/library/oar/handle/123456789/378 2026-08-02T20:41:32Z /library/oar/handle/123456789/148252 Title: Phylogenomic discordance among plastid genes in endangered Maltese Limonium Authors: Agius, Dorita; Poczai, Peter Abstract: Chloroplast genomes are widely used in plant phylogenetics, yet plastome-wide analyses increasingly reveal heterogeneity among gene trees. Limonium, a genus of over 600 species, centred in the Mediterranean basin, exhibits substantial taxonomic complexity driven by hybridization, apomixis, and polyploidy, but plastome data from its centre of diversity have been lacking. We report the first complete plastomes from Mediterranean Limonium, sequencing the endangered Maltese endemics L. melitense (154,139 bp) and L. zeraphae (154,142 bp), and compare them with seven plastomes from the Irano-Turanian and Chinese-Japanese regions. Genome sizes range from 150,515 to 174,033 bp, with variation primarily associated with inverted repeat (IR) expansion and contraction and differences in repeat content. Highly variable coding genes (ndhF, ycf1, rpl32) and several intergenic regions were identified as candidate molecular markers, and 382 simple sequence repeats were detected across nine plastomes. Structural comparisons revealed IR boundary shifts, repeat variation, and pseudogenization of rpl22 in L. zeraphae. Plastome-wide maximum likelihood analyses strongly supported the monophyly of Limonium and recovered geographically structured clades. To evaluate phylogenetic concordance, we analysed individual plastid protein-coding genes and inferred a species tree under the multispecies coalescent. Gene-tree conflict was localized to specific nodes, particularly involving the placement of L. otolepis and relationships among East Asian taxa, indicating heterogeneous plastome signal despite strong concatenated support. Selection analyses based on Ka/Ks ratios and complementary site-mode approaches identified six genes (ccsA, rpl22, rpoA, rps8, ycf1, ycf2) exhibiting signatures of positive selection. These results demonstrate dynamic plastome evolution and localized phylogenetic discordance within Limonium, refining the evolutionary framework of the genus and informing plastome-based inference in recent plant radiations. 2026-01-01T00:00:00Z /library/oar/handle/123456789/136669 Title: Gaining insights into epigenetic memories through artificial intelligence and omics science in plants Authors: Dobránszki, Judit; Vassileva, Valya; Agius, Dorita; Moschou, Panagiotis Nikolaou; Gallusci, Philippe; Berger, Margot M. J.; Farkas, Dóra; Basso, Marcos Fernando; Martinelli, Federico Abstract: Plants exhibit remarkable abilities to learn, communicate, memorize, and develop stimulus-dependent decision-making circuits. Unlike animals, plant memory is uniquely rooted in cellular, molecular, and biochemical networks, lacking specialized organs for these functions. Consequently, plants can effectively learn and respond to diverse challenges, becoming used to recurring signals. Artificial intelligence (AI) and machine learning (ML) represent the new frontiers of biological sciences, offering the potential to predict crop behavior under environmental stresses associated with climate change. Epigenetic mechanisms, serving as the foundational blueprints of plant memory, are crucial in regulating plant adaptation to environmental stimuli. They achieve this adaptation by modulating chromatin structure and accessibility, which contribute to gene expression regulation and allow plants to adapt dynamically to changing environmental conditions. In this review, we describe novel methods and approaches in AI and ML to elucidate how plant memory occurs in response to environmental stimuli and priming mechanisms. Furthermore, we explore innovative strategies exploiting transgenerational memory for plant breeding to develop crops resilient to multiple stresses. In this context, AI and ML can aid in integrating and analyzing epigenetic data of plant stress responses to optimize the training of the parental plants. 2025-01-01T00:00:00Z /library/oar/handle/123456789/129223 Title: Plant memory and communication of encounters Authors: Dobránszki, Judit; Agius, Dorita; Berger, Margot M.J.; Moschou, Panagiotis N.; Gallusci, Philippe; Martinelli, Federico Abstract: Plants can communicate with each other and other living organisms in a very sophisticated manner. They use biological molecules and even physical cues to establish a molecular dialogue with beneficial organisms as well as with their predators and pathogens. Several studies were recently published that explore how plants communicate with each other about their previous encounters or stressful experiences. However, there is an almost complete lack of knowledge about how these intra- and interspecies communications are directly regulated at the epigenetic level. In this perspective article we provide new hypotheses for the possible epigenetic modifications that regulate plant responses at the communication level. 2024-01-01T00:00:00Z /library/oar/handle/123456789/124307 Title: Ischnura genei (Rambur, 1842) Authors: Boudot, Jean-Pierre; Degabriele, Godwin Abstract: Distribution World: Ischnura genei is an insular species endemic to the western Mediterranean.; Europe: Ischnura genei is endemic to the Tuscan archipelago and the Tyrrhenian and Maltese islands, and is common and widespread within its range. It is absent from mainland Europe and replaces I. elegans on the above islands, except in Giglio where both species cohabit. A male and female were caught on the Italian island of Linosa, between the Maltese islands and the Tunisian coast, in 2010 (Corso et al. 2012). Whether they belonged to a local population breeding in the few man-made water tanks present on the island or were vagrants is unknown. 2015-01-01T00:00:00Z