Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of WGD, allo- or autopolyploidization, lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are important for understanding the early stages of genome evolution. However, assembling neopolyploid is a challenging task due to the presence of 2 homologous (or homeologous) chromosome sets and therefore the existence of the extended paralogous regions in its genome. Post-WGD evolution of polyploids includes cytogenetic diploidization leading to the formation of species, whose polyploid origin might be hidden by disomic inheritance. Earlier we uncovered the hidden polyploid origin of the free-living flatworms of the genus Macrostomum (Macrostomum lignano, M. janickei, and M. mirumnovem). Cytogenetic diploidization in these species is accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we unravel the M. lignano genome organization through generation and sequencing of 2 sublines of the commonly used inbred line of M. lignano (called DV1) differing only in a copy number of the largest chromosome (MLI1). Using nontrivial assembly free comparative analysis of their genomes, we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano, which consists of (i) presence of 3 subgenomes, which emerged via formation of large fused chromosomes and its variants, and (ii) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.

Геномика и протеомика возбудителя описторхоза Opisthorchis felineus

The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers. RatDEGdb is novel in that, unlike any other biomedical database, it offers the manually curated annotations of DEGs in model rats with the use of independent clinical data on equal changes in the expression of homologous genes revealed in people with pathologies. The rat DEGs put in RatDEGdb were annotated with equal changes in the expression of their human homologs in affected people. In its current release, RatDEGdb contains 94,873 such annotations for 321 human genes in 836 diseases based on 959 original scientific papers found in the current PubMed. RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.

Most lepidopteran species have a WZ/ZZ sex chromosome system, suggesting a common origin. However, the exceptional variability of W chromosomes supports their multiple independent origins. Here, we investigated the genome of the recently formed species, Dendrolimus sibiricus, which is one of the most devastating pests of the boreal forests in Northern Asia. We found that its karyotype consists of 30 pairs of chromosomes and follows the WZ/ZZ sex chromosome system. We produced a chromosome-scale assembly of its female genome and identified the sequences of both sex chromosomes. With the exception of the W chromosome, the D. sibiricus genome displays a very high degree of synteny with genomes of other Dendrolimus representatives. The non-conserved W chromosome is composed entirely of recently acquired sequences, mainly young genomic repeats and a few unique loci derived from subtelomeric regions of the same species' Z chromosome as well as from the genome of the endosymbiotic Wolbachia bacterium. It shares no common ancestral sequences with the W chromosomes of two related species, Dendrolimus tabulaeformis and Lasiocampa quercus. They, in turn, display a similar organization relative to the W of D. sibiricus, including Z-derived loci. The W of D. tabulaeformis also contained multiple fragments of the mitochondrial genome, as seen in classical B chromosomes. We conclude that W chromosomes arose from their Z counterparts recently and independently in these three species. We propose that this mechanism may be a common feature of lepidopteran evolution, counteracting the inevitable degeneration of a non-recombining chromosome through its repeated, complete turnover.

The parasitic flatworm Opisthorchis felineus is one of the causative agents of opisthorchiasis in humans. Recently, we assembled the O. felineus genome, but the correct genome annotation by means of standard methods was hampered by the presence of spliced leader trans-splicing (SLTS). As a result of SLTS, the original 5’-end (outron) of the transcripts is replaced by a short spliced leader sequence donated from a specialized SL RNA. SLTS is involved in the RNA processing of more than half of O. felineus genes, making it hard to determine the structure of outrons and bona fide transcription start sites of the corresponding genes and operons, being based solely on mRNA-seq data. In the current study, we tested various experimental approaches for identifying the sequences of outrons in O. felineus using massive parallel sequencing. Two of them were developed by us for targeted sequencing of already processed branched outrons. One was based on sequence-specific reverse transcription from the SL intron toward the 5’-end of the Y-branched outron. The other used outron hybridization with an immobilized single-stranded DNA probe complementary to the SL intron. Additionally, two approaches to the sequencing of rRNA-depleted total RNA were used, allowing the identification of a wider range of transcripts compared to mRNAseq. One is based on the enzymatic elimination of overrepresented cDNAs, the other utilizes exonucleolytic degradation of uncapped RNA by Terminator enzyme. By using the outron-targeting methods, we were not able to obtain the enrichment of RNA preparations by processed outrons, which is most likely indicative of a rapid turnover of these trans-splicing intermediate products. Of the two rRNA depletion methods, a method based on the enzymatic normalization of cDNA (Zymo-Seq RiboFree) showed high efficiency. Compared to mRNA-seq, it provides an approximately twofold increase in the fraction of reads originating from outrons and introns. The results suggest that unprocessed nascent transcripts are the main source of outron sequences in the RNA pool of O. felineus.

Whole genome duplication (WGD) is an evolutionary event resulting in a redundancy of genetic material. Different mechanisms of genome doubling through allo- or autopolyploidization could lead to distinct evolutionary trajectories of newly formed polyploids. Genome studies on such species are undoubtedly important for understanding one of the crucial stages of genome evolution. However, assembling neopolyploid appears to be a challenging task because its genome consists of two homologous (or homeologous) chromosome sets and therefore contains the extended paralogous regions with a high homology level. Post-WGD evolution of polyploids includes rediploidization, first part of which is cytogenetic diploidization led to the formation of species, whose polyploid origin might be hidden by disomic inheritance and diploid-like meiosis. Earlier we uncovered the hidden polyploid origin of free-living flatworms of the genus Macrostomum ( Macrostomum lignano, M. janickei , and M. mirumnovem ). Despite the different mechanisms for their genome doubling, cytogenetic diploidization in these species accompanied by intensive chromosomal rearrangements including chromosomes fusions. In this study, we reported unusual subgenomic organization of M. lignano through generation and sequencing of two new laboratory sublines of DV1 that differ only by a copy number of the large chromosome MLI1. Using non-trivial assembly-free comparative analysis of their genomes, including adapted multivariate k-mer analysis, and self-homology within the published genome assembly of M. lignano , we deciphered DNA sequences belonging to MLI1 and validated them by sequencing the pool of microdissected MLI1. Here we presented the uncommon mechanism of genome rediplodization of M. lignano , which consists in (1) presence of three subgenomes, emerged via formation of large fused chromosome and its variants, and (2) sustaining their heterozygosity through inter- and intrachromosomal rearrangements.