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Purifying selection is expected to prevent the accumulation of transposable elements (TEs) within their host, especially when located in and around genes and if affected by epigenetic silencing. However, positive selection may favor the spread of TEs, causing genomic imprinting under parental conflict, as genomic imprinting allows parent-specific influence over resource accumulation to the progeny. Concomitantly, the number and frequency of TE insertions in natural populations are conditioned by demographic events. In this study, we aimed to test how demography and selective forces interact to affect the accumulation of TEs around genes, depending on their epigenetic silencing, with a particular focus on imprinted genes. To this aim, we compared the frequency and distribution of TEs in Arabidopsis lyrata from Europe and North America. Generally, we found that TE insertions showed a lower frequency when they were inserted in or near genes, especially TEs targeted by epigenetic silencing, suggesting purifying selection at work. We also found that many TEs were lost or got fixed in North American populations during the colonization and the postglacial range expansion from refugia of the species in North America, as well as during the transition to selfing, suggesting a potential “TE load.” Finally, we found that silenced TEs increased in frequency and even tended to reach fixation when they were linked to imprinted genes. We conclude that in A. lyrata, genomic imprinting has spread in natural populations through demographic events and positive selection acting on silenced TEs, potentially under a parental conflict scenario.

Reproductive strategies play a major role in plant speciation. Notably, transitions from outcrossing to selfing may lead to relaxed sexual selection and parental conflict. Shifts in mating systems can affect maternal and paternal interests, and thus parent–specific influence on endosperm development, leading to reproductive isolation: if selfing and outcrossing species hybridize, the resulting seeds may not be viable due to endosperm failure. Nevertheless, it remains unclear how the switch in mating systems can impact reproductive isolation between recently diverged lineages, that is, during the process of speciation. We investigated this question using Arabidopsis lyrata, which recently transitioned to selfing (10,000 years ago) in certain North American populations, where European populations remain outcrossing. We performed reciprocal crosses between selfers and outcrossers, and measured seed viability and endosperm development. We show that parental genomes in the hybrid seed negatively interact, as predicted by parental conflict. This leads to extensive hybrid seed lethality associated with endosperm cellularization disturbance. Our results suggest that this is primarily driven by divergent evolution of the paternal genome between selfers and outcrossers. In addition, we observed other hybrid seed defects, suggesting that sex-specific interests are not the only processes contributing to postzygotic reproductive isolation.

Bacteria that positively interact with plant roots are defined as plant growth promoting rhizobacteria (PGPR). Although the positive effect of PGPR on plant growth has been widely studied, their impact on genetic regulation during plant growth processes remains largely unknown. Therefore, this study aimed to gain a deeper understanding of the regulatory role of miRNA and redox enzymes in response to PGPR at the maize seedling stage in leaf growth zone which consists of the meristem, elongation and mature zones. For this purpose, growth of the third leaf was monitored in response to Pseudomonas putida ( P. putida ) KT2440 at phenotypic, physiological, cellular, kinematic, and transcriptional levels. This application resulted in an increase of 15% in shoot length, 56% in both shoot fresh/dry weight, 10% in chlorophyll amount, 8% in mature cell length, 15% in leaf elongation rate, and 7% in cell production; meanwhile final leaf length was unchanged, while leaf area and leaf width decreased by 22% and 16%, respectively. Ascorbate peroxidase and glutathione reductase activity increased throughout the leaf growth zone indicating a possible role in PGPR-plant interaction during transition between cell division, expansion and differentiation processes. The expression analysis of cell cycle check point marker genes revealed that CycA2_1 was mainly responsible for promoting cell proliferation in meristem. miR160, miR169 and miR408 were differentially expressed in the meristem, indicating their indirect regulatory roles in the cell division response to PGPR. In addition, miR160, miR319 and miR396 were downregulated in the elongation zone, which draws attention to their possible role in regulating cell elongation processes. In summary, cell cycle, redox and miRNA regulation in maize seedling growth zones in response to P. putida were investigated for the first time in this study.

Genomic imprinting is a form of gene regulation leading to the unequal expression of maternal and paternal alleles. The main hypothesis invoked to explain the evolution of imprinted genes is the kinship theory, which posits a conflict between parental genomes over resource allocation in progeny. According to this theory, imprinted genes are expected to undergo a shift from balancing to directional selection, in coding or regulatory regions. However, most studies addressing selection in imprinted genes have focused on self-fertilizing species, where conflicts over resource allocation are predicted to be weak. Consequently, the impact of kinship theory on the evolution of imprinted genes remains largely untested. Furthermore, the predicted coevolution between certain imprinted genes under kinship theory has not been tested yet empirically. Combined phylogenetic and population genomic approaches, we investigated signatures of selection on imprinted genes across the Brassicaceae family and in autogamous and allogamous populations of , and searched for evidence of coevolution among imprinted genes. We found that endosperm-expressed genes exhibited signals of balancing selection across Brassicaceae and within allogamous populations, consistent with unresolved intralocus conflicts. Supporting the kinship theory, these signals varied with mating system. Moreover, phylogenetic analyses further indicated negative directional selection acting on imprinted genes. However, population-level signals were independent of mating system and showed limited concordance with kinship predictions, possibly due to stronger selection acting on expression than on coding sequences. Finally, we identified coevolution between imprinted genes, although not at specific sites, suggesting that interactions beyond protein sequence drive this process.

Genomic imprinting is a form of gene regulation resulting in the unequal expression of the two parental alleles. Two main hypotheses are usually mentioned to explain it, the kinship and the sexual antagonism theories, together related to a conflict over resource allocation. Between the different common assumptions expected under these theories, directional selection on imprinted genes could help to discriminate the best theory to explain imprinting because the selection is expected, in regulatory or in coding regions respectively. But, so far, most researches that studied selection in imprinted genes have focused on autogamous species, whose conflict for ressource’s allocation is expected to be low. Moreover, kinship theory is expected to promote intense antagonistic coevolution between imprinted genes, but this has never been tested so far. To address these knowledge gaps, using phylogenetic and population genomics approaches, we searched for signals of selection on imprinted genes across the Brassicaceae family and in allogamous and autogamous populations of Arabidopsis lyrata, and we investigated signals of coevolution across imprinted genes. Overall, we found that non-imprinted endosperm genes presented signals of balancing selection, as expected in the case of unresolved intralocus conflict. Moreover, according to kinship theory, the PEGs exhibited signals of directional selection but not in coding regions and this signal was sensitive to mating systems. Finally, we found imprinted genes showing signals of coevolution, but not related to specific sites, suggesting that the coevolution is driven by other interactions than protein, as predicted by kinship theory.