Endogenous giant viruses shape intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii

Chlamydomonas reinhardtii is an important eukaryotic alga that has been studied as a model organism for decades. Despite extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of numerous C. reinhardtii isolates, and in six strains we discovered endogenous genomes of giant viruses reaching over several hundred kilobases in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, one of the closest sequenced phylogenetic relatives of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and inter-strain genomic variability of C. reinhardtii. Our findings suggest that endogenization of giant viruses can have profound implications in shaping the population dynamics and ecology of protists in the environment.

Utilization of specific primers in legume allergens based polymorphism screening

Different types of allergies became a part of life of many people around the world. The research activities connecting to allergens are actually not oriented only for protein and immunological interactions, but to the genomic and transcriptomic background of them, too. Analysis and description of genomic variability of allergens in plant food resources will help to manage the allergen based strategies in the future. Here, the bioinformatic approach was used to develop and validate the specific primers for genomic screening of polymorphism of profilins (Profilin Based Amplicon Polymorphism; PBAP) and vicilins (Vicilin Based Amplicon Polymorphism; VBAP) among the legumes. The alignment of existing public databases data for these allergens in the group of legumes was performed. Subsequently, specific primers were designed and their ability to generate polymorphic amplicons were tested for three legumes – bean, lentil and chickpeas. In all cases, amplicons were generated and polymorphism was detected in all three species for profilin as well as for vicilin.

BBAP amplification profiles of apple varieties

Several types of allergies are currently known and are characterized by an exaggerated response of the immune system to substances from various sources called allergens. One of them is a food allergy, which is becoming more common in the population. For this reason, it is necessary to describe the issue from several aspects including genomic variability of plant allergens. The objective of this study was to analyse intraspecific variability of Bet v 1 of 10 different varieties of apple species (Malus domestica Borkh.). BBAP technique for genomic determination of the presence of Bet v 1 homologs at the DNA level was performed. Degenerate primers that anneal a variable and conserved part of PR-10 protein homologues genes were used in the analyse. Amplicons were generated and formed relatively monomorphic profiles, indicating the stability of the given isoforms of Bet v 1 within the selected apple varieties. To evaluate the potential allergenicity of selected varieties further studies on another molecular level such as a comparison of gene expression of the PR-10 family members and their protein expression levels are needed.

Intra-genomic rDNA gene variability of Nassellaria and Spumellaria (Rhizaria, Radiolaria) assessed by Sanger, MinION and Illumina sequencing

Ribosomal DNA (rDNA) genes are known to be valuable markers for the barcoding of eukaryotic life and its phylogenetic classification at various taxonomic levels. The large scale exploration of environmental microbial diversity through metabarcoding approaches have been focused mainly on the hypervariable regions V4 and V9 of the 18S rDNA gene. Yet, the accurate interpretation of such environmental surveys is hampered by technical (e.g., PCR and sequencing errors) and biological biases (e.g., intra-genomic variability). Here we explored the intra-genomic diversity of Nassellaria and Spumellaria specimens (Radiolaria) by comparing Sanger sequencing with two different high-throughput sequencing platforms: Illumina and Oxford Nanopore Technologies (MinION). Our analysis determined that intra-genomic variability of Nassellaria and Spumellaria is generally low, yet in some Spumellaria specimens we found two different copies of the V4 with a similarity lower than 97%. From the different sequencing methods, Illumina showed the highest number of contaminations (i.e., environmental DNA, cross-contamination, tag-jumping), revealed by its high sequencing depth; and Minion showed the highest sequencing rate error (~14%). Yet the long reads produced by MinION (~2900 bp) allowed accurate phylogenetic reconstruction studies. These results, highlight the requirement for a careful interpretation of Illumina based metabarcoding studies, in particular regarding low abundant amplicons, and open future perspectives towards full environmental rDNA metabarcoding surveys.

Revisiting the heterogeneous global genomic population structure of Leishmania infantum

Leishmania infantum is the main causative agent responsible for visceral leishmaniasis (VL), a disease with global distribution. The genomic structure and genetic variation of this species have been widely studied in different parts of the world. However, in some countries, this information is still yet unknown, as is the genomic behaviour of the main antigens used in VL diagnosis (rK39 and rK28), which have demonstrated variable sensitivity and specificity in a manner dependent on the geographic region analysed. The objective of this study was to explore the genomic architecture and diversity of four Colombian L. infantum isolates obtained in this study and to compare these results with the genetic analysis of 183 L. infantum isolates from across the world (obtained from public databases), as well as to analyse the whole rK39 and rK28 antigen sequences in our dataset. The results showed that, at the global level, L. infantum has high genetic homogeneity and extensive aneuploidy. Furthermore, we demonstrated that there are distinct populations of L. infantum circulating in various countries throughout the globe and that populations of distant countries have close genomic relationships. Additionally, this study demonstrated the high genetic variability of the rK28 antigen worldwide. In conclusion, our study allowed us to (i) expand our knowledge of the genomic structure of global L. infantum; (ii) describe the intra-specific genomic variability of this species; and (iii) understand the genomic characteristics of the main antigens used in the diagnosis of VL. Additionally, this is the first study to report whole-genome sequences of Colombian L. infantum isolates.

Origin, Phylogeny, Variability and Epitope Conservation of SARS-CoV-2 Worldwide

The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges include understanding what triggered SARS-CoV-2 emergence, how this RNA virus is evolving or how the genomic variability may impact the primary structure of proteins that are targets for vaccine. We analyzed 19471 SARS-CoV-2 genomes and 199,984 spike glycoprotein sequences available at the GISAID database from all over the world and 3335 genomes of other Coronoviridae family members available at Genbank, collecting SARS-CoV-2 high-quality genomes and distinct Coronoviridae family genomes. Here, we identify a SARS-CoV-2 emerging cluster containing 13 closely related genomes isolated from bat and pangolin that showed evidence of recombination, which may have contributed to the emergence of SARS-CoV-2. The analyzed SARS-CoV-2 genomes presented 9632 single nucleotide polymorphisms (SNPs) corresponding to a variant density of 0.3 over the genome, and a clear geographic distribution. SNPs are unevenly distributed throughout the genome and hotspots for mutations were found for the spike gene and ORF 1ab. We describe a set of predicted spike protein epitopes whose variability is negligible. All predicted epitopes for the structural E, M and N proteins are highly conserved. This result favors the continuous efficacy of the available vaccines.