Transposable elements drive rapid phenotypic variation in Capsella rubella Xiao-Min Niua,b,1, Yong-Chao Xua,b,1, Zi-Wen Lia, Yu-Tao Biana,b, Xing-Hui Houa,b, Jia-Fu Chena,b, Yu-Pan Zoua,b, Juan Jianga,b, Qiong Wua, Song Gea,b, Sureshkumar Balasubramanianc, and Ya-Long Guoa,b,2 aState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China; bUniversity of Chinese Academy of Sciences, 100049 Beijing, China; and cSchool of Biological Sciences, Monash University, VIC 3800, Australia Edited by Ian T. Baldwin, Max Planck Institute for Chemical Ecology, Jena, Germany, and approved February 19, 2019 (received for review July 4, 2018) Rapid phenotypic changes in traits of adaptive significance are of invasion with a much wider distribution than that of its out- crucial for organisms to thrive in changing environments. How crossing sister species Capsella grandiflora (16). C. rubella provides such phenotypic variation is achieved rapidly, despite limited an excellent opportunity to unravel the underlying mechanisms, in genetic variation in species that experience a genetic bottleneck addition to its transition to selfing that helps with rapid coloni- is unknown. Capsella rubella, an annual and inbreeding forb (Bras- zation, for the genetic paradox of invasion (14, 15, 17). sicaceae), is a great system for studying this basic question. Its In this study, we reasoned that, if TEs are critical for rapid distribution is wider than those of its congeneric species, despite phenotypic variation and adaptation, their distribution in the C. an extreme genetic bottleneck event that severely diminished its rubella genome might reflect this. Through population genomics genetic variation. Here, we demonstrate that transposable ele- analyses, we show that TEs are highly enriched in promoters and ments (TEs) are an important source of genetic variation that could downstream regions of genes in C. rubella compared with C. account for its high phenotypic diversity. TEs are (i) highly grandiflora. TEs are also highly polymorphic in natural pop- enriched in C. rubella compared with its outcrossing sister species ulations of C. rubella, and 4.2% of polymorphic TE insertions are Capsella grandiflora, and (ii) 4.2% of polymorphic TEs in C. rubella associated with significant changes in expression levels of their are associated with variation in the expression levels of their ad- adjacent genes. In particular, we demonstrate that frequent TE jacent genes. Furthermore, we show that frequent TE insertions at insertions at the FLOWERING LOCUS C (FLC) locus in natural FLOWERING LOCUS C (FLC) in natural populations of C. rubella populations of C. rubella affect its expression and could explain could explain 12.5% of the natural variation in flowering time, a 12.5% of the variation in flowering time, one of the most important key life history trait correlated with fitness and adaptation. In life history traits correlated with adaptation. We also reveal that a ′ particular, we show that a recent TE insertion at the 3 UTR of TE insertion in the 3′ UTR affects mRNA stability. Overall, our FLC affects mRNA stability, which results in reducing its steady- results indicate that TEs play a crucial role in rapid phenotypic state expression levels, to promote the onset of flowering. Our variation, which could potentially promote adaptation to changing results highlight that TE insertions can drive rapid phenotypic var- iation, which could potentially help with adaptation to changing environments in a species with limited standing genetic variation. Significance Brassicaceae | Capsella rubella | natural variation | rapid phenotypic The mechanisms underlying rapid adaptation to changing en- variation | transposable elements vironments in species with reduced genetic variation, referred to as the “genetic paradox of invasion,” are unknown. We re- port that transposable elements (TEs) are highly enriched in the apid phenotypic changes in traits of adaptive significance gene promoter regions of Capsella rubella compared with its provide organisms with potentials for local adaptation, which R outcrossing sister species Capsella grandiflora. We also show is critical for both survival and range expansion of organisms. that a number of polymorphic TEs in C. rubella are associated This becomes even more crucial in the context of global climate with changes in gene expression. Frequent TE insertions at change (1). Species often experience a genetic bottleneck after FLOWERING LOCUS C of C. rubella affect flowering-time vari- speciation or introduction into a new area that diminishes their ation, an important life history trait correlated with fitness. genetic variation, but rapidly adapt and become invasive there- These results indicate that TE insertions drive rapid phenotypic after, which is referred to as the “genetic paradox of invasion” – variation, which could potentially help adapting to novel en- (2 4). However, the underlying mechanisms mediating these vironments in species with limited genetic variation. rapid diversification phenotypes, in traits that are correlated with adaptation, are unclear. Author contributions: Y.