Pocheina and Acrasis are two genera of heterolobosean sorocarpic amoebae within Acrasidae that have historically been considered close relatives. The two genera were differentiated based on their differing fruiting body morphologies. The validity of this taxonomic distinction was challenged when a SSU rRNA phylogenetic study placed an isolate morphologically identified as "Pocheina" rosea within a clade of Acrasis rosea isolates. The authors speculated that pocheinoid fruiting body morphology might be the result of aberrant Ac. rosea fruiting body development, which, if true, would nullify this taxonomic distinction between genera. To clarify Acrasidae systematics, we analyzed SSU rRNA and ITS region sequences from multiple isolates of Pocheina, Acrasis, and Allovahlkampfia generated by Polymerase Chain Reaction (PCR) and transcriptomics. We demonstrate that the initial SSU sequence attributed to "P. rosea" originated from an Ac. rosea DNA contamination in its amplification reaction. Our analyses, based on morphology, SSU and 5.8S rRNA gene phylogenies, as well as comparative analyses of ITS1 and ITS2 sequences, resolve Acrasidae into three major lineages: Allovahlkampfia and the strongly supported clades comprising Pocheina and Acrasis. We confirm that the latter two genera can be identified by their fruiting body morphologies.

• Klíčová slova
• Acrasis, Allovahlkampfia, Guttulina, acrasid, amoeba, cellular slime mold, multicellularity, protist, social amoeba, sorocarpic amoeba,
• MeSH
• fylogeneze * MeSH
• mezerníky ribozomální DNA genetika   chemie   MeSH
• polymerázová řetězová reakce MeSH
• protozoální DNA genetika   MeSH
• ribozomální DNA genetika   chemie   MeSH
• RNA ribozomální 18S genetika   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• mezerníky ribozomální DNA MeSH
• protozoální DNA MeSH
• ribozomální DNA MeSH
• RNA ribozomální 18S MeSH

Nucleases of the S1/P1 family have important applications in biotechnology and molecular biology. We have performed structural analyses of SmNuc1 nuclease from Stenotrophomonas maltophilia, including RNA cleavage product binding and mutagenesis in a newly discovered flexible Arg74-motif, involved in substrate binding and product release and likely contributing to the high catalytic rate. The Arg74Gln mutation shifts substrate preference towards RNA. Purine nucleotide binding differs compared to pyrimidines, confirming the plasticity of the active site. The enzyme-product interactions indicate a gradual, stepwise product release. The activity of SmNuc1 towards c-di-GMP in crystal resulted in a distinguished complex with the emerging product 5'-GMP. This enzyme from an opportunistic pathogen relies on specific architecture enabling high performance under broad conditions, attractive for biotechnologies.

• Klíčová slova
• Stenotrophomonas maltophilia, RNA, S1/P1 nuclease, X‐ray crystallography, c‐di‐GMP cleavage,
• MeSH
• bakteriální proteiny metabolismus   chemie   genetika   MeSH
• guanosinmonofosfát cyklický metabolismus   analogy a deriváty   chemie   MeSH
• katalytická doména * MeSH
• krystalografie rentgenová MeSH
• molekulární modely MeSH
• RNA metabolismus   chemie   genetika   MeSH
• Stenotrophomonas maltophilia * enzymologie   genetika   metabolismus   MeSH
• substrátová specifita MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• bakteriální proteiny MeSH
• guanosinmonofosfát cyklický MeSH
• RNA MeSH

The nuclear lamina is a dense network of intermediate filaments beneath the inner nuclear membrane. Composed of A-type lamins (lamin A/C) and B-type lamins (lamins B1 and B2), the nuclear lamina provides a scaffold for the nuclear envelope and chromatin, thereby maintaining the structural integrity of the nucleus. A-type lamins are also found inside the nucleus where they interact with chromatin and participate in gene regulation. Viruses replicating in the cell nucleus have to overcome the nuclear envelope during the initial phase of infection and during the nuclear egress of viral progeny. Here, we focused on the role of lamins in the replication cycle of a dsDNA virus, mouse polyomavirus. We detected accumulation of the major capsid protein VP1 at the nuclear periphery, defects in nuclear lamina staining and different lamin A/C phosphorylation patterns in the late phase of mouse polyomavirus infection, but the nuclear envelope remained intact. An absence of lamin A/C did not affect the formation of replication complexes but did slow virus propagation. Based on our findings, we propose that the nuclear lamina is a scaffold for replication complex formation and that lamin A/C has a crucial role in the early phases of infection with mouse polyomavirus.

