Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

International audienceReconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements , and protein divergence into a single evolutionary framework

Evolution des répertoires de gènes et nouveaux gènes chez les levures

Les répertoires de gènes sont des objets extrêmement dynamiques : Des gènes sont dupliqués et perdus, transférés d’un génome à l’autre et des nouveaux gènes sont créés. L’étude de ces processus et de leur impact sur l’évolution des répertoires de gènes est fondamentale pour notre compréhension de l’énorme diversité de la vie sur terre. J’ai reconstruit les familles des gènes homologues chez les levures du clade Lachancea et je les ai classées en trois catégories selon leur présence chez les espèces en dehors du clade en: transmises verticalement (98.2 %), transmises horizontalement (0.15 %) et spécifiques aux Lachancea (1.63 %). Ensuite, j’ai reconstruit l’évolution de chaque famille de gènes le long de l’arbre phylogénétique des Lachancea en terme de gains et de pertes depuis l’origine du clade. Mes résultats suggèrent que les réarrangements chromosomiques balancés (translocations, inversions) peuvent interrompre, au niveau de leurs points de cassure, la séquence codante des gènes, et entraîner jusqu’à 14 % des pertes de gènes observées (rupture de gène). En outre, j’ai observé des corrélations entre le taux de divergence des séquences codant pour des protéines et les taux de duplication de gènes, de translocations et d’inversions, et de rupture de gène, suggérant l’existence d’une horloge génomique qui coordonnerait ces processus. Par la suite, je me suis focalisé sur l’émergence de nouveaux gènes de novo à partir de séquences non-codantes, dont l’impact global sur les génomes n’est pas encore connu. J’ai pour cela analysé les gènes taxonomiquement restreints aux levures des clades Lachancea et Saccharomyces sensu stricto et j’ai pu identifier un ensemble de 596 gènes ayant fort probablement émergé de novo. Le taux d’émergence de novo est constant chez les levures au sein du même clade mais varie d’un ordre de grandeur entre les 2 clades (2.8 gènes/ma chez les Saccharomyces et 0.27 gènes/ma chez les Lachancea). Ces nouveaux gènes sont distribués uniformément sur les chromosomes. Ils sont le plus souvent orientés de façon divergente par rapport à leur voisin en 5’, ce qui suggère que leur transcription pourrait être initiée au niveau de promoteurs divergents, favorisant ainsi la transition d’une séquence intergénique non transcrite à une séquence codante transcrite (puis traduite). Enfin, j’ai montré que dans certains cas, seul un petit nombre de mutations permettent la création d’un gène bien adapté à son environnement génomique, en comparaison avec des gènes plus «anciens». Cela signifie que sous certaines conditions la transition d’une séquence non-codante vers une séquence codante peut être relativement rapide. Globalement, mes résultats suggèrent que l’émergence de novo est un processus évolutif non négligeable, représentant une source importante de création de nouvelles protéines.Gene repertoires are highly dynamic : Genes are duplicated, lost, transferred from one genome toanother and new genes are formed. Studying these processes and how they shape gene repertoireevolution is fundamental to our understanding of how the enormous diversity of life on earth came to be. I reconstructed the homologous gene families of the yeasts of the Lachancea genus and categorized them based on their conservation in species outside the genus into vertically inherited (98.2%), horizontally transferred (0.15%) and taxonomically restricted (1.63%). Then, I inferred the evolution of each family along the genus’ phylogeny and identified the gene gain and loss events that occurred since the genus’ origin. I found that balanced chromosomal rearrangements may be responsible for up to 14% of gene losses by disrupting the coding sequence at their breakpoints and detected 3 cases with clear traces of the disruption at the sequence level. Additionally, I found that correlations exist between the rate of protein-coding sequence divergence and the rates of gene duplication, chromosomal inversions and translocations, and gene disruptions by balanced rearrangements, suggesting the existence of a genomic clock coordinating these processes. Next, I focused on the emergence of new genes de novo from non-coding sequences, a process whose overall impact remains a matter of debate. I thus analyzed taxonomically restricted genes in the two model yeast genera Lachancea and Saccharomyces sensu stricto and identified a robust set of 596 genes that have likely emerged de novo. I found that de novo emergence rates are constant among yeasts of the same genus but differ by an order of magnitude between the two genera with 2.8 genes/my in the Saccharomyces and 0.27 genes/my in the Lachancea. De novo genes are uniformly distributed on yeast genomes and are found divergently oriented relative to their 5’ neighbors suggesting that divergent transcription might play a role in their transition from non-transcribed intergenic sequences to transcribed (and translated) coding sequences. Moreover, through specific examples I was able to show that a few enabling mutations are sufficient for a young de novo gene to emerge already well-adapted relative to older genes, indicating that the transition from non-coding to coding can happen rapidly. Overall, my results support de novo emergence as a ubiquitous evolutionary process and a potent source of novel proteins

Atopic Dermatitis and Water: Is There an Optimum Water Intake Level for Improving Atopic Skin?

Water is a vital nutrient with innumerable functions for every living cell. The functions of human skin include protection against dehydration of the body. Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease that presents with dry skin, erythematous and eczematous lesions, and lichenification. This paper discusses the question of whether extra water intake in children with AD affects skin hydration and the skin barrier function. Among the methods used to treat dry skin, topical leave-on products are the first-line treatment, intended to improve hydration and the skin barrier function. The effectiveness of adequate water intake as a measure to treat dry skin is still under debate. Normal skin hydration increases with dietary water intake, particularly in those with prior lower water consumption. Skin dryness in AD is instrumental to the itch and inflammation cycle, contributing to barrier impairment and aggravating disease severity and flares. Certain emollients provide significant hydration to AD skin, with relief of dryness and reduction in barrier impairment, disease severity, and flares. Further investigations are needed to evaluate the optimum water intake levels in children with AD, as important questions remain unanswered, namely, does oral hydration provide relief of skin dryness and reduce barrier impairment, disease severity, and flares; is there any additional benefit from using mineral or thermal spring water; or is there a need to specifically study the fluid/water intake in children with AD and food allergy (FA) restrictions

Atopic Dermatitis and Water: Is There an Optimum Water Intake Level for Improving Atopic Skin?

Water is a vital nutrient with innumerable functions for every living cell. The functions of human skin include protection against dehydration of the body. Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease that presents with dry skin, erythematous and eczematous lesions, and lichenification. This paper discusses the question of whether extra water intake in children with AD affects skin hydration and the skin barrier function. Among the methods used to treat dry skin, topical leave-on products are the first-line treatment, intended to improve hydration and the skin barrier function. The effectiveness of adequate water intake as a measure to treat dry skin is still under debate. Normal skin hydration increases with dietary water intake, particularly in those with prior lower water consumption. Skin dryness in AD is instrumental to the itch and inflammation cycle, contributing to barrier impairment and aggravating disease severity and flares. Certain emollients provide significant hydration to AD skin, with relief of dryness and reduction in barrier impairment, disease severity, and flares. Further investigations are needed to evaluate the optimum water intake levels in children with AD, as important questions remain unanswered, namely, does oral hydration provide relief of skin dryness and reduce barrier impairment, disease severity, and flares; is there any additional benefit from using mineral or thermal spring water; or is there a need to specifically study the fluid/water intake in children with AD and food allergy (FA) restrictions

New and Upcoming Topical Treatments for Atopic Dermatitis: A Review of the Literature

Atopic dermatitis (AD) is a chronic inflammatory dermatosis with periods of exacerbation and remissions. AD is characterized by intense, persistent pruritus and heterogeneity in clinical symptomatology and severity. Therapeutic goals include the amelioration of cutaneous eruptions, diminishing relapses and eventually the disease burden. To date, topical corticosteroids (TCS) and calcineurin inhibitors (TCI) have yet been deemed the mainstay of topical treatments in AD management. Nevertheless, despite their indisputable efficiency, TCS and TCI are not indicated for continuous long-term use given their safety profile. While research in AD has concentrated predominantly on systemic therapies, more than 30 novel topical compounds are under development. The existing data appear encouraging, with some regimens that are already FDA-approved (ruxolitinib was the most recent in September 2021) and several pharmaceutical pipeline products for mild-to-moderate AD that are in an advanced stage of development, such as tapinarof, difamilast and roflumilast. Larger, long-term studies are still required to evaluate the efficacy and safety of these novel compounds in the long run and weigh their advantages over present treatments. In this review, we aim to provide an overview of the latest knowledge about AD topical treatments, echoing upcoming research trends

A Molecular Portrait of De Novo Genes in Yeasts

International audienc