-L.G. designed research; X.-M.N., Y.-C.X., Z.-W.L., Y.-T.B., X.-H.H., Transposable elements (TEs) are among the most variable J.-F.C., and J.J. performed research; Y.-L.G. contributed new reagents/analytic tools; components of the genome, which can replicate and integrate X.-M.N., Y.-C.X., Z.-W.L., Y.-P.Z., and Q.W. analyzed data; and X.-M.N., S.G., S.B., and into new positions. Changes in the environment, such as climate Y.-L.G. wrote the paper. change, can alter both the copy number of TEs and their effects The authors declare no conflict of interest. on gene regulation, generating novel genetic and phenotypic This article is a PNAS Direct Submission. variation of potential adaptive significance (5). Therefore, TEs This open access article is distributed under Creative Commons Attribution-NonCommercial- have the potential to quickly create abundant genetic diversity NoDerivatives License 4.0 (CC BY-NC-ND). and thus be agents of rapid adaptation (6–10). Despite extensive Data deposition: The data described in the paper have been deposited in the National Center for Biotechnology Information Sequence Read Archive under accession nos. studies on their phenotypic effects, the extent to which TEs can PRJNA392709, PRJNA392711, and PRJNA511520 and in GenBank under accession nos. contribute to the process of rapid adaptation is largely unknown MF422379–MF422413, MF422414–MF422449, MF422450–MF422525, MF142149–MF142156, (11–13). and MG492014–MG492020. To explore whether TEs could drive rapid phenotypic di- 1X.-M.N. and Y.-C.X. contributed equally to this work. versification in species with limited genetic variation, we focused 2To whom correspondence should be addressed. Email: [email protected]. on Capsella rubella (Brassicaceae), an annual and inbreeding This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. forb that experienced a genetic bottleneck during speciation (14, 1073/pnas.1811498116/-/DCSupplemental. 15). C. rubella provides a typical example of the genetic paradox Published online March 15, 2019. 6908–6913 | PNAS | April 2, 2019 | vol. 116 | no. 14 www.pnas.org/cgi/doi/10.1073/pnas.1811498116 Downloaded by guest on October 1, 2021 environments in plants and could explain the genetic paradox regions (SI Appendix,Fig.S2B). The number of polymorphic TEs of invasion. in these accessions ranged from 1,024 to 1,688, and 1,731 in the reference MTE (SI Appendix, Fig. S3 and Table S1). The poly- Results morphic TEs that are present in at least two accessions were TEs Are Highly Enriched in C. rubella and Affect the Expression Levels considered as common. In total, of the 3,808 polymorphic TEs, of Its Adjacent Genes. We hypothesized that if TEs are among the 2,558 (67.17%) were present in at least two accessions, suggesting key determinants of phenotypic variation, their distribution may a common allelic variation (Fig. 1C). differ between C. rubella and its outcrossing congeneric sister To assess the functional implications of this variation, we species C. grandiflora. To test this, we compared the distribution performed transcriptome sequencing for three representative of TEs in 19,795 orthologous gene pairs between C. rubella and accessions of C. rubella, MTE, 86IT1, and 879 (SI Appendix, C. grandiflora. TEs are highly enriched in different genic regions Table S2), based on their positions on the phylogenetic tree of 28 of the C. rubella compared with the corresponding regions of C. C. rubella accessions (SI Appendix, Fig. S1). In these three ac- grandiflora (Fig. 1A). Our analysis with orthologous regions cessions there are 1,309 polymorphic TEs, of which 5.45% were unmasked these divergent distribution patterns compared with located in genic regions and 94.55% were in intergenic regions. the previous study (18), since the genomes of these two species We found that 55 of 1,309 polymorphic TE loci in these three have varied coverages/assemblies. In addition, TEs are highly accessions (4.2%) were associated with significant changes in the enriched in the promoter and downstream regions of genes in C. expression levels of their adjacent genes [Wilcoxon sum test, rubella compared with C. grandiflora (Fig. 1B), indicating that false discovery rate (FDR) corrected, P < 0.05, SI Appendix, TEs could potentially contribute to the diversification of gene Table S3]. Among these TEs that are associated with changes in expression in C. rubella. gene expression, retrotransposons are more common (36.37%, To assess whether TEs are polymorphic in C. rubella,we SI Appendix, Fig. S4). A Gene Ontology enrichment analysis (21) scanned 28 C. rubella genomes, which included 27 accessions (18, of the genes that are affected by the TEs using the Arabidopsis 19) (SI Appendix, Table S1), with MTE accession as a reference orthologous genes suggested that these genes are involved in (20). A phylogenetic tree based on whole-genome sequences lateral root formation and defense response (SI Appendix, Fig.