• Klíčová slova
• VP1, lamin A/C, lamin B, mouse polyomavirus, viral replication centres,
• MeSH
• buněčné jádro metabolismus   virologie   MeSH
• fosforylace MeSH
• infekce onkogenními viry virologie   patologie   metabolismus   genetika   MeSH
• jaderná lamina * metabolismus   virologie   MeSH
• jaderný obal metabolismus   virologie   MeSH
• lamin typ A * metabolismus   genetika   MeSH
• lamin typ B metabolismus   genetika   MeSH
• myši MeSH
• polyomavirové infekce * virologie   metabolismus   genetika   patologie   MeSH
• Polyomavirus * genetika   patogenita   fyziologie   MeSH
• replikace viru * MeSH
• virové plášťové proteiny metabolismus   genetika   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• lamin typ A * MeSH
• lamin typ B MeSH
• virové plášťové proteiny MeSH
• VP1 protein, polyomavirus MeSH Prohlížeč

Anaeramoebae is a recently described phylum of anaerobic, marine amoebae, and amoeboflagellates belonging to the Metamonada supergroup. So far, six species have been described based on light microscopic morphology and sequences of the SSU rRNA gene. Here we present three new strains of Anaeramoeba with a description of their morphology, ultrastructure, and phylogenetic position based on the analysis of SSU rRNA gene sequences. Two of the strains represent a new species, Anaeramoeba pumila sp. nov., that has the smallest cells of all known Anaeramoeba species, and one that represents a species from the newly recognized Anaeramoeba flamelloides complex. Anaeramoebae are known to have a syntrophic relationship with prokaryotes. Our strains display two novel, remarkable types of symbioses, previously unknown from Anaeramoebae.

• Klíčová slova
• SSU rRNA gene, anaerobiosis, marine, morphology, new taxa, phylogeny, ultrastructure,
• MeSH
• Amoeba * genetika   MeSH
• Eukaryota MeSH
• fylogeneze MeSH
• mikroskopie MeSH
• RNA ribozomální 16S genetika   MeSH
• sekvenční analýza DNA MeSH
• symbióza * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• RNA ribozomální 16S MeSH

Plant species diversity may be considerably underestimated, especially in evolutionarily complex genera and in diversity hotspots that have enabled long-term species persistence and diversification, such as the Balkan Peninsula. Here, we address the topic of underexplored plant diversity and underlying evolutionary and biogeographic processes by investigating the hygrophytic mountain species complex of Cardamine acris s.l. distributed in the Balkans (three subspecies within C. acris) and northwestern Anatolia (C. anatolica). We performed a series of phylogenetic and phylogeographic analyses based on restriction-site associated DNA sequencing (RADseq) and target enrichment (Hyb-Seq) data in combination with habitat suitability modelling. We found C. anatolica as a clade nested within the Balkan C. acris, probably resulting from a founder event, and uncovered three allopatric cryptic lineages within C. acris subsp. acris, allowing us to recognise a total of six entities in this complex. We observed the deepest genetic split within C. acris subsp. acris in the western Balkans, which was at odds with taxonomy and showed no distribution gap. We inferred vicariance as the most likely process for population divergence in the Balkans, accompanied by gene flow between the recognised entities, which was consistent with the modelled habitat suitability dynamics. Furthermore, we discovered several polyploid populations in C. acris, representing both pure intra- and inter-lineage hybrid polyploids, but detected only minor traces of hybridization with related congeners. Overall, our results illustrate that diverse evolutionary processes may influence the history of mountain plant species in the Balkan Peninsula, including vicariance, reticulation, polyploidization and cryptic diversification.

