Papers by Igor V Sharakhov
Far Eastern entomologist, Feb 21, 2018
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Lecture Notes in Computer Science, 2023
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Genes, May 28, 2022
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Journal of Visualized Experiments, May 26, 2023
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Insects, Sep 17, 2018
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Proceedings of The Royal Society B: Biological Sciences, Jul 10, 2019
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Research Square (Research Square), Apr 25, 2022
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Biokhimiya, Apr 1, 2018
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Pathogens and Global Health, Oct 2, 2020
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Methods in molecular biology, Nov 10, 2018
The development of genomic resources and tools is an important step in designing novel approaches... more The development of genomic resources and tools is an important step in designing novel approaches to genetic control of mosquitoes. Physical genome maps enhance the quality of the genome assemblies, improve gene annotation, and provide a better framework for comparative and population genomics studies in mosquitoes. In this chapter, we describe protocols for an important procedure in physical genome mapping-fluorescence in situ hybridization (FISH). We provide details on (1) dissection of salivary glands, ovaries, and imaginal discs for obtaining high-quality polytene or mitotic chromosome preparations; (2) DNA-labeling procedures and extraction of repetitive DNA fractions; and (3) approaches to FISH on polytene and mitotic chromosomes.
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Parasites & Vectors, Oct 19, 2011
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Pathogens and Global Health, 2020
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BackgroundAnopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among t... more BackgroundAnopheles coluzzii and An. arabiensis belong to the An. gambiae complex and are among the major malaria vectors in Sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species.FindingsIn this study, we produced de novo chromosome-level genome assemblies for An. coluzzii and An. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 Mbp and 256.8 Mbp of the total assemblies for An. coluzzii and An. arabiensis, respectively. Each assembly consists of three chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomiccoordinates for the b...
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Multiple studies have demonstrated a negative correlation between gene expression and the positio... more Multiple studies have demonstrated a negative correlation between gene expression and the positioning of genes at the nuclear envelope (NE) lined by nuclear lamina. In this paper, we ask whether there is a causal, systematic relationship between the expression level of the groups of genes in topologically associating domains (TADs) of Drosophila nuclei and the probabilities of TADs to be found at the NE. To investigate the nature of this possible relationship, we combine a coarse-grained dynamic model of the entire Drosophila nucleus with genome-wide gene expression data; we analyze the TAD averaged transcription levels of genes against the probabilities of individual TADs to be near the NE in the control and lamins-depleted nuclei. Our findings demonstrate that, within the statistical error margin, the stochastic positioning ofDrosophila melanogasterTADs at the NE does not, by itself, systematically affects the mean level of gene expression in these TADs, while the expected negativ...
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Frontiers in Ecology and Evolution, Jun 10, 2021
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InTech eBooks, May 20, 2016
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BMC Biology, Mar 12, 2020
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Papers by Igor V Sharakhov