Grass evolution inferred from chromosomal rearrangements and geometrical and statistical features in RNA structure

The grasses (Poaceae) represent a monophyletic lineage that arose about 70 million years ago. The lineage contains about 10,000 species that differ widely in morphology and physiology. Species show striking differences in genome size, a feature important in the context of conservation of gene content and order (synteny and colinearity) and in the extension of genomic information directly from one grass species to another using comparative approaches. Grass diversification has been a contentious issue, as the exact branching order of the various subfamilies has been difficult to establish with standard methods. This motivated an evolutionary study of deep phylogenctic relationships based on the structure of coding and non-coding RNA molecules and on chromosomal rearrangements. Phylogenetic relationships in the grass family were inferred directly from the structure of RNA using cladistic principles and considerations in statistical mechanics. Coded attributes describing topological and thermodynamic information embedded in RNA molecules were treated as linearly ordered multi-state characters and were polarized by fixing the direction of character transformation toward molecular order. Intrinsically rooted phylogenies derived from the structure of signal recognition particle (SRP) RNA, the mRNA encoded by the early nodulation gene enod40, the small subunit of ribosomal RNA (rRNA), and the internal transcribed spacer ITS1 of rRNA established an order for the diversification of major grass lineages, suggesting a sister relationship of the Pooideae and the PACCAD clade. This same conclusion was reached when large-scale chromosomal rearrangements derived from the comparative genetic mapping of cereal genomes were studied. Chromosomal complements aligned in the most parsimonious manner allowed identification and coding of characters depicting chromosomal translocations, insertions, and linkage block arrangements and the reconstruction of phylogenetic trees based on large-scale chromosomal structure. Congruent reconstruction of deep branching relationships using geometrical and statistical features of RNA structure and orthology and large scale chromosomal recombination events support assumptions of polarization in character argumentation, and fail to falsify the claim that extant grass chromosomes can be considered combinations of linkage blocks of an ancestor of the rice genome. Congruence also suggests that the universal tendency toward order in RNA and the search for the most parsimonious organization of be genome architecture appear to be mutually supported drivers of molecular evolution. The study clarifies the relationship of major clades in the grasses, shows that phylogenetic history can be reconstructed effectively from the combinatorial exchange of chromosomal linkage blocks, and reveals considerable phylogenetic signal embedded in the structure of signal polypeptide-coding mRNA molecules, describing an instance where mRNA structure is the subject of strong evolutionary constraint.