Animal husbandry is increasing yearly due to the growing demand for meat and livestock products, among other reasons. To meet these demands, prophylactic antibiotics are used in the livestock industry (i.e., poultry farming) to promote health and stimulate animal growth. However, antibiotics are not fully metabolized by animals, and they are evacuated to the environment with excreta. Animal manure is used as fertilizer to reduce the volume of waste generated in the livestock sector. However, manure often contains microorganisms harboring antibiotic resistance genes (ARGs). Then, the microbiome of manure applicate to the soil may contribute to the spread of antibiotic resistance in the environment, including autochthonous soil-dwelling microorganisms. The present study was conducted during the crops growing season in Poland (May to September 2019) to determine the influence of poultry manure as well as poultry manure supplemented with selected antibiotics on the diversity of the soil microbiome in treatments that had not been previously fertilized with manure and the ability of antibiotic-resistant bacteria to transfer ARGs to other soil bacteria. Antibiotic concentrations were elevated at the beginning of the study and decreased over time. Poultry manure induced significant changes in the structure of microbial communities in soil; the diversity of the soil microbiome decreased, and the abundance of bacterial genera Bradyrhizobium, Streptomyces, and Pseudomonas, which are characteristic of the analyzed manure, increased. Over time, soil microbial diversity was restored to the state observed before the application of manure. Genes conferring resistance to multiple drugs as well as genes encoding resistance to bacitracin and aminoglycosides were the most frequently identified ARGs in the analyzed bacteria, including on mobile genetic elements. Multidrug resistance was observed in 17 bacterial taxa, whereas ARGs were identified in 32 bacterial taxa identified in the soil microbiome. The results of the study conclude that the application of poultry manure supplemented with antibiotics initially affects soil microbiome and resistome diversity but finally, the soil shows resilience and returns to its original state after time, with most antibiotic resistance genes disappearing. This phenomenon is of great importance in sustainable soil health after manure application.

Synonymous codon usage bias, a significant factor in gene expression and genome evolution, was extensively studied in genomics and molecular biology. Although the genetic code is universal, significant variations in synonymous codon usage have been observed among and within organisms. This bias was linked to various factors, including gene expression levels, tRNA abundance, protein structure, and environmental adaptation. Relative Synonymous Codon Usage (RSCU), a normalized measure, was used to quantify this bias. By analyzing RSCU values, researchers uncovered patterns and trends related to the underlying mechanisms driving codon usage bias. We present an R package named RSCUcaller designed for the analysis of coding nucleotide sequences at the level of relative synonymous codon usage (RSCU). The package enables both visualization of data and the performance of advanced statistical analyses. RSCUcaller accepts as input a multi-fasta file containing coding sequences (CDS) and an accompanying description table. Alternatively, the user may provide separate fasta files for each sequence along with the corresponding table. The program merges the provided sequences and calculates RSCU values for each. Implemented visualization features include creating heatmaps and dendrograms based on these heatmaps. Furthermore, the package allows for the presentation of data in the form of histograms. The calculated RSCU values can also be used to create matrices that can be subjected to further analysis by the user. RSCUcaller offers the functionality of correlation analysis between any two organisms. Additionally, to compare the frequency of amino acid occurrence between different groups of sequences, statistical tests have been implemented. RSCUcaller enabled comparative RSCU analysis between coding sequences of different organisms or individuals of the same species. It facilitated visualization and statistical analysis among codons and user-defined groups. The RSCUcaller package is available at https://github.com/Mordziarz/RSCUcaller under the GPL-3 license.

