Genomic analysis reveals cryptic diversity in aphelids and sheds light on the emergence of Fungi.

Over the past decade, molecular phylogenetics has reshaped our understanding of the fungal tree of life by unraveling a hitherto elusive diversity of the protistan relatives of Fungi. Aphelida constitutes one of these novel deep branches that precede the emergence of osmotrophic fungal lifestyle and hold particular significance as the pathogens of algae. Here, we obtain and analyze the genomes of aphelid species Amoeboaphelidium protococcarum and Amoeboaphelidium occidentale.

Comparative analysis of alignment-free genome clustering and whole genome alignment-based phylogenomic relationship of coronaviruses.

The SARS-CoV-2 is the third coronavirus in addition to SARS-CoV and MERS-CoV that causes severe respiratory syndrome in humans. All of them likely crossed the interspecific barrier between animals and humans and are of zoonotic origin, respectively. The origin and evolution of viruses and their phylogenetic relationships are of great importance for study of their pathogenicity and development of antiviral drugs and vaccines.

The Mitochondrial Genome of a Freshwater Pelagic Amphipod Is among the Longest in Metazoa.

There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals.

Bioinformatic tools for tRNA gene analyses in mitochondrial DNA sequence data.

The data presented here are related to the research article entitled "Hidden cases of tRNA genes duplication and remolding in mitochondrial genomes of amphipods" (Romanova et al., 2020) [1]. Correct tRNA gene sequence annotation in mitochondrial (mt) and nuclear genomes sometimes can be a challenging task because of the differential performances of tRNA annotation/prediction programmes.

The diversity of the Baikal lineage of Pallas, 1766: molecular and morphological evidence.

In this paper, molecular analyses of Baikal hydras from the ' group', based on COI and ITS1-5.8S-ITS2, and morphological analysis of their holotrichous isorhizas, were performed. Low genetic diversity and shared haplotypes were found between Pallas, 1766 and Swarczewsky, 1923 specimens, which is evidence of the mixing of these lineages.

Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods.

The evolution of tRNA genes in mitochondrial (mt) genomes is a complex process that includes duplications, degenerations, and transpositions, as well as a specific process of identity change through mutations in the anticodon (tRNA gene remolding or tRNA gene recruitment). Using amphipod-specific tRNA models for annotation, we show that tRNA duplications are more common in the mt genomes of amphipods than what was revealed by previous annotations. Seventeen cases of tRNA gene duplications were detected in the mt genomes of amphipods, and ten of them were tRNA genes that underwent remolding.

"886-84-like" tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics.

Tick-borne encephalitis virus (TBEV) can cause severe meningitis, encephalitis, and meningoencephalitis. TBEV represents a pathogen of high zoonotic potential and an emerging global threat. There are three known subtypes of TBEV: Far-Eastern, Siberian and European.

Population genetic structure and phylogeography of sterlet (Acipenser ruthenus, Acipenseridae) in the Ob and Yenisei river basins.

The sterlet (Acipenser ruthenus Linnaeus, 1758) is a relatively small sturgeon widely distributed in Eurasian rivers from the Danube to the Yenisei. During the twentieth century, all wild sterlet populations have declined due to anthropogenic factors including: overfishing, poaching, construction of dams, and pollution. Despite the necessity of characterization both wild and captive stocks, few studies of population genetics have been performed thus far.

Evolution of mitochondrial genomes in Baikalian amphipods.

Background: Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences.

The complete mitochondrial genome of (Lubomirskiidae): description and phylogenetic analysis.

The complete mitochondrial genome of the Lake Baikal sponge was sequenced. The circular mitochondrial genome is 28,327 bp in length and includes 14 protein-coding genes, 2 ribosomal RNA genes and 25 transfer RNA genes. Bayesian comparative analysis of molecular evolution rates was found no acceleration of the mtDNA evolution of .

A new, genetically divergent species of Pseudobaikalia Lindholm, 1909 (Caenogastropoda, Baicaliidae).

A new gastropod species, Pseudobaikalia michelae Sitnikoiva & Kovalenkova, sp. n., (family Baicaliidae) is described from Lake Baikal.

The complete mitochondrial genome of a deep-water Baikalian amphipoda Brachyuropus grewingkii (Dybowsky, 1874).

In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B.

The complete mitochondrial genome of Baikalian amphipoda Eulimnogammarus vittatus Dybowsky, 1874.

A complete mitochondrial genome sequence of amphipoda Eulimnogammarus vittatus Dybowsky, 1874 from Lake Baikal was obtained using next-generation sequencing approach. Mitochondrial DNA with the length of 15,534 bp contains 13 protein-coding genes, 2 ribosomal RNA, 23 transfer RNA and non-coding sequences: a putative control region and 7 intergenic spacers. A brief comparative analysis of mitochondrial genomes of E.

Genotyping of Capreolus pygargus fossil DNA from Denisova cave reveals phylogenetic relationships between ancient and modern populations.

Background: The extant roe deer (Capreolus Gray, 1821) includes two species: the European roe deer (C. capreolus) and the Siberian roe deer (C. pygargus) that are distinguished by morphological and karyotypical differences.

When environmental changes do not cause geographic separation of fauna: differential responses of Baikalian invertebrates.

Background: While the impact of climate fluctuations on the demographic histories of species caused by changes in habitat availability is well studied, populations of species from systems without geographic isolation have received comparatively little attention. Using CO1 mitochondrial sequences, we analysed phylogeographic patterns and demographic histories of populations of five species (four gastropod and one amphipod species) co-occurring in the southwestern shore of Lake Baikal, an area where environmental oscillations have not resulted in geographical isolation of habitats.

Results: Species with stronger habitat preferences (gastropods B.

Genetic flows in a structured one-dimensional population: simulation and real data on Baikalian polychaetes M. godlewskii.

In this work, we apply population dynamic approach enhanced with simulation of the fate of neutrally evolving "DNA sequences" included into each individual in the computer experiment to the case of the Baikalian endemic polychaetes Manavunkia. These animals inhabit a narrow littoral zone around whole the lake perimeter and are of very limited mobility. Accordingly, the general model was modified by addition of a "geographic barrier" of different isolating power and length of existence.