MADS-box transcription factors (TFs) are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here, we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs that are bound by PHE1 have been distributed by RC/Helitron transposable elements. Our data provide an example of the molecular domestication of these elements which, by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.

Transposable elements (TEs) constitute major fractions of plant genomes. Their potential to be mobile provides them with the capacity to cause major genome rearrangements. Those effects are potentially deleterious and enforced the evolution of epigenetic suppressive mechanisms controlling TE activity. However, beyond their deleterious effects, TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. Indeed, TEs are increasingly recognized as major drivers of evolutionary novelties by regulating the expression of nearby genes. TEs frequently contain binding motifs for transcription factors and capture binding motifs during transposition, which they spread through the genome by transposition. Thus, TEs drive the evolution and diversification of gene regulatory networks by recruiting lineage-specific targets under the regulatory control of specific transcription factors. This process can explain the rapid and repeated evolution of developmental novelties, such as C4 photosynthesis and a wide spectrum of stress responses in plants. It also underpins the convergent evolution of embryo nourishing tissues, the placenta in mammals and the endosperm in flowering plants. Furthermore, the gene regulatory network underlying flower development has also been largely reshaped by TE-mediated recruitment of regulatory elements; some of them being preserved across long evolutionary timescales. In this review, we highlight the potential role of TEs as evolutionary toolkits in plants by showcasing examples of TE-mediated evolutionary novelties.

Summary Gene duplication is a prominent and recurrent process in plant genomes. Among the possible fates of duplicated genes, subfunctionalization refers to duplicates taking on different parts of the function or expression pattern of the ancestral gene. This partitioning could be accompanied by changes in subcellular localization of the protein products. When alternative splicing of gene products leads to protein products with different subcellular localizations, we propose that after gene duplication there will be partitioning of the alternatively spliced forms such that the products of each duplicate are localized to only one of the original locations, which we refer to as sublocalization. We identified the plastid ascorbate peroxidase (cpAPX) genes across angiosperms and analyzed their duplication history, alternative splicing, and subcellular targeting patterns to identify cases of sublocalization. We found angiosperms typically have one cpAPX gene that generates both thylakoidal APX (tAPX) and stromal APX (sAPX) through alternative splicing. We identified several independent lineage‐specific sublocalization cases with specialized paralogues of tAPX and sAPX. We determined that the sublocalization happened through two types of sequence evolution patterns. Our findings suggest that the divergence through sublocalization is key to the retention of paralogous cpAPX genes in angiosperms.

MADS-box transcription factors (TFs) are present in nearly all major eukaryotic groups. They are divided into Type I and Type II that differ in domain structure, functional roles, and rates of evolution. In flowering plants, major evolutionary innovations like flowers, ovules and fruits have been closely connected to Type II MADS-box TFs. The role of Type I MADS-box TFs in angiosperm evolution remains to be identified. Here, we show that the formation of angiosperm-specific Type I MADS-box clades of Mγ and Mγ-interacting Mα genes (Mα*) can be tracked back to the ancestor of all angiosperms. Angiosperm-specific Mγ and Mα* genes were preferentially expressed in the endosperm, consistent with their proposed function as heterodimers in the angiosperm-specific embryo-nourishing endosperm tissue. We propose that duplication and diversification of Type I MADS-genes underpins the evolution of the endosperm, a developmental innovation closely connected to the origin and success of angiosperms.

SUMMARY The Arabidopsis MEKK1‐MKK1/MKK2‐MPK4 kinase cascade is monitored by the nucleotide‐binding leucine‐rich‐repeat immune receptor SUMM2. Disruption of this kinase cascade leads to activation of SUMM2‐mediated immune responses. MEKK2, a close paralog of MEKK1, is required for defense responses mediated by SUMM2, the molecular mechanism of which is unclear. In this study, we showed that MEKK2 serves as a negative regulator of MPK4. It binds to MPK4 to directly inhibit its phosphorylation by upstream MKKs. Activation of SUMM2‐mediated defense responses induces the expression of MEKK2, which in turn blocks MPK4 phosphorylation to further amplify immune responses mediated by SUMM2. Intriguingly, MEKK2 locates in a tandem repeat consisting of MEKK1, MEKK2 and MEKK3, which was generated from a recent gene duplication event, suggesting that MEKK2 evolved from a MAPKKK to become a negative regulator of MAP kinases.

Duplicated genes are a major contributor to genome evolution and phenotypic novelty. There are multiple possible evolutionary fates of duplicated genes. Here, we provide an example of concerted divergence of simultaneously duplicated genes whose products function in the same complex. We studied POLYCOMB REPRESSIVE COMPLEX2 (PRC2) in Brassicaceae. The VERNALIZATION (VRN)-PRC2 complex contains VRN2 and SWINGER (SWN), and both genes were duplicated during a whole-genome duplication to generate FERTILIZATION INDEPENDENT SEED2 (FIS2) and MEDEA (MEA), which function in the Brassicaceae-specific FIS-PRC2 complex that regulