The Selaginella genome identifies genetic changes associated with the evolution of vascular plants

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.

Figure 1

Selaginella morphology. (A) The diploid sporophyte body. Bar, 10 mm. (B) A shoot with two ranks of microphylls (“leaves”) and strobili. Each microphyll of a strobilus has either a mega- or microsporangium where mega- or microspores are produced. Bar, 2 mm. (C) An orange microspore on top of a dark megaspore. These single celled haploid spores represent the beginning of the independent haploid gametophyte generation. The microgametophye produces motile sperm and the megagametophyte eggs. Bar, 0.1 mm.

Figure 2

(A) Phylogeny of plants. Taxa in red have sequenced genomes. (B) Gene family gains (+) and losses (−) mapped onto the plant phylogenetic tree. The minimum numbers of gene families present in the ancestors of different plant lineages are circled.

Figure 2

(A) Phylogeny of plants. Taxa in red have sequenced genomes. (B) Gene family gains (+) and losses (−) mapped onto the plant phylogenetic tree. The minimum numbers of gene families present in the ancestors of different plant lineages are circled.