Biology subjects

Schelkunov, M. I.

Publications and source records attributed to Schelkunov, M. I..

8 recordsLinked to original sources

bioRxiv2025

The plastid genome of the non-photosynthetic plant Rhopalocnemis phalloides is one of the most polymorphic genomes known

The common ancestor of plants in the Balanophoraceae family lost the ability to photosynthesize, and all several dozen extant species of this family feed exclusively by parasitizing other plants. Previous studies have shown that the plastid genomes of Balanophoraceae present numerous unusual features, including an extraordinarily increased rate of mutation accumulation without an observable weakening of natural selection acting on the genes. This study aims to test the hypothesis that the increased rate of mutation accumulation could have led to exceptionally high levels of intraspecific polymorphism in Balanophoraceae. To this end, we studied the plastid genomes of 7 samples of the species Rhopalocnemis phalloides. Although all 7 plastid genomes possessed the same genes arranged in the same order, the level of polymorphism was indeed extremely high, possibly the highest among all known genomes of any living organisms. Specifically, the average genome-wide percent identity of the plastid genomes of Rhopalocnemis phalloides was 68.7%, and the average percent identity of the CDSs was 68.9%. Additionally, during this study, we discovered 60 taxonomically misclassified plastid genomes in NCBI databases; this result has independent value.

genomics↗

bioRxiv2024

Trans2express - de novo transcriptome assembly pipeline optimized for gene expression analysis

BackgroundAs genomes of many eukaryotic species, especially plants, are large and complex, their de novo sequencing and assembly is still a difficult task despite progress in sequencing technologies. An alternative to genome assembly is the assembly of transcriptome, the set of RNA products of the expressed genes. While a bunch of de novo transcriptome assemblers exists, the challenges of transcriptomes (the existence of isoforms, the uneven expression levels across genes) complicates the generation of high-quality assemblies suitable for downstream analyses. ResultsWe developed Trans2express - a web-based tool and a pipeline of de novo hybrid transcriptome assembly and postprocessing based on rnaSPAdes with a set of subsequent filtrations. The pipeline was tested on Arabidopsis thaliana cDNA sequencing data obtained using Illumina and Oxford Nanopore Technologies platforms. The comparison of structural characteristics of the transcriptome assembly with reference Arabidopsis genome revealed the high quality of assembled transcriptome with 86.1% of Arabidopsis expressed genes assembled as a single contig. We tested the applicability of the transcriptome assembly for gene expression analysis and showed high congruence of gene expression levels and sets of differentially expressed genes between analyses based on genome and based on the transcriptome assembly. ConclusionsWe present Trans2express - a protocol for de novo hybrid transcriptome assembly aimed at recovering of a single transcript per gene. We expect this protocol to promote the characterization of transcriptomes and gene expression analysis in non-model plants and web-based tool to be of use to a wide range of plant biologists.

bioinformatics↗

bioRxiv2023

The genome of the toxic invasive species Heracleum sosnowskyi carries an increased number of genes despite the absence of recent whole-genome duplications

Heracleum sosnowskyi, belonging to a group of giant hogweeds, is a plant with large effects on ecosystems and human health. It is an invasive species that contributes to the deterioration of grassland ecosystems. The ability of H. sosnowskyi to produce linear furanocoumarins (FCs), photosensitizing compounds, makes it very dangerous. At the same time, linear FCs are compounds with high pharmaceutical value that are used in skin disease therapies. Despite this high importance, it has not been the focus of genetic and genomic studies. Here, we report a chromosome-scale assembly of the Sosnowskys hogweed genome. Genomic analysis revealed an unusually high number of genes (55 206) in the hogweed genome, in contrast to the 25-35 thousand found in most plants. However, we did not find any traces of recent whole genome duplications not shared with its confamiliar, Daucus carota (carrot), which has approximately thirty thousand genes. The analysis of the genomic proximity of duplicated genes indicates tandem duplications as a main reason for this increase. We performed a genome-wide search of the genes of the FC biosynthesis pathway and their expression in aboveground plant parts. Using a combination of expression data and phylogenetic analysis, we found candidate genes for psoralen synthase and experimentally showed the activity of one of them using a heterologous yeast expression system. These findings expand our knowledge on the evolution of gene space in plants and lay a foundation for further analysis of hogweed as an invasive plant and as a source of FCs.

