B Chromosomes’ Sequences in Yellow-Necked Mice Apodemus flavicollis—Exploring the Transcription

B chromosomes (Bs) are highly polymorphic additional chromosomes in the genomes of many species. Due to the dispensability of Bs and the lack of noticeable phenotypic effects in their carriers, they were considered genetically inert for a long time. Recent studies on Bs in Apodemus flavicollis revealed their genetic composition, potential origin, and spatial organization in the interphase nucleus. Surprisingly, the genetic content of Bs in this species is preserved in all studied samples, even in geographically distinct populations, indicating its biological importance. Using RT-PCR we studied the transcription activity of three genes (Rraga, Haus6, and Cenpe) previously identified on Bs in A. flavicollis. We analysed mRNA isolated from spleen tissues of 34 animals harboring different numbers of Bs (0–3). The products of transcriptional activity of the analysed sequences differ in individuals with and without Bs. We recorded B-genes and/or genes from the standard genome in the presence of Bs, showing sex-dependent higher levels of transcriptional activity. Furthermore, the transcriptional activity of Cenpe varied with the age of the animals differently in the group with and without Bs. With aging, the amount of product was only found to significantly decrease in B carriers. The potential biological significance of all these differences is discussed in the paper.

The Effect of the Application of Stimulants on the Photosynthetic Apparatus and the Yield of Winter Wheat

The use of stimulation preparations seems to be a promising means for mitigating the effects of abiotic and biotic stressors. Their significance includes plant organism stimulation and metabolism optimisation, water regime, and nutrition during periods of stress. They help bridge it over and create conditions for rapid regeneration. In a field experiment, the effect of the application of stimulation preparations on cultivars Triticum aestivum L. with different genetic composition was evaluated (donor of blue aleurone colour KM-72-18; donor of a multi-row spike (MRS) KM-94-18). Our results show a predominantly positive effect of the application of stimulants on the yield and thousand-grain weight (TKW). The results obtained were influenced by the year, based on different temperatures and precipitation. Higher yields were achieved in 2020 with higher total precipitation during the grain filling period and with a higher maximum quantum yield of the photosystem II (Fv/Fm). In 2019, this period was significantly dry and warm, which was reflected in a lower yield and TKM, higher proline content in the leaves, and lower Fv/Fm values. In both experimental years, there was a higher yield of the cultivar with blue aleurone (KM-72-18). In the case of cultivars with coloured grains, the promising use of the content substances in cultivars as natural means of increasing resistance to abiotic and biotic stressors seems to be promising.

The rise and spread of the SARS-CoV-2 AY.122 lineage in Russia

BackgroundDelta has outcompeted most preexisting variants of SARS-CoV-2, becoming the globally predominant lineage by mid-2021. Its subsequent evolution has led to emergence of multiple sublineages, many of which are well-mixed between countries.AimHere, we aim to study the emergence and spread of the Delta lineage in Russia.MethodsWe use a phylogeographic approach to infer imports of Delta sublineages into Russia, and phylodynamic models to assess the rate of their spread.ResultsWe show that nearly the entire Delta epidemic in Russia has probably descended from a single import event despite genetic evidence of multiple Delta imports. Indeed, over 90% of Delta samples in Russia are characterized by the nsp2:K81N+ORF7a:P45L pair of mutations which is rare outside Russia, putting them in the AY.122 sublineage. The AY.122 lineage was frequent in Russia among Delta samples from the start, and has not increased in frequency in other countries where it has been observed, suggesting that its high prevalence in Russia has probably resulted from a random founder effect.ConclusionThe apartness of the genetic composition of the Delta epidemic in Russia makes Russia somewhat unusual, although not exceptional, among other countries.

Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish

Asexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.

Viral Phrenology

We introduce Viral Phrenology, a new scheme for understanding the genomic composition of spherical viruses based on the locations of their structural protrusions. We used icosahedral point arrays to classify 135 distinct viral capsids collected from over 600 capsids available in the VIPERdb. Using gauge points of point arrays, we found 149 unique structural protrusions. We then show how to use the locations of these protrusions to determine the genetic composition of the virus. We then show that ssDNA, dsDNA, dsRNA and ssRNA viruses use different arrangements for distributing their protrusions. We also found that Triangulation number is also partially dependent on the structural protrusions. This analysis begins to tie together Baltimore Classification and Triangulation number using point arrays.

Changes in the genetic composition of Myzus persicae nicotianae populations in Chile and frequency of insecticide resistance mutations

Myzus persicae is a cosmopolitan aphid that is highly polyphagous and an important agricultural pest. The subspecies M. persicae nicotianae has been described for highly specialized phenotypes adapted to tobacco (Nicotiana tabacum). In Chile, the population of M. persicae nicotianae was originally composed of a single red genotype that did not possess insecticide resistance mutations. However, in the last decade, variation in the colour of tobacco aphids has been observed in the field. To determine whether this variation stems from the presence of new genotypes, sampling was carried out across the entire distribution of tobacco cultivation regions in Chile. The aphids collected were genotyped, and the frequency of kdr (L1014F), super-kdr (M918T), modification of acetylcholinesterase (MACE) and nicotinic acetylcholine receptor β subunit (nAChRβ) mutations associated with insecticide resistance was determined. A total of 16 new genotypes of M. persicae nicotianae were detected in Chile: four of them possessed the MACE mutation, and none of them possessed the kdr, super-kdr or nAChRβ mutation. The previously described red genotype was not detected in any of the sampled fields over two seasons. These results raise questions about the mechanisms underlying changes in the genetic structure of M. persicae nicotianae populations in Chile. Future research aimed at addressing these questions could provide new insight into aphid evolution and agricultural practices.

Characterization of a blaNDM-1-Bearing IncHI5-Like Plasmid From Klebsiella pneumoniae of Infant Origin

The spread of plasmid-mediated carbapenem-resistant clinical isolates is a serious threat to global health. In this study, an emerging NDM-encoding IncHI5-like plasmid from Klebsiella pneumoniae of infant patient origin was characterized, and the plasmid was compared to the available IncHI5-like plasmids to better understand the genetic composition and evolution of this emerging plasmid. Clinical isolate C39 was identified as K. pneumoniae and belonged to the ST37 and KL15 serotype. Whole genome sequencing (WGS) and analysis revealed that it harbored two plasmids, one of which was a large IncHI5-like plasmid pC39-334kb encoding a wide variety of antimicrobial resistance genes clustered in a single multidrug resistance (MDR) region. The blaNDM-1 gene was located on a ΔISAba125-blaNDM-1-bleMBL-trpF-dsbC structure. Comparative genomic analysis showed that it shared a similar backbone with four IncHI5-like plasmids and the IncHI5 plasmid pNDM-1-EC12, and these six plasmids differed from typical IncHI5 plasmids. The replication genes of IncHI5-like plasmids shared 97.06% (repHI5B) and 97.99% (repFIB-like) nucleotide identity with those of IncHI5 plasmids. Given that pNDM-1-EC12 and all IncHI5-like plasmids are closely related genetically, the occurrence of IncHI5-like plasmid is likely associated with the mutation of the replication genes of pNDM-1-EC12-like IncHI5 plasmids. All available IncHI5-like plasmids harbored 262 core genes encoding replication and maintenance functions and carried distinct MDR regions. Furthermore, 80% of them (4/5) were found in K. pneumoniae from Chinese nosocomial settings. To conclude, this study expands our knowledge of the evolution history of IncHI5-like plasmids, and more attention should be paid to track the evolution pathway of them among clinical, animal, and environmental settings.