Architecture and evolution of a minute plant genome

Abstract

It has been argued that the evolution of plant genome size is principally unidirectional and increasing owing to the varied action of whole-genome duplications (WGDs) and mobile element proliferation1. However, extreme genome size reductions have been reported in the angiosperm family tree. Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. Unexpectedly, we identified at least three rounds of WGD in U. gibba since common ancestry with tomato (Solanum) and grape (Vitis). The compressed architecture of the U. gibba genome indicates that a small fraction of intergenic DNA, with few or no active retrotransposons, is sufficient to regulate and integrate all the processes required for the development and reproduction of a complex organism.

Long-read sequencing uncovers the adaptive topography of a carnivorous plant genome

“…Carnivorous plants are interesting model systems not only for understanding the molecular mechanisms underlying nutrient acquisition strategies, but also for discovering the regulatory underpinnings of their unique trapping morphologies. U. gibba is of particular interest given the previous publication of an ∼82-Mb short-read assembly (10), which revealed that its genome gained and deleted gene duplicates significantly faster than those of other genomes (11). Given that the U. gibba genome likely descended via considerable shrinkage from an ancestral genome up to 1.5 Gb in size (12), duplicates that survived deletion during its evolutionary history arguably evolved under greater purifying selection pressure compared with the more expansive genomes of most angiosperms.…”

“…Utricularia gibba is an aquatic carnivorous plant with an unusually small but highly dynamic nuclear genome that experienced at least two whole-genome duplication (WGD) events during its evolutionary history since divergence from grapevine, tomato, and other species (10). Carnivorous plants are interesting model systems not only for understanding the molecular mechanisms underlying nutrient acquisition strategies, but also for discovering the regulatory underpinnings of their unique trapping morphologies.…”

Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum

“…It was thought that plants have a 'one-way ticket to genome obesity' due to the retention of proliferating transposable elements 21 . However, analysis of carnivorous plants Utricularia gibba (bladderwort, 82 Mb) 22 and Genlisea aurea (corkscrew, 63.6 Mb) 23 provided evidence that almost all intergenic space can be purged. Small genomes also arise from a reduction in gene number as seen in the aquatic monocotyledon Spirodela polyrhiza, which has the fewest predicted protein coding genes at 19,623 (ref.…”

Genome of wild olive and the evolution of oil biosynthesis

“…Within the Lamiales, multiple WGD independent from the paleopolyploidy in the Solanales have been described: two or three in the lineage leading to U. gibba (one of which could be shared with M. guttatus) (18), and one in the lineage leading to S. indicum (estimated age similar to tomato) (19). This latter one and the oldest WGD in U. gibba could denote the same event, possibly even shared with the older WGD in the oleaster and ash lineage, or both could be independent ones, partly depending on their phylogenetic relationship (SI Appendix, section 3.2).…”