Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage.

Thousands of yeast genomes have been sequenced with both traditional and long-read technologies, and multiple observations about modes of genome evolution for both wild and laboratory strains have been drawn from these sequences. In our study, we applied Oxford Nanopore and Illumina technologies to assemble complete genomes of two widely used members of a distinct laboratory yeast lineage, the Peterhof Genetic Collection (PGC), and investigate the structural features of these genomes including transposable element content, copy number alterations, and structural rearrangements. We identified numerous notable structural differences between genomes of PGC strains and the reference S288C strain. We discovered a substantial enrichment of mid-length insertions and deletions within repetitive coding sequences, such as in the SCH9 gene or the NUP100 gene, with possible impact of these variants on protein amyloidogenicity. High contiguity of the final assemblies allowed us to trace back the history of reciprocal unbalanced translocations between chromosomes I, VIII, IX, XI, and XVI of the PGC strains. We show that formation of hybrid alleles of the FLO genes during such chromosomal rearrangements is likely responsible for the lack of invasive growth of yeast strains. Taken together, our results highlight important features of laboratory yeast strain evolution using the power of long-read sequencing.

Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa.

Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.

Comparative Genomic Analysis of Holospora spp., Intranuclear Symbionts of Paramecia.

While most endosymbiotic bacteria are transmitted only vertically, Holospora spp., an alphaproteobacterium from the Rickettsiales order, can desert its host and invade a new one. All bacteria from the genus Holospora are intranuclear symbionts of ciliates Paramecium spp. with strict species and nuclear specificity. Comparative metabolic reconstruction based on the newly sequenced genome of Holospora curviuscula, a macronuclear symbiont of Paramecium bursaria, and known genomes of other Holospora species shows that even though all Holospora spp. can persist outside the host, they cannot synthesize most of the essential small molecules, such as amino acids, and lack some central energy metabolic pathways, including glycolysis and the citric acid cycle. As the main energy source, Holospora spp. likely rely on nucleotides pirated from the host. Holospora-specific genes absent from other Rickettsiales are possibly involved in the lifestyle switch from the infectious to the reproductive form and in cell invasion.

Redescription of an early-derivative mite, Pentasetacus araucariae (Eriophyoidea, Phytoptidae), and new hypotheses on the eriophyoid reproductive anatomy.

A unique set of plesiomorphic characters, and its association with an ancient gymnosperm, Araucaria araucana, have made Pentasetacus araucariae a putative relict of a lineage of gymnosperm-associated mites, itself possibly basal to all extant eriophyoids. However, the suboptimal description of this species is impeding morphological comparisons with other species, which are fundamental to eriophyoid systematics. Herein, we designate a female lectotype from syntype specimens and use additional non-type material to redescribe P. araucariae based on external and internal anatomy using different microscopic and 3D reconstruction techniques. Contrarily to statements in the literature, P. araucariae has undivided empodia in all instars, short spermathecal tubes, and large, globose spermathecae in females, as well as rudimentary genital fovea in immatures. In addition, males of P. araucariae were shown to have genitalic attributes similar to a species of Trisetacus studied in parallel, including two reservoir-like structures, which may represent parts of the genital chamber and of the ductus ejaculatorius, respectively, as well as paired testes and ducti deferentes. This is contrary to previous, limited knowledge on eriophyoids indicating that they possess a single testis. Although their short spermathecal tubes weaken the cladistic relationship between P. araucariae (Pentasetacinae) and conifer-associated Nalepellinae (e.g. Trisetacus) having long tubes, the structural similarities in male genitalia may reinforce it.