• Klíčová slova
• Hyb‐Seq, RAD sequencing, habitat suitability modelling, phylogeography, polyploidy, vicariance,
• MeSH
• Cardamine * genetika   klasifikace   MeSH
• DNA rostlinná genetika   MeSH
• ekosystém MeSH
• fylogeneze * MeSH
• fylogeografie * MeSH
• genetická variace MeSH
• genom rostlinný MeSH
• populační genetika MeSH
• sekvenční analýza DNA MeSH
• tok genů MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Balkánský poloostrov MeSH
• Turecko MeSH
• Názvy látek
• DNA rostlinná MeSH

Haemoglobin is a key molecule for oxygen transport in vertebrates. It exhibits remarkable gene diversity in teleost fishes, reflecting adaptation to various aquatic environments. In this study, we present the dynamic evolution of haemoglobin subunit genes based on a comparison of high-quality genome assemblies of 24 vertebrate species, including 17 teleosts (of which six are cichlids). Our findings indicate that teleost genomes contain a range of haemoglobin genes, from as few as five in fugu to as many as 43 in salmon, with the latter being the largest repertoire found in vertebrates. We find evidence that the teleost ancestor had at least four Hbα and three or four Hbβ subunit genes, and that the current gene diversity emerged during teleost radiation, driven primarily by (tandem) gene duplications, genome compaction, and rearrangement dynamics. We provide insights into the genomic organisation of haemoglobin clusters in different teleost species. We further show that the evolution of paralogous rhbdf1 genes flanking both teleost clusters (LA and MN) supports the hypothesis for the origin of the LA cluster by rearrangement within teleosts, rather than by the teleost specific whole-genome duplication. We specifically focus on cichlid fishes, where adaptation to low oxygen environment plays role in species diversification. Our analysis of six cichlid genomes, including Pungu maclareni from the Barombi Mbo crater lake, for which we sequenced a representative genome, reveals 18-32 copies of the Hb genes, and elevated rates of non-synonymous substitutions compared to other teleosts. Overall, this work facilitates a deeper understanding of how haemoglobin genes contribute to the adaptive potential of teleosts.

• Klíčová slova
• cichlids, duplication, evolution, haemoglobin, synteny, teleosts,
• MeSH
• cichlidy * genetika   MeSH
• duplikace genu * genetika   MeSH
• fylogeneze * MeSH
• genom genetika   MeSH
• genová přestavba genetika   MeSH
• hemoglobiny * genetika   MeSH
• molekulární evoluce * MeSH
• ryby * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• hemoglobiny * MeSH

Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1-D1' helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed.

• Klíčová slova
• Dulcicalothrix, 16S‐23S ITS rRNA region, Brunnivagina gen. nov., Calotrichaceae, Cyanobacteria, ITS rRNA region percent dissimilarity, multiple ribosomal operons,
• MeSH
• fylogeneze * MeSH
• mezerníky ribozomální DNA analýza   genetika   MeSH
• operon MeSH
• RNA ribozomální 16S analýza   genetika   MeSH
• RNA ribozomální 23S genetika   MeSH
• rRNA operon genetika   MeSH
• sinice * genetika   klasifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Indie MeSH
• Názvy látek
• mezerníky ribozomální DNA MeSH
• RNA ribozomální 16S MeSH
• RNA ribozomální 23S MeSH

Interbreeding and introgression between recently diverged species is common. However, the processes that prevent these species from merging where they co-occur are not well understood. We studied the mechanisms that allowed an isolated group of populations of the snail Helix thessalica to persist within the range of the related Helix pomatia despite high gene flow. Using genomic cline analysis, we found that the nuclear gene flow between the two taxa across the mosaic hybrid zone was not different from that expected under neutral admixture, but that the exchange of mtDNA was asymmetric. Tests showed that there is relaxed selection in the mitochondrial genome of H. thessalica and that the substitution rate is elevated compared to that of H. pomatia. A lack of hybrids that combine the mtDNA of H. thessalica with a mainly (>46%) H. pomatia genomic background indicates that the nuclear-encoded mitochondrial proteins of H. pomatia are not well adapted to the more rapidly evolving proteins and RNAs encoded by the mitochondrion of H. thessalica. The presumed reduction of fitness of hybrids with the fast-evolving mtDNA of H. thessalica and a high H. pomatia ancestry, similar to 'Darwin's Corollary to Haldane's rule', resulted in a relative loss of H. pomatia nuclear ancestry compared to H. thessalica ancestry in the hybrid zone. This probably prevents the H. thessalica populations from merging quickly with the surrounding H. pomatia populations and supports the hypothesis that incompatibilities between rapidly evolving mitochondrial genes and nuclear genes contribute to speciation.

