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Background: Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. Results: In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. Conclusions: At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience. † Benjamin Noel and France Denoeud have equal contribution.

Telomeres are environment-sensitive regulators of health and aging. Here,we present telomere DNA length analysis of two reef-building coral genera revealing that the long- and short-term water thermal regime is a key driver of between-colony variation across the Pacific Ocean. Notably, there are differences between the two studied genera. The telomere DNA lengths of the short-lived, more stress-sensitive Pocillopora spp. colonies were largely determined by seasonal temperature variation, whereas those of the long-lived, more stress-resistant Porites spp. colonies were insensitive to seasonal patterns, but rather influenced by past thermal anomalies. These results reveal marked differences in telomere DNA length regulation between two evolutionary distant coral genera exhibiting specific life-history traits. We propose that environmentally regulated mechanisms of telomere maintenance are linked to organismal performances, a matter of paramount importance considering the effects of climate change on health. published

The linearity of eukaryotic chromosomes requires the presence of a particular terminal chromatin structure, named telomere, to control the stability and function of genomes. Changes in telomere structure during life can determine longevity, stress resistance and disease susceptibility. Our knowledge on the contribution of environmental factors on telomere length (TL) variability remains at its infancy, as well as the diversity of telomere maintenance mechanisms and ageing strategies existing in the tree of life. In this regard reef building corals are an interesting but yet poorly investigated model to tackle the question of telomere response to environment. Indeed those long lived animals cannot escape external environmental stressors due to their fixed life mode nor internal ones due to the symbiosis, within their gastrodermal cells, with a photosynthetic microalgae. Here I combined an extensive field case study on 3 coral genera (two scleractinians, Pocillopora sp. and Porites sp. and the hydrozoan Millepora sp.) as well as controlled conditions test on the coral model Stylophora pistillata to unravel the possible links between telomere DNA length variation and environmental stress. I found that an absence of TL shortening with age and size in all the investigated corals. I observed a possible impact of dark induced bleaching on TL and different TL dynamics in wild populations. Pocillopora sp. mean TL is constrained both by genetic and environment while Porites sp. has a remarkable ability to maintain its TL regardless of size, genetic and some environment disturbance. Yet both of genera TLs were negatively correlated with seasonal deviations, identifying this environmental parameter as a factor overcoming TL maintenance in genera with different TL dynamics and life-history strategies.; La linéarité des chromosomes eucaryotes implique la présence d’une chromatine à la structure particulière, appelée télomère, pour contrôler la stabilité du génome et conserver sa fonction. Des changements dans la structure des télomères peuvent déterminer la longévité, la résistance au stress et la susceptibilité de développer certaines pathologies. Notre compréhension sur la contribution des facteurs environnementaux sur la longueur des télomères n’en est qu’à ses balbutiements, tout comme notre connaissance de la diversité des mécanismes de régulation de la taille des télomères dans l’arbre de la vie. Les coraux constructeurs de récifs sont à cet égard des modèles de choix, leurs conditions de vie fixée les empêchant de fuir des conditions défavorables et leur endosymbiose obligatoire avec une micro-algue photosynthétique les exposant à un stress oxydant quotidien. Leurs télomères ne sont pourtant que peu étudiés. Dans ce travail de thèse, j’ai combiné une large étude de terrain sur 3 genres de coraux (deux scléractiniaires, Pocillopora sp. et Porites sp., et un hydrozoaire Millepora sp.) et une étude en conditions contrôlées sur l’espèce modèle Stylophora pistillata dans le but de comprendre le lien entre la variation de la taille des télomères et l'environnement. J’ai observé que la taille des télomères des coraux ne diminuait pas avec l’âge, ni avec la taille des colonies, mais qu’une rupture de la symbiose induite à l’obscurité pouvait induire un raccourcissement des télomères. J’ai aussi montré que des espèces avec des stratégies évolutives différentes avaient des régulations de leurs tailles de télomères différentes, le genre Pocillopora sp. étant contraint à la fois par la génétique et l'environnement tandis que le genre Porites sp. démontrant un incroyable maintien de la taille des télomères en dépit des variations génétiques ou des catégories d'environnements. Cependant, malgré leurs différentes stratégies, la taille des télomères des deux genres étaient négativement corrélées aux variations environnementales, mettant à jour ce paramètre comme crucial et potentiellement perturbateur des mécanismes de maintien de la taille des télomères.