The modification of adenosine to inosine at the first position of transfer RNA (tRNA) anticodons (I34) is widespread among bacteria and eukaryotes. In bacteria, the modification is found in tRNA^Arg and is catalyzed by tRNA adenosine deaminase A, a homodimeric enzyme. In eukaryotes, I34 is introduced in up to eight different tRNAs by the heterodimeric adenosine deaminase acting on tRNA. This substrate expansion significantly influenced the evolution of eukaryotic genomes in terms of codon usage and tRNA gene composition. However, the selective advantages driving this process remain unclear. Here, we have studied the evolution of I34, tRNA adenosine deaminase A, adenosine deaminase acting on tRNA, and their relevant codons in a large set of bacterial and eukaryotic species. We show that a functional expansion of I34 to tRNAs other than tRNA^Arg also occurred within bacteria, in a process likely initiated by the emergence of unmodified A34-containing tRNAs. In eukaryotes, we report on a large variability in the use of I34 in protists, in contrast to a more uniform presence in fungi, plans, and animals. Our data support that the eukaryotic expansion of I34-tRNAs was driven by the improvement brought by these tRNAs to the synthesis of proteins highly enriched in certain amino acids.

The olive tree (Olea europaea L.) is a wind-pollinated crop that exhibits an extreme alternate bearing habit. To improve fruit set, several methods have been used to determine the most successful compatible combinations of cultivars. In this study, priority is given to seed paternity analysis based on simple sequence repeats (SSRs), microsatellite markers used for the identification of potential pollen donors of cultivar ‘Oblica’ in a mixed olive orchard during two consecutive years. Seven microsatellite primers were successfully used to examine the paternity of olive embryos from ‘Oblica’ mother trees. Embryos were considered as a product of self-fertilization if only maternal alleles were present, but not a single case of self-fertilization was found among all the embryos analyzed. Two dominant pollen donors were not the closest nor the cultivars with the highest number of trees in the orchard, suggesting that cross-compatibility may have a key role in determining pollen donor success. In our earlier studies, pollen tube growth and fertilization success correlated with fruit set when controlled crosses between cultivars were performed; however, some discrepancy might appear compared to paternity analyses when mother trees have a free choice among different pollen sources from cultivars growing in their surroundings.

Trendy high-density olive fields are often monovarietal orchards, mostly using the cultivar Arbequina. However, Arbequina shows a strong self-incompatibility response, and its yields depend on wind cross-pollination, which is not always available. With the aim of finding suitable self-compatible cultivars that can replace Arbequina, we evaluated pollen–pistil interaction, fruit set and seed paternity in Arbosana under different pollination treatments: self-pollination, open-pollination and three cross-pollination treatments: × Arbequina, × Sikitita and × Koroneiki. All these cultivars are low-vigor cultivars suitable for high-density orchards, making them potential pollinizers for Arbosana. The results show that Arbosana is also self-incompatible with a strong reduction in fruit set due to a lower fertilization level caused by a strong inhibition of pollen tube growth in self-pollinated flowers. Seed-paternity analyses confirmed the self-incompatibility response of Arbosana and suggest that some fruit obtained in bagged shoots under self-pollination were, in fact, a product of cross-fertilization. In conclusion, we recommend against the use of Arbosana in large monovarietal orchards. On the contrary, good results were obtained under cross-pollination with Sikitita, Arbequina and Koroneiki pollen, allowing us to recommend them as pollinizers for Arbosana in appropriate pollination designs. This is the first time Arbosana self-incompatibility has been reported.

Backcrossing between Sikitita and its male parent Arbequina, offers the possibility to check the suitability of different self-incompatibility models proposed for olive. To determine Sikitita’s response to self- and cross-pollination treatments, including pollination with its father Arbequina, we compared the parameters following pollen–pistil interaction, the resulting initial and final fruit set, and the paternity of the seeds produced under different crosses. The results showed that Sikitita behaves as a self-incompatible cultivar due to the inhibition of pollen tube growth in the pistil of self-pollinated flowers. This incompatibility reaction led to a significant reduction of self-fertilization and fruit set. Seed paternity analyses confirmed the self-incompatibility response of Sikitita. A similar incompatibility response was observed in Sikitita flowers when hand-pollinated with pollen of Arbequina and Koroneiki. On the contrary, cross-pollination with Arbosana gave excellent results, with analyses showing that pollen of Arbosana is largely preferred by Sikitita to father its seeds more than the pollen of other cultivars presented in the orchard. The backcross failure of Sikitita with Arbequina pollen suggests that the self-incompatibility system in olives is not of the gametophytic type. In contrast, pollination tests fit features of previously reported sporophytic self-incompatibility systems. However, some amendments are proposed, among them the incompatibility groups for Sikitita and Koroneiki.

Two bacteria belonging to the Pseudomonas and Pantoea genera were isolated from olive knots. Both bacterial strains were omnipresent in this study’s olive orchard with high susceptibility of the autochthonous olive genotypes indicating coevolution of bacteria with host plants. Genomes of two endemic bacteria show conserved core genomes and genome plasticity. The Pseudomonas ST1 genome has conserved virulence-related genes including genes for quorum sensing, pilus, and flagella biosynthesis, two copies of indole acetic acid biosynthesis (IAA) operons, type I-VI secretions systems, and genes for alginate and levan biosynthesis. Development of knots depends only on the presence of the Pseudomonas ST1 strain which then allows Pantoea paga strain co-infection and cohabitation in developed knots. The two bacteria are sensitive to a large number of antimicrobials, antibiotics, H₂O₂, and Cu (II) salts that can be efficiently used in propagation of bacterial free olive cultivars.

Here, we present the total genome sequence of Pantoea sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of Pantoea sp. paga is 5.08 Mb, with a G+C content of 54%. The genome contains 4,776 predicted coding DNA sequences (CDSs), including 70 tRNA genes and 1 ribosomal operon. Obtained genome sequence data will provide insight on the physiology, ecology, and evolution of Pantoea spp.