—The study of molecular and genetic mechanisms of sex determination in the poplar is of interest not only in the fundamental science, but also in the applied research. In landscaping of large ...settlements, it is advisable to use male individuals of the
Populus
genus due to their hypoallergenicity and increased resistance to environmental pollution, stress conditions, and pathogens. However, sex determination in poplars is complicated by the complex genetic structure of the sex-determining region of the genome (SDR). In this review, the emergence, evolution, structure, and function of the SDR in the genus
Populus
are discussed. Current insights into the structure and function of the key regulator of sex selection in poplars, orthologue of the
ARR16
/
ARR17
gene and the possible roles of other genes that are differentially expressed between male and female plants, including microRNAs, in this process are discussed in detail. The great diversity of species and the high complexity of SDR organization justify the need for further study of the molecular mechanisms of sex determination in poplars.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Regulation of gene expression via microRNA is the key mechanism of response to biotic and abiotic stresses in plants. There are a lot of experimental data on the biological function of microRNAs in ...response to different stresses in various plant species. This review contains up-to-date information on molecular mechanisms of microRNA action in plants in response to abiotic stresses, including drought, salinity, mineral nutrient deficiency or imbalance.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Understanding the molecular mechanisms of plant response to unfavorable conditions is necessary for the effective selection of tolerant genotypes. Earlier, using high-throughput transcriptome ...sequencing of flax plants after exposure to aluminum ions (Al
3+
) and high soil acidity, we detected stress-induced alteration in the expression of several genes, including
CAX3
, which encodes Ca
2+
/H
+
-exchanger involved in calcium ion transport. Here we describe
CAX3
mRNA levels in flax cultivars either tolerant (Hermes and TMP1919) or sensitive (Lira and Orshanskiy) to Al
3+
. Stress-induced increased expression of
CAX3
was detected only in aluminum-tolerant flax cultivars. The product of
CAX3
gene may participate in flax response to high soil acidity and high Al
3+
concentration through Ca
2+
-mediated intracellular regulation.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Flax (
Linum usitatissimum
L.) is a valuable agricultural crop grown for seed and fiber. Complete and accurate genome assemblies are the basis for molecular genetic studies and efficient breeding of ...flax. In the present work, we aimed to improve the accuracy of the Nanopore-assembled genome of line 3896, which is currently a reference genome for
L. usitatissimum
in the NCBI database. We sequenced the DNA of this line on the Illumina platform and obtained about 50× flax genome coverage. High-precision Illumina reads were used to polish the genome assembly of line 3896 by the POLCA tool. This significantly increased the accuracy of the assembly, which was reflected in the QUAST reference-based statistics, primarily in a drastic reduction in the number of single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). We also demonstrated the effect of polishing with Illumina reads on individual gene sequences. This procedure allowed us to correct erroneous SNPs and InDels in 14 of 25 examined genes of the
SAD
and
FAD
families, including those causing erroneous frameshifts and amino acid substitutions. Thus, we significantly improved the genome assembly of flax line 3896 and increased its value for basic and applied research on
L. usitatissimum
.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
—
The peculiarities of meiosis, C-heterochromatin (C-HC) distribution, and the activity of nucleolus organizer regions (NORs) of the chromosomes were studied in the
Pisum sativum
L. pea and
Triticum ...compactum
Host. club wheat grown from the seeds obtained in Lada space greenhouse on the board of RS ISS. It was noted that the analysis of meiosis detected no significant violations in the “space” plant cells, and the total amount of C-HC did not differ significantly from the control, despite the polymorphism of the chromosome C-banding pattern. Paracentric inversion on the chromosome 4A was found for the first time in the
T. compactum,
while no additional active NOR chromosomes were found.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OBVAL, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
6.
Genome: Origins and evolution of the term Zelenin, A. V.; Rodionov, A. V.; Bolsheva, N. L. ...
