SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

BACKGROUND

The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained.

RESULTS

To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers.

CONCLUSIONS

The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature.

Unique and ancestral features in trunk kidney microanatomy and ultrastructure of omul Coregonus migratorius

This study presents novel data on the microanatomy and ultrastructure of the omul Coregonus migratorius trunk kidney. Adult individuals of C. migratorius were sampled in the Barguzin Bay of Lake Baikal. Active leuko- and erythropoiesis were found in the interstitium of the mesonephros. For the first time, cells with radially arranged vesicles have been described in the renal interstitium of C. migratorius. The quantitative characteristics of blood cells and ultrastructural parameters of leukocytes reflected the functioning of the non-specific defence system in the organism. The share of the renal interstitium, morphological diversity of the epithelial cells of the nephron tubules, the ultrastructural features of the renal corpuscles and nephron tubules and the number of mitochondria in leukocytes and ion-transporting cells were typical for representatives of the whitefish Coregonus lavaretus complex and thus considered ancestral features of the present-day C. migratorius population reflecting its adaptive potential to living in an ultra-deep Lake Baikal.

Structural features of the mesonephros of semianadromous fish on the example of the European smelt (Osmerus eperlanus)

At present, special attention is drawn to the study of the adaptation of aquatic organisms to a complex of environmental factors precisely at the cellular level. It is very important to study the structural and functional features of the kidney, which not only plays a key role in osmoregulation, but also makes a significant contribution to maintaining homeostasis at the level of functioning of a single nonspecific defense system of the body. In this aspect, the study of species belonging to a unique ancient group, united in the order salmoniformes, is highly relevant. Using the methods of light and electron microscopy, we investigated the morphology and ultrastructure of the mesonephros of the population of the semianadromous ecological form European smelt Osmerus eperlanus inhabiting the Gulf of Finland of the Baltic Sea and performing spawning migrations in the Luga River of the Leningrad Region. The general scheme of the trunk kidney organization is given, the structural features and the ratio of leukocytes and structures of the smelt nephron are revealed. It is shown that the development of hematopoietic tissue in the mesonephros, the number of mature forms of granulocytes are systematic signs which do not depend on the ecology of the species. The ratio of leukocytes, the width of the cisterns of the rough endoplasmic reticulum of plasma cells, the structure and number of granules in granulocytes are associated with the peculiarities of the functioning of the cellular link of the immune system under certain conditions of the species habitat. The ultrafine structure of the ion-transporting interstitial cells, as well as the ultrastructural features found in the smelt nephron, can be considered cytological markers of smelt adaptation to a semianadromous lifestyle.

The Center of Origin and Colonization Routes of Noble Salmons of the Genus Salmo (Salmonidae, Actinopterigii)

Genetic diversity and colonization routes of noble salmons were studied using a partial nucleotide sequence of the mitochondrial COI gene. The brown trout S. trutta, which is the most ancient species of the genus, was concluded to originate from the modern southeastern Pontic-Caspian area, which is currently inhabited by members of the subspecies S. trutta oxianus. Migrating westward while the Paratethys was in existence (5-34 million years ago), species of the genus colonized ancient water bodies in the modern Mediterranean basin and formed many isolated populations that survived desiccation of the Mediterranean Sea (5-6 million years ago). The Strait of Gibraltar mediated brown trout migrations to Northern Europe; the subspecies S. trutta trutta belongs to a relatively young phylogenetic lineage of the species. A separate brown trout lineage, currently classified as the subspecies S. trutta labrax, formed most likely in the area of the modern Danube basin, which was a relatively separate part of the Paratethys and was sometimes isolated as the Pannonian Lake. A highly divergent phylogenetic lineage of Atlantic salmon (S. salar) haplotypes originates from a haplotype of the brown trout that inhabited the area of the modern Strait of Gibraltar.

Fish hosts, glochidia features and life cycle of the endemic freshwater pearl mussel Margaritifera dahurica from the Amur Basin

Margaritiferidae is a small freshwater bivalve family with 16 species. In spite of a small number of taxa and long-term history of research, several gaps in our knowledge on the freshwater pearl mussels still exist. Here we present the discovery of host fishes for Margaritifera dahurica, i.e. Lower Amur grayling, sharp-snouted lenok, and blunt-snouted lenok. The host fishes were studied in rivers of the Ussuri Basin. The identification of glochidia and fish hosts was confirmed by DNA analysis. The life cycle of M. dahurica and its glochidia are described for the first time. The SEM study of glochidia revealed that the rounded, unhooked Margaritifera dahurica larvae are similar to those of the other Margaritiferidae. Margaritifera dahurica is a tachytictic breeder, the larvae of which attach to fish gills during the Late August – September and finish the metamorphosis in June. Ancestral host reconstruction and a review of the salmonid - pearl mussel coevolution suggest that the ancestral host of the Margaritiferidae was a non-salmonid fish, while that of the genus Margaritifera most likely was an early salmonid species or their stem lineage. The overfishing of lenoks and graylings appears to be the most significant threat for this rare mussel species.