Ancient whole-genome duplications (WGDs) characterize many large angiosperm lineages, including angiosperms themselves. Prominently, the core eudicot lineage accommodates 70% of all angiosperms and shares ancestral hexaploidy, termed gamma. Gamma arose via two WGDs that occurred early in eudicot history; however, the relative timing of these is unclear, largely due to the lack of high-quality genomes among early-diverging eudicots. Here, we provide complete genomes for Buxus sinica (Buxales) and Tetracentron sinense (Trochodendrales), representing the lineages most closely related to core eudicots. We show that Buxus and Tetracentron are both characterized by independent WGDs, resolve relationships among early-diverging eudicots and their respective genomes, and use the RACCROCHE pipeline to reconstruct ancestral genome structure at three key phylogenetic nodes of eudicot diversification. Our reconstructions indicate genome structure remained relatively stable during early eudicot diversification, and reject hypotheses of gamma arising via inter-lineage hybridization between ancestral eudicot lineages, involving, instead, only stem lineage core eudicot ancestors.

No abstract

The RACCROCHE pipeline reconstructs ancestral gene orders and chromosomal contents of the ancestral genomes at all internal vertices of a phylogenetic tree. The strategy is to accumulate a very large number of generalized adjacencies, phylogenetically justified for each ancestor, to produce long ancestral contigs through maximum weight matching. It constructs chromosomes by counting the frequencies of ancestral contig co-occurrences on the extant genomes, clustering these for each ancestor and ordering them. The main objective of this paper is to closely simulate the evolutionary process giving rise to the gene content and order of a set of extant genomes (six distantly related monocots), and to assess to what extent an updated version of RACCROCHE can recover the artificial ancestral genome at the root of the phylogenetic tree relating to the simulated genomes.

No abstract

To reconstruct the ancestral genome of a set of phylogenetically related descendant species, we use the raccroche pipeline for organizing a large number of generalized gene adjacencies into contigs and then into chromosomes. Separate reconstructions are carried out for each ancestral node of the phylogenetic tree for focal taxa. The ancestral reconstructions are monoploids; they each contain at most one member of each gene family constructed from descendants, ordered along the chromosomes. We design and implement a new computational technique for solving the problem of estimating the ancestral monoploid number of chromosomes x. This involves a “g-mer” analysis to resolve a bias due long contigs, and gap statistics to estimate x. We find that the monoploid number of all the rosid and asterid orders is $$x=9$$ x = 9 . We show that this is not an artifact of our method by deriving $$x\approx 20$$ x ≈ 20 for the metazoan ancestor.