A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana

Abstract

The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA, largely composed of transposable elements. Transposable elements persist through self-replication, but some genes once encoded by transposable elements have, through a process called molecular domestication, evolved new functions that increase fitness. Although they have conferred numerous adaptations, the number of such domesticated transposable element genes remains unknown, so their evolutionary and functional impact cannot be fully assessed. Systematic searches that exploit genomic signatures of natural selection have been employed to identify potential domesticated genes, but their predictions have yet to be experimentally verified. To this end, we investigated a family of domesticated genes called MUSTANG (MUG), identified in a previous bioinformatic search of plant genomes. We show that MUG genes are functional. Mutants of Arabidopsis thaliana MUG genes yield phenotypes with severely reduced plant fitness through decreased plant size, delayed flowering, abnormal development of floral organs, and markedly reduced fertility. MUG genes are present in all flowering plants, but not in any non-flowering plant lineages, such as gymnosperms, suggesting that the molecular domestication of MUG may have been an integral part of early angiosperm evolution. This study shows that systematic searches can be successful at identifying functional genetic elements in noncoding regions and demonstrates how to combine systematic searches with reverse genetics in a fruitful way to decipher eukaryotic genomes.

Figure 1. MUSTANG phylogeny and gene structure in A. thaliana.

(A) MUG phylogeny in nine angiosperm species. At, Arabidopsis thaliana; Bd, Brachypodium distachyon; Cp, Carica papaya; Mg, Mimulus guttatus; Mt, Medicago truncatula; Os, Oryza sativa; Sb, Sorghum bicolor; Vv, Vitis vinifera; Zm, Zea mays. See Figure S1 for sequences and Table S5 for locus IDs. All bootstrap values are >70% (not shown). Cp7 is truncated; its position is approximate. (B) Graphical representation of At-MUG1, At-MUG2, At-MUG7, and At-MUG8 gene transcripts. Bold horizontal lines represent transcripts, dips introns, and rectangles coding sequences.

Figure 2. Phenotypic analysis of mug1 mug2 and mug7 mug8 in A. thaliana.

(A) Phenotypes of wild-type (Col-0), mug1 mug2, and mug7 mug8 based on the following traits: 1) Germination (%); 2) First leaves recorded as number of days after sterilization (DAS); 3) Flowering time (DAS); 4) Rosette leaf coloration; 5) Rosette diameter (cm) at 42 DAS; 6) Height (cm) of primary inflorescence at 42 DAS; 7) Average number of aborted seeds. Measurements based on 60 plants per genotype. Statistical significance based on two-sample student t-test; α = 0.05; * p<0.01; ** p<0.001. (B) Growth phenotype of Col-0, mug1 mug2, and mug7 mug8 at 40 DAS. Scale = 1 cm. (C) Image of an MS plate (0.8% agar w/v; 1% sucrose w/v) containing 17-day-old Col-0 and mug1 mug2 seedlings. (D) Chlorophyll accumulation in Col-0 and mug1 mug2 seedlings. Bars represents standard deviations of quadruple experiments. 200 mg or approximately 10 Col-0 or 30 mug1 mug2 seedlings per experiment. (E) Phenotypes of mug1 mug2 under sucrose conditions. Twelve-day-old seedlings of Col-0 and mug1 mug2 were grown on standard MS medium without sucrose or with 100 mM sucrose. (F) Close up of a dissected mug1 mug2 silique showing a normal funiculus from which the attached mature seed was released (green arrow) and a funiculus attached to undeveloped ovule tissues (red arrow).

Figure 3. Flower structure of wild-type, mug1 mug2, and mug7 mug8 in A. thaliana.

(A–C) Bright-field micrographs of dissected flowers shown of (A) wild-type, (B) mug1 mug2, and (C) mug7 mug8. Scale = 0.5 mm. (D–F) SEM micrographs of dissected flowers of (D) wild-type, (E) mug1 mug2, and (F) mug7 mug8. Scale = 0.5 mm. (G–I) SEM micrographs of dissected flowers at higher magnification showing the stigma papillae of (G) wild-type, (H) mug1 mug2, and (I) mug7 mug8. Scale = 100 µm. (J–L) SEM micrographs of dissected flowers at higher magnification showing one anther and pollen of (J) wild-type, (K) mug1 mug2, and (L) mug7 mug8. Scale = 50 µm.