• Klíčová slova
• Darwin's Corollary, genomic cline, hybrid zone, land snail, mitonuclear incompatibility, speciation,
• MeSH
• genetická zdatnost MeSH
• genom mitochondriální MeSH
• Helix (hlemýždi) * genetika   MeSH
• hybridizace genetická * MeSH
• mitochondriální DNA * genetika   MeSH
• mitochondrie genetika   MeSH
• molekulární evoluce MeSH
• populační genetika MeSH
• selekce (genetika) MeSH
• tok genů * MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• mitochondriální DNA * MeSH

Nodular gill disease (NGD) is an emerging condition associated with amoeba trophozoites in freshwater salmonid farms. However, unambiguous identification of the pathogens still must be achieved. This study aimed to identify the amoeba species involved in periodic NGD outbreaks in two rainbow trout (Oncorhynchus mykiss) farms in Northeastern Italy. During four episodes (February-April 2023), 88 fish were euthanized, and their gills were evaluated by macroscopic, microscopic and histopathological examination. The macroscopic and microscopic severity of the lesions and the degree of amoebae infestation were scored and statistically evaluated. One gill arch from each animal was put on non-nutrient agar (NNA) Petri dishes for amoeba isolation, cultivation and subsequent identification with SSU rDNA sequencing. Histopathology confirmed moderate to severe lesions consistent with NGD and mild to moderate amoeba infestation. The presence of amoebae was significantly correlated with lesion severity. Light microscopy of cultured amoebae strains and SSU rDNA analysis revealed the presence of a previously characterized amoeba Naegleria sp. strain GERK and several new strains: two strains from Hartmannelidae, three vannelid amoebae from the genus Ripella and cercozoan amoeba Rosculus. Despite the uncertainty in NGD etiopathogenesis and amoebae pathogenic role, identifying known and new amoebae leans towards a possible multi-aetiological origin.

• Klíčová slova
• Oncorhynchus mykiss, Italy, SSU rDNA, amphizoic amoeba, nodular gill disease (NGD), rainbow trout,
• MeSH
• amébiáza * veterinární   parazitologie   MeSH
• Amoeba genetika   izolace a purifikace   klasifikace   MeSH
• Amoebozoa genetika   izolace a purifikace   klasifikace   fyziologie   MeSH
• fylogeneze MeSH
• nemoci ryb * parazitologie   epidemiologie   MeSH
• Oncorhynchus mykiss * parazitologie   MeSH
• vodní hospodářství MeSH
• žábry * parazitologie   patologie   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Itálie MeSH

While metopids (Armophorea: Metopida) represent the most species-rich group of free-living anaerobic ciliates thriving in hypoxic environments, our understanding of their true diversity remains incomplete. Most metopid species are still characterized only morphologically. Particularly, the so-called IAC clade (named in the past after some of the taxa included, Idiometopus, Atopospira, and Clevelandellida), comprising free-living members as well as the endosymbiotic ones (order Clevelandellida), is in serious need of revision. In our study, we establish a new free-living genus in the IAC clade, Pidimetopus n. gen., with descriptions of two new species, P. nanus n. sp., and P. permonicus n. sp., using up-to-date molecular and morphologic methods. The genus is characterized by small cells (up to 75 μm long), not more than 10 adoral membranelles and eight somatic kineties, and usually, four long caudal cilia that can stiffen. In addition to morphologic and molecular characterizations, we also conducted a statistical morphotype analysis of the polymorphic species P. nanus n. sp. We discuss the relevance of the earlier morphologically described species Metopus minor as a putative collective taxon for several small metopids less than 50 μm long.

• Klíčová slova
• 18S rRNA gene, Armophorea, Metopida, phylogeny, transmission electron microscopy,
• MeSH
• biodiverzita MeSH
• Ciliophora * klasifikace   genetika   cytologie   MeSH
• fylogeneze * MeSH
• protozoální DNA genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• protozoální DNA MeSH