys Seaway and the reduction in mangrove distribution followed by Mid-Miocene cooling were key factors that caused the linage diversification. Phylogeographic analyses also suggested the formation of the distinctive genetic structure at the AEP region across the American continents around Pliocene. Furthermore, long-distance trans-pacific dispersal occurred from the Pacific coast of American continents to the South Pacific and formed F1 hybrid, resulting in gene exchange between the IWP and AEP lineages after 11 million years of isolation. Considering the phylogeny and phylogeography with divergence time, a comprehensive picture of the historical scenario behind the pantropical distribution of Rhizophora is updated.

Уточнение видовой принадлежности некоторых видов щелкунов (Coleoptera: Elateridae) на основе молекулярно-генетического анализа

The article is devoted to data on the approbation of modern methods and the refinement of species affiliation of soil-inhabiting larvae of click beetles (wireworm) based on the molecular genetic analysis (DNAbarcoding). For the first time, data obtained on the complete identity of certain DNA sequences of a number of species of click beetles living in the Kostanay Region (Kazakhstan) — dangerous pests of agricultural crops. At the same time, the World genetic bank (GenBank) did not find identical DNA sequences of decoded DNA nucleotide sequences for a number of studied specimens. The basis for this study was the materials collected in 2018 in the subzone of ordinary black earth on sandy loam soils (Mendykarinsky district). The selection of larvae was carried out by the method of standard soil-zoological samples. The fixation and storage of the selected click beetles larvae was carried out according to the method of preparing samples for molecular genetic analysis with fixation in 96 % alcohol. After the classic identification of the taxonomic position of the collected specimens, the species were identified by genetic analysis on the nucleotide sequence of the cytochrome C oxidase I subunit gene (COI). The assembly and decoding of the DNA nucleotide sequences of the studied samples were carried out using the programs «Codon Code Aligner» and «MEGA-X». As a result of the work carried out in the DNA laboratory of the Museum of Natural History (University of Oslo, Norway), it was possible to identify the complete identity of the DNA sequences of several mass species of click beetles, while a number of decoded DNA sequences of model specimens were absent in the genetic bank, which requires replenishment in it with new data.

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic genetics is conventional Sanger sequencing; however, this is gradually being replaced by high-throughput sequencing (HTS) approaches which can generate millions of individual reads in a single experiment. HTS sequencing, which now dominates molecular biology research, has already been demonstrated for use in a number of forensic genetic analysis applications, including species identification. However, the generation of HTS data to date requires expensive equipment and is cost-effective only when large numbers of samples are analysed simultaneously. The Oxford Nanopore Technologies (ONT) MinION™ is an affordable and small footprint DNA sequencing device with the potential to quickly deliver reliable and cost effective data. However, there has been no formal validation of forensic species identification using high-throughput (deep read) sequence data from the MinION making it currently impractical for many wildlife forensic end-users. Here, we present a MinION deep read sequence data validation study for species identification. First, we tested whether the clustering-based bioinformatics pipeline NGSpeciesID can be used to generate an accurate consensus sequence for species identification. Second, we systematically evaluated the read variation distribution around the generated consensus sequences to understand what confidence we have in the accuracy of the resulting consensus sequence and to determine how to interpret individual sample results. Finally, we investigated the impact of differences between the MinION consensus and Sanger control sequences on correct species identification to understand the ability and accuracy of the MinION consensus sequence to differentiate the true species from the next most similar species. This validation study establishes that ONT MinION sequence data used in conjunction with the NGSpeciesID pipeline can produce consensus DNA sequences of sufficient accuracy for forensic genetic species identification.