While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

Sequences of the internal transcribed spacers (ITS) of nuclear ribosomal DNA were acquired for 112 species of Balsaminaceae worldwide and five species of its closest relatives Marcgraviaceae and Tetrameristaceae. Phylogenetic analyses applying parsimony and distance estimates confirmed the monophyly of Balsaminaceae and suggest the monophyly of Impatiens. Within Impatiens, a few clades are recognized with strong support. Two of the most important clades are the spurless Madagascan endemic group, and the one comprising species with broadly fusiform fruits and the basic chromosome number x = 8, that shows a Southeast Asia, southern India, Africa, and Madagascar connection. Despite recognition of several strongly supported small lineages, ITS data alone could not resolve relationships among most of the lineages with confident support values. ITS phylogenies are therefore of limited taxonomic value for Impatiens. However, ITS phylogenies do reveal that extant Impatiens species are of Southeast Asian origin, from where dispersals to boreal Eurasia and North America, to central Asia and eastern Europe via the Himalayas, and to India and Africa have occurred. The Madagascan Impatiens show an African origin. Molecular phylogenies suggest the ancestral basic chromosome number to be x = 10, and the spurred flowers and elongated linear fruits to be plesiomorphic states in Impatiens. A predominantly descending dysploid chromosome evolution, following dispersal of the clade with broadly fusiform fruits from Southeast Asia to India, Africa, and Madagascar, is also suggested.

MADS-domain transcription factors have been shown to act as key repressors or activators of the transition to flowering and as master regulators of reproductive organ identities. Despite their important roles in plant development, the origin of several MADS-box subfamilies has remained enigmatic so far. Here we demonstrate, through a combination of genome synteny and phylogenetic reconstructions, the origin of three major, apparently angiosperm-specific MADS-box gene clades: FLOWERING LOCUS C- (FLC-), SQUAMOSA- (SQUA-) and SEPALLATA- (SEP-)-like genes. We find that these lineages derive from a single ancestral tandem duplication in a common ancestor of extant seed plants. Contrary to common belief, we show that FLC-like genes are present in cereals where they can also act as floral repressors responsive to prolonged cold or vernalization. This opens a new perspective on the translation of findings from Arabidopsis to cereal crops, in which vernalization was originally described.

Comparative genome biology has unveiled the polyploid origin of all angiosperms and the role of recurrent polyploidization in the amplification of gene families and the structuring of genomes. Which species share certain ancient polyploidy events, and which do not, is ill defined because of the limited number of sequenced genomes and transcriptomes and their uneven phylogenetic distribution. Previously, it has been suggested that most, but probably not all, of the eudicots have shared an ancient hexaploidy event, referred to as the gamma triplication. In this study, detailed phylogenies of subfamilies of MADS-box genes suggest that the gamma triplication has occurred before the divergence of Gunnerales but after the divergence of Buxales and Trochodendrales. Large-scale phylogenetic and K(S)-based approaches on the inflorescence transcriptomes of Gunnera manicata (Gunnerales) and Pachysandra terminalis (Buxales) provide further support for this placement, enabling us to position the gamma triplication in the stem lineage of the core eudicots. This triplication likely initiated the functional diversification of key regulators of reproductive development in the core eudicots, comprising 75% of flowering plants. Although it is possible that the gamma event triggered early core eudicot diversification, our dating estimates suggest that the event occurred early in the stem lineage, well before the rapid speciation of the earliest core eudicot lineages. The evolutionary significance of this paleopolyploidy event may thus rather lie in establishing a species lineage that was resilient to extinction, but with the genomic potential for later diversification. We consider that the traits generated from this potential characterize extant core eudicots both chemically and morphologically.

ABSTRACT. Balsaminaceae are a morphologically diverse family with ca. 1,000 representatives that are mainly distributed in the Old World tropics and subtropics. To understand the relationships of its members, we obtained chloroplast atpB-rbcL sequences from 86 species of Balsaminaceae and five outgroups. Phylogenetic reconstructions using parsimony and Bayesian approaches provide a well-resolved phylogeny in which the sister group relationship between Impatiens and Hydrocera is confirmed. The overall topology of Impatiens is strongly supported and is geographically structured. Impatiens likely originated in South China from which it colonized the adjacent regions and afterwards dispersed into North America, Africa, India, the Southeast Asian peninsula, and the Himalayan region.