NEW YORK (GenomeWeb News) – In the online version of Science today, an international research group reported that it has sequenced the first non-seed vascular plant genome — that of the spikemoss, Selaginella moellendorffii.
With the genome in hand, researchers were able to do genomic and proteomic comparisons with several non-vascular, vascular, and flowering plant species that helped them identify sets of genes corresponding to the advent of various plant features — from the acquisition of vascular tissues to the arrival of flowering plants
"We have used the compact Selaginella genome sequence to uncover genes associated with major evolutionary transitions in land plants," senior author Igor Grigoriev, head of fungal genomics at the US Department of Energy's Joint Genome Institute, and co-authors wrote.
"Understanding their functions in Selaginella and other taxa, as well as acquiring the genome sequences of other informative taxa … will be key to understanding the evolution of plant form and function," they added.
Vascular plants — plants with specialized, vein-like tissues for transporting water and nutrients — are thought to have evolved roughly 410 million years ago. Although past studies suggest there were once many vascular plant lineages, just two remain today: one containing seed plants and ferns and another containing spore-producing plants known as lycophytes.
By focusing on the latter vascular plant group, researchers explained, they hoped to get a better handle on the genetic changes involved in plant evolution.
"Because the lycophytes are an ancient lineage that diverged shortly after land plants evolved vascular tissues, we sequenced the Selaginella genome to provide a resource for identifying genes that may have been important in the early evolution of development and metabolic processes unique to vascular plants," they wrote.
Using a whole-genome shotgun sequencing approach, the researchers generated a 212.6 million base genome sequence, which appears to represent two distinct haplotypes with sequences of around 106 million base pairs apiece.
Their analysis of one of the haplotyes suggests that the Selaginella genome contains some 58 microRNAs and 22,285 protein-coding genes, including several genes predicted to code for secondary metabolites.
In contrast to land plants sequenced before, the researchers didn't see any signs of polyploidy or whole-genome duplication in Selaginella.
Similar to the pattern previously reported for Arabidopsis, the team uncovered a preponderance of transposable elements in the Selaginella genome, particularly in some regions with relatively few protein-coding genes.
The genome lacks some genes typically used to help generate a type of small RNA called trans-acting small interfering RNA, or tasiRNA, which regulate gene expression at a post-transcriptional stage.
In flowering plants, these tasiRNAs regulate developmental processes such as leaf polarity, the team explained, suggesting the spikemoss uses some alternative regulatory strategies.
By comparing proteome patterns in Selaginella with those reported for the green alga Chlamydomonas, a moss called Physcomitrella, and 15 different flowering plant species — and looking at how this proteome data related to plant phylogeny — the team homed in on groups of genes that coincide with certain lineages and stages of vascular plant evolution.
That, in turn, allowed them to trace the number of additional genes acquired during the transition from unicellular green algae to multi-cellular land plants, from non-vascular land plants to vascular land plants, and so on.
For example, proteome data hints that roughly three times as many new genes cropped up when seed plant, fern, and flowering plant traits appeared than were acquired during an earlier transition involving a shift in the primary mode of plant reproduction. Their comparison also highlights groups of gene families that expanded in specific plant groups as they took on various lineage-specific features and developmental patterns.