genomics↗

bioRxiv2022

Mabs, a suite of tools for gene-informed genome assembly

MotivationDespite constantly improving genome sequencing methods, error-free eukaryotic genome assembly has not yet been achieved. Among other kinds of problems of eukaryotic genome assembly are so-called "haplotypic duplications", which may manifest themselves as cases of alleles being mistakenly assembled as paralogues. Haplotypic duplications are dangerous because they create illusions of gene family expansions and, thus, may lead scientists to incorrect conclusions about genome evolution and functioning. ResultsHere, I present Mabs, a suite of tools that serve as parameter optimizers of the popular genome assemblers Hifiasm and Flye. By optimizing the parameters of Hifiasm and Flye, Mabs tries to create genome assemblies with the genes assembled as accurately as possible. Tests on 6 eukaryotic genomes showed that in 6 out of 6 cases, Mabs created assemblies with more accurately assembled genes than those generated by Hifiasm and Flye when they were run with default parameters. When assemblies of Mabs, Hifiasm and Flye were postprocessed by a popular tool for haplotypic duplication removal, Purge_dups, genes were better assembled by Mabs in 5 out of 6 cases. Availability and implementationMabs has been written in Python and is available at https://github.com/shelkmike/Mabs

bioinformatics↗

bioRxiv2020

Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives.

The plant family Balanophoraceae consists entirely of species that have lost the ability to photosynthesize. Instead, they obtain nutrients by parasitizing other plants. Recent studies have shown that plastid genomes of Balanophoraceae have a number of interesting features, one of the most prominent of those being a tremendous AT content close to 90%. Also, the nucleotide substitution rate in the plastid genomes of Balanophoraceae is greater by an order of magnitude compared to photosynthetic relatives, without signs of relaxed selection. All these features have no definite explanations. Given these unusual features, we supposed that it would be interesting to gain insight into the characteristics of nuclear genomes of Balanophoraceae. To do this, in the present study we analysed transcriptomes of two species from Balanophoraceae, namely Rhopalocnemis phalloides and Balanophora fungosa, and compared them with transcriptomes of their close photosynthetic relatives Daenikera sp., Dendropemon caribaeus, Malania oleifera. The analysis showed that the AT content of nuclear genes of Balanophoraceae does not markedly differ from that of photosynthetic relatives. The nucleotide substitution rate in genes of Balanophoraceae is for an unknown reason several times larger than in genes of photosynthetic Santalales, though the negative selection in Balanophoraceae is likely stronger. We observed an extensive loss of photosynthesis-related genes in Balanophoraceae. Also, for Balanophoraceae we did not see transcripts of several genes whose products participate in plastid genome repair. This implies their loss or very low expression, which may explain the increased nucleotide substitution rate and AT content of the plastid genomes.

genomics↗

bioRxiv2019

Mitochondrial genome of non-photosynthetic mycoheterotrophic plant Hypopitys monotropa: unusual structure and extensive RNA editing

Heterotrophic plants - the plants that lost the ability to photosynthesis - are characterized by a number of changes at all levels of organization. Heterotrophic plants divide into two large categories - parasitic and mycoheterotrophic. The question of to what extent these changes are similar in these two categories is still open. Plastid genomes of non-photosynthetic plants are well characterized and they demonstrate similar patterns of reduction in both groups. In contrast, little is known about mitochondrial genomes of mycoheterotrophic plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a mycoheterotrophic member of Ericaceae, and the expression of mitochondrial genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, its complete size is ~810 Kbp. We found an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations on parasitic non-photosynthetic plants. Transcriptome sequencing revealed trans-splicing of several genes and RNA editing in 33 genes of 38. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites which extensively integrate genetic material from their hosts.

evolutionary biology↗

bioRxiv2018

Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their genomes, especially plastid genomes, markedly differ from the genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing on other plants. The genome is highly reduced (18 622 base pairs versus approximately 150 kilobase pairs in autotrophic plants) and possesses an outstanding AT content, 86.8%, the highest of all sequenced plant plastid genomes. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologues from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

genomics↗

bioRxiv2017

RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of holo-mycoheterotrophic plants

* While photosynthesis is the most notable trait of plants, several lineages of plants (so-called holo-heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels.\n\n* Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related holo-heterotrophic plants.\n\n* In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated mutations twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H.monotropa.\n\n* Holo-heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.

genomics↗