Molecular Biology,
07/2016, Volume:
50, Issue:
4
Journal Article, Book Review
Peer reviewed
The appearance of a new scientific term is a significant event in the human cognitive process and the result of the realization of the separateness of an object or a phenomenon. Our article ...concentrates on the origins of basic genetic terms, such as
genetics
,
gene
,
genotype
,
genome
,
gene pool
, and
genomics
. We propose using the term
karyogenomics
for the special direction of genomics related to the study of the organization and evolution of eukaryotic genomes by means of modern chromosome analysis, as well as by full genome sequencing.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
High-quality genome sequences help to elucidate the genetic basis of numerous biological processes and track species evolution. For flax (Linum usitatissimum L.)—a multifunctional crop, high-quality ...assemblies from Oxford Nanopore Technologies (ONT) data were unavailable, largely due to the difficulty of isolating pure high-molecular-weight DNA. This article proposes a scheme for gaining a contiguous L. usitatissimum assembly using Nanopore data. We developed a protocol for flax nuclei isolation with subsequent DNA extraction, which allows obtaining about 5 μg of pure high-molecular-weight DNA from 0.5 g of leaves. Such an amount of material can be collected even from a single plant and yields more than 30 Gb of ONT data in two MinION runs. We performed a comparative analysis of different genome assemblers and polishers on the gained data and obtained the final 447.1-Mb assembly of L. usitatissimum line 3896 genome using the Canu—Racon (two iterations)—Medaka combination. The genome comprised 1695 contigs and had an N50 of 6.2 Mb and a completeness of 93.8% of BUSCOs from eudicots_odb10. Our study highlights the impact of the chosen genome construction strategy on the resulting assembly parameters and its eligibility for future genomic studies.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Chromosome C-banding and two-color fluorescent in situ hybridization (FISH) were used to compare the chromosomes, to identify the chromosomal localization of the 45S and 5S rRNA genes, and to analyze ...the sequences of internal transcribed spacers 1 and 2 (ITS1 and ITS2) of the 45S rRNA genes in the genomes of grasses Zingeria biebersteiniana (2n = 4), Z. pisidica, Z. trichopoda (2n = 8), Colpodium versicolor (2n = 4), and Catabrosella variegata (syn. Colpodium variegatum) (2 n = 10). Differences in C-banding pattern were observed for two Z. biebersteiniana accessions from different localities. Similar C-banding patterns of chromosomes 1 and 2 were demonstrated for the Z. pisidica and Z. biebersteininana karyotypes. Chromosome C banding and localization of the 45S and 5S rRNA genes on the chromosomes of the two Zingeria species confirmed the assumption that Z. pisidica is an allotetraploid with one of the subgenomes similar to the Z. biebersteiniana genome. ITS comparisons showed that the unique two-chromosome grasses (x = 2)—Z. biebersteiniana (2n = 4), Z. trichopoda (2n = 8), Z. pisidica (2n = 8), and C. versicolor (2n = 4), which were earlier assigned to different tribes of subtribes of the family Poaceae—represent two closely related genera, the genetic distance (p-distance) between their ITSs being only 1.2-4.4%. The Zingeria species and C. versicolor formed a common clade with Catabrosella araratica (2n = 42, x = 7) on a molecular phylogenetic tree. Thus, the karyotypes of Zingeria and Colpodium, which have the lowest known basic chromosome number (x = 2), proved to be monophyletic, rather than originating from different phylogenetic lineages.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Poplars are widely used in landscaping of Moscow due to the ability to effectively purify the air from harmful impurities and to release a large amount of oxygen. The genus
Populus
is characterized ...by a high level of intraspecies polymorphism, as well as the presence of natural interspecies hybrids. The aim of our work was to evaluate the genetic diversity of poplars, which are growing on the territory of Moscow city by high-throughput sequencing of internal transcribed spacers of 45S rRNA genes (ITS sequences). Sequencing of ITS of 40 poplar plants was performed on Illumina platform (MiSeq) and about 3 000 reads were obtained for each sample in average. Bioinformatics analysis was performed using CLC Genomics Workbench tool. The involved set of poplars had a high level of genetic diversity – the number of single nucleotide polymorphisms (SNPs) detected in each genotype relative to the reference ITS1 and ITS2 sequences of
P. trichocarpa
varying from 4 to 44. We showed that even trees which had been planted on the same territory and, probably, at the same time had significant genetic differences. It can be speculated that highly polymorphic plant material was used for planting poplars in Moscow. For some sites with SNPs, several variants of nucleotides were found in the same individual and the ratio of SNPs was different. We assume that close to 50/50 ratio is observed in interspecific hybrids due to genetic differences in the ITS sequences between maternal and paternal genotypes. For SNPs with a predominance of one of the variants, the presence of paralogues among numerous genomic copies of ITS sequences is more likely. The results of our work can provide a framework for molecular genetic markers application with the purpose of
Populus
species and interspecific hybrids identification, determination the origin of a number of natural hybrids, and monitoring the diversity of genus
Populus
in the Moscow city.
The karyotype of the common ice plant Mesembryanthemum crystallinum L. (Aizoaceae) was studied using Chromomycin A
3
(CMA)/4′,6-diamidino-2-phenylindole (DAPI) staining, fluorescence in situ ...hybridization with 5S and 18S-5.8S-25S rDNA probes, DAPI/C-banding and immunodetection of 5-methylcytosine. A single bright CMA-band was revealed on the satellite chromosome, whose location was coincided with a position of a site of 18S-5.8S-25S rRNA genes. A site of 5S rRNA genes was observed on one of the other chromosomes. Relatively large DAPI/C-bands were mainly localized in the pericentromeric regions of the chromosomes. DAPI/C-banding patterns allowed us to identify all the chromosomes in the karyotype of M. crystallinum. The methylation of euchromatic chromosome regions was weaker as compared with heterochromatic DAPI/C-bands, which were hypermethylated. The obtained results may provide opportunities for investigating, at the chromosomal level, the genomic changes occurring in M. crystallinum either under salinization or under the action of other stress factors.
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