PMID: 21551031;PMCID: PMC3166216;Abstract:
Vascular plants appeared ∼410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community.
From the set of all pairwise homologies, weighted by sequence similarities, among a set of genomes, we seek disjoint orthology sets of genes, in which each element is orthogonal to all other genes (on a different genome) in the same set. In a graph-theoretical formulation, where genes are vertices and weighted edges represent homologies, we suggest three criteria, with three different biological motivations, for evaluating the partition of genes produced by deletion of a subset of edges: i) minimum weight edge removal, ii) minimum degree-zero vertex creation, and iii) maximum number of edges in the transitive closure of the graph after edge deletion. For each of the problems, all either proved or conjectured to be NP-hard, we suggest approximate and heuristic algorithms of finding orthology sets satisfying the criteria, and show how to incorporate genomes that have a whole genome duplication event in their immediate lineage. We apply this to ten flowering plant genomes, involving 160,000 different genes in given pairwise homologies. We evaluate the results in a number of ways and recommend criterion iii) as best suited to applications to multiple gene order alignment. © 2011 Springer-Verlag.