Membrane-bound organelles, such as mitochondria and chloroplasts, have played a crucial role in the evolution of plant cells. In this study, we investigate the presence of heteroplasmy and genomic variation in liverworts, a group of non-vascular plants, using nanopore sequencing technology. We selected four liverwort species representing different lineages: Riccia fluitans, Apopellia endiviifolia, Aneura pinguis, and Scapania undulata. Through nanopore sequencing, we sequenced, assembled, and annotated the organellar genomes of selected liverwort species. The plastid genomes of Riccia fluitans, Apopellia endiviifolia, Aneura pinguis, and Scapania undulata exhibited high conservation with previously published genomes, while the mitogenome of Scapania undulata represents the first report for this species. The analysis of the liverwort organellar genomes revealed conserved gene content, structure, and order. We further investigated heteroplasmy within the liverwort species. The plastome analysis did not detect structural heteroplasmy, which is observed in some angiosperms but seems limited to seed plants. However, in the mitogenomes, we found evidence of heteroplasmy in Aneura pinguis, Apopellia endiviifolia, and Scapania undulata. The heteroplasmic sites in the mitogenomes were mainly represented by substitutions, indels, and short tandem repeat polymorphisms. Some of the identified substitutions resembled RNA editing patterns observed in liverworts. This study highlights the utility of nanopore sequencing for studying organellar genomes and detecting heteroplasmy in liverworts. The findings expand our understanding of organellar genomic variation in non-vascular plants and provide insights into the mechanisms underlying heteroplasmy in liverwort mitogenomes. Further research is needed to explore the functional significance of heteroplasmy and its implications for liverwort evolution and adaptation.

In this comprehensive review, we explore the significant role that nanopore sequencing technology plays in the study of plant organellar genomes, particularly mitochondrial and chloroplast DNA. To date, the application of nanopore sequencing has led to the successful sequencing of over 100 plant mitochondrial genomes and around 80 chloroplast genomes. These figures not only demonstrate the technology’s robustness but also mark a substantial advancement in the field, highlighting its efficacy in decoding the complex and dynamic nature of these genomes. Nanopore sequencing, known for its long-read capabilities, significantly surpasses traditional sequencing techniques, especially in addressing challenges like structural complexity and sequence repetitiveness in organellar DNA. This review delves into the nuances of nanopore sequencing, elaborating on its benefits compared to conventional methods and the groundbreaking applications it has fostered in plant organellar genomics. While its transformative impact is clear, the technology’s limitations, including error rates and computational requirements, are discussed, alongside potential solutions and prospects for technological refinement.

Summary: The genus Riccia is the most speciose of the Marchantiopsida, the complex thalloid liverworts. In contrast to the predicted ancestral liverwort and the majority of extant liverworts that are dioicous, most Riccia species are monoicous. Both the gametophyte and the sporophyte generations have undergone regressive evolution in Riccia, with the sporophyte lacking many adaptations for spore dispersal. Phylogenetic reconstructions suggest multiple transitions between dioicy and monoicy, and vice versa, within the Riccia. We analysed the genomes of two Riccia species and the transcriptomes of two additional Riccia species to explore the evolution of sexual systems and investigate genomic signatures of regressive evolution. Genomic analyses suggest a transition from dioicy to monoicy at the base of the Riccia clade and a subsequent reversion to dioicy with the concomitant evolution of a new sex chromosome, followed by further transitions back to monoicy. Additionally, Riccia species exhibit significant losses of transcription factors known to control aspects of sporophyte and gametophyte development. Comparisons with the monotypic sister genus, Ricciocarpos, suggest independent evolutions to both monoicy and reductive morphologies in the two genera. The reductive morphology has facilitated their colonization of extreme habitats but has perhaps canalized them to remain there.

Ribes genus from the Grossulariaceae family, have been used in the food industry and for medicinal purposes for years. Despite the valuable medicinal values and the widespread occurrence of Ribes, many species remain understudied. One of these is the alpine currant Ribes alpinum L., which occurs natively in Europe. The study aimed to thoroughly understand and characterize the organelle genomes of R. alpinum, conduct their comparative analysis with available data for other representatives of Grossulariaceae and, in the case of the chloroplast genome, also with Saxifraga insolens Irmsch., a representative of the closely related Saxifragaceae family. The analysis of plastome interspecific variation revealed several hotspots of variation which could be useful as potential phylogenetic markers or specific DNA barcodes. The phenomenon of sequence transfer between the chloroplast and mitochondrial genomes and the relative synonymous codon usage between the plastome and mitogenome were also analyzed. A phylogenetic inference based on the chloroplast genome sequence questioned earlier reports of a close relationship of R. alpinum to R. rubrum and confirmed its affiliation with an early-diverged phylogenetic line together with R. fasciculatum. Analysis of hotspots of variation in chloroplast genome allowed us to indicate petN-psbM and trnS-trnG as high-utility barcode sequences, competitive with standard barcodes and the ycf1 gene.