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Vol 20, No 2 (2022)

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Genetic basis of ecosystems evolution

Contribution of the intron retained in the Nxf1 gene transcript to the phylogeny of the order Chiroptera

Bondaruk D.D., Golubkova E.V., Mamon L.A.


This work is devoted to the possibilities of using a specific intron-containing block of the Nxf1 gene in phylogenetic studies.

Our attention was drawn to the conservative intron of the Nxf1 (nuclear export factor) gene. This intron is a part of an evolutionarily conserved block formed with flanking 110 bp and 37 bp exons, similar in representatives of various taxonomic groups. This evolutionary conservative block in our previous works was designated “cassette intron”. The Nxf1 genes are found in all representatives of Opisthokonta, and may be a convenient object for phylogenetic studies.

The Nxf1 gene sequences of seventeen representatives of the order Chiroptera obtained from publicly available databases (ensembl, ncbi). Alignment algorithm: MUSCLE. Programs: MEGA-X version 10.1.7, IQTree, Mesquite, MrBayes, and FigTree.v1.4.4. Estimation methods: Maximum Likelihood and Bayes Inference.

The use of Nxf1 gene sequences that include only exons or only introns leads to unequal loss of accuracy in establishing evolutionary relationships in comparison with the model based on the complete gene sequence. Sequences involving all exons plus a cassette intron give the same result as the complete Nxf1 gene sequence.

The obtained results indicate the importance of the cassette intron in the evolution of the Nxf1 gene of Chiroptera.

Ecological genetics. 2022;20(2):73-88
pages 73-88 views

DNA-metabarcoding analyses of the grapevine wood fungal community in the Krasnodar Region and Crimea

Blinova S.A., Shvartsev A.A., Alekseev Y.I., Stranishevskaya E.P., Ilnitskaya E.T., Makarkina M.V., Soloviev A.A.


Grapes are an economically important agricultural plant. Studies of the Grapevine microbiota and rhizosphere have become increasingly important in the last decade. The importance of such research is also supported by the fact that grapes are a perennial, long-used crop.

In this work, we present the results of a DNA-metabarcoding analysis of the fungal community of grape wood, collected from vineyards in the Krasnodar Territory and the Southern Coast of Crimea, and considered approaches to the analysis of DNA-metabarcoding data. Classifier is Naïve base (“sklearn”) based on machine learning is more informative metagenomic data classifier than BLAST+ (local alignment) and Vsearch (global alignment). Analysis of the ITS locus revealed the largest number of taxa, which was confirmed for all types of classifiers used in the study. Primers for the ITS locus showed a high specificity of fungal DNA in comparison with the LSU and SSU loci. The most common genera in the fungal community are Acidea, Alternaria, Cladosporium and Fusarium. Significant differences were revealed in the assessment of alpha and beta diversity in the analysis of samples from different regions. This article presents an analysis of the wood grapevine fungal community and ways to ASV classification. This study is the first to describe the endophytic fungal communities of the Krasnodar Territory and the Crimea vines using the analysis of DNA metabarcoding data.

Ecological genetics. 2022;20(2):89-100
pages 89-100 views

Identification of the eam8 allele associated with photoperiod insensitivity in barley accessions from Japan

Zveinek I.A., Abdullaev R.A., Matvienko I.I., Radchеnko E.E., Alpatieva N.


BACKGROUND: Cultivated plants grown in the northern regions of Russia are subject to strict requirements in terms of their ability to produce a high yield during short growing season. Important adaptive traits that affect crop yield are early maturity and insensitivity to photoperiod. The search and involvement in breeding programs of new sources of these valuable traits is a necessary step for the creation of new ecologically plastic varieties.

THE AIM: To identify alleles of the Eam8 gene, which determine weak photoperiodic sensitivity, among Japanese barley accessions from the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) collection.

MATERIALS AND METHODS: Screening of 200 barley accessions from Japan was carried out in a climatic chamber in order to identify plants with yellow color of seedlings — a marker sign of the influence of the eam8 allele, which controls early maturity and low sensitivity to the photoperiod. The presumably photoperiod-insensitive accession was studied under conditions of long and short photoperiods and was studied by molecular methods.

RESULTS: Phenotypic screening identified a presumably photoperiod-insensitive accession k-17545 (Jap.456). The photoperiodic sensitivity of the accession and the variety Mari (carrier of the recessive eam8 allele) were similar. Using molecular analysis, the eam8.k allele, occurred naturally in the cultivars Kinai 5 and Kagoshima Gold from Japan, was found in the k-17545 line. The Jap.456 was polymorphic by srorage proteins (hordein) patterns and RAPD profiles. In addition, previously undescribed SNPs in the eam8.k sequence were identified in individual plants.

CONCLUSIONS: As a result of the study of 200 accessions of barley from Japan, accession k-17545 (Jap.456) was found, in which the eam8.k allele was identified, which controls weak sensitivity to the photoperiod.

Ecological genetics. 2022;20(2):101-109
pages 101-109 views

Human ecological genetics

Telomeres as dynamic structures of human genome: the effect of endogenous and exogenous factors

Krapivin M.I., Sagurova Y.M., Efimova O.A., Tikhonov A.V., Pendina A.A.


In this review, we summarize data on the structural and functional characteristics of human telomeres and analyze how endo- and exogenous factors influence telomere length. We elucidate the history of telomere investigation, describe their structure and functions, methods of their study. We also characterize the mechanisms of telomere lengthening and shortening. We discuss in detail endo- and exogenous factors affecting telomere length during gametogenesis, embryogenesis and in the postnatal period of human development. We describe how oxidative stress influences telomere length through guanine oxidation, single-strand breaks in DNA, decrease of telomerase activity and suppression of recombination in telomeric sequences. We conclude that the multidirectional effect of various factors, both sporadic and determined by the developmental program, ensures the dynamic equilibrium of telomere length. A shift in this balance due to increased influence of one or several factors can lead to telomere lengthening or shortening. Understanding the mechanisms underlying the telomere length changes and the critical periods of exposure to both protective and negative factors is important to contribute to the knowledge about telomere functions and to develop approaches of telomere length correction.

Ecological genetics. 2022;20(2):111-140
pages 111-140 views

Opinions, discussions

On spontaneity, variability and directed evolution. Whether it is necessary to push foreheads inherited or acquired features?

Daev E.V.


It seems, that historically the problem of oppose inherited features vs acquired is mainly two-causes problem. The first is an insufficient knowledge about mechanisms how acquired phenotypic feature could became inherited.

The second is semiotic or more precisely semantic. Any “language itself contained the seeds of the problem” because of ambiguous interpreting of same terms by different scientists. Human specific understanding of any term, which depends on their different education, specificity of different languages, usage of metaphors and analogies, etc., create “unintended illusions” of real truth.

This brief theoretical study attempts to consider adaptively significant traits as gradually moving from the category of non-heritable to heritable ones. The conceptual approach used makes it possible to erase the contradictions between the interrelated concepts of “acquired” and “inherited” features.

Ecological genetics. 2022;20(2):141-150
pages 141-150 views

Phylogeny problems of the genus Vaccinium L. and ways to solve them

Zhidkin R.R., Matveeva T.V.


The genus Vaccinium includes almost 500 species, among which there are economically important species of cranberries V. macrocarpon Ait. and V. oxycoccos L., lingonberries V. vitis-idaea L., bilberries V. myrtillus L. and blueberries V. uliginosum L., V. angustifolium Ait., V. corymbosum L., V. virgatum Ait. Despite the fact that many of these species were actively used by humans in medicine and food, their active selection began in the 20th century, in connection with which a classification of the genus according to morphological characters was developed. Many of these data remain relevant to the present day. The development of the ideas of molecular phylogeny prompted a revision of the old classification, identifying a number of difficulties that do not allow one to unambiguously determine phylogenetic relationships within the genus. Today, the genus includes 33 sections, while the species composition of the sections and the evolutionary relationships between them remain controversial. This review discusses various approaches to the study of the structure of the genus Vaccinium: from classical to phylogenomic, the main results of using these approaches and their prospects.

Ecological genetics. 2022;20(2):151-164
pages 151-164 views

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