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Advances in optical transmission technology are driving the evolution from legacy opaque toward transparent backbone networks. Aiming at reducing the costs and energy consumption, transparent networks allow the data to be kept optical end to end and thus removing the majority of the expensive optical-electrical-optical (OEO) devices. Nonetheless, physical impairments accumulate on the signal along optical transparent paths, therefore limiting the system reach and the overall network performance. Furthermore, failures propagate in a transparent network environment and they cannot be easily localized and isolated. So then, transparent networks need to deal with a number of challenges impacting both planning and operation phases. Such challenges require the use of cross-layer approaches, which involve dynamic interactions between the physical layer and the network layer to enable the compensation for mismatching of requirements and resources. In this paper, we aim to provide an overview of such challenges, reporting comparative analysis with a selection of existing solutions and to cast a glance at the open issues for future research.