The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified developmental stage correspondences across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.

Gene expression programs define shared and species-specific phenotypes, but their evolution remains largely uncharacterized beyond the transcriptome layer 1 . Here we report an analysis of the co-evolution of translatomes and transcriptomes using ribosome-profling and matched RNA-sequencing data for three organs (brain, liver and testis) in fve mammals (human, macaque, mouse, opossum and platypus) and a bird (chicken). Our within-species analyses reveal that translational regulation is widespread in the diferent organs, in particular across the spermatogenic cell types of the testis. The between-species divergence in gene expression is around 20% lower at the translatome layer than at the transcriptome layer owing to extensive buffering between the expression layers, which especially preserved old, essential and housekeeping genes. Translational upregulation specifcally counterbalanced global dosage reductions during the evolution of sex chromosomes and the efects of meiotic sex-chromosome inactivation during spermatogenesis. Despite the overall prevalence of bufering, some genes evolved faster at the translatome layer—potentially indicating adaptive changes in expression; testis tissue shows the highest fraction of such genes. Further analyses incorporating mass spectrometry proteomics data establish that the co-evolution of transcriptomes and translatomes is refected at the proteome layer. Together, our work uncovers co-evolutionary patterns and associated selective forces across the expression layers, and provides a resource for understanding their interplay in mammalian organs.

Boraginaceae s.str. is a subcosmopolitan family of 1600 to 1700 species in around 90 genera, and recent phylogenetic studies indicate that the infrafamilial classification as currently used is highly obsolete. The present study addresses the relationships of the major clades in Boraginaceae s.str. with an emphasis on monophyly of, and relationships between previously recognized clades and the position of various unplaced genera such as Afrotysonia, Anoplocaryum, Brachybotrys, Chionocharis, Craniospermum, Thyrocarpus, and Trigonocaryum using three plastid markers and a taxon sampling with four outgroup and 170 ingroup species from 73 genera. The phylogeny shows high statistical support for most nodes on the backbone and within individual clades. Echiochileae are confirmed as sister to the remainder of Boraginaceae s.str., which, in turn, fall into two well‐supported clades, the Boragineae + Lithospermeae and the Cynoglosseae s.l. The latter is highly resolved and includes the Lasiocaryum‐clade (Chionocharis, Lasiocaryum, Microcaryum) and the Trichodesmeae (Caccinia, Trichodesma) as sister to the remainder of the group. Rochelieae (formerly the Eritrichieae s.str., also including Eritrichium, Hackelia, and Lappula) form a poorly supported polytomy together with the Mertensia‐clade (also including Anoplocaryum, Asperugo, and Memoremea) and the Omphalodes‐clade. The enigmatic genus Craniospermum (Craniospermeae) is sister to an expanded Myosotideae (also including Brachybotrys, Decalepidanthus, Trigonocaryum, and Trigonotis) and these two clades are in turn sister to the Core‐Cynoglosseae, in which Afrotysonia glochidiata and Thyrocarpus sampsonii are included. Core‐Cynoglosseae again fall into two pairs of well‐supported subclades. The majority of generic placements are now resolved satisfactorily and the remaining phylogenetic questions can be clearly delimited. Based on the extensive phylogenetic data now available we propose a new infrafamilial classification into three subfamilies and 11 tribes, representing a consensus among the participating authors, according to which major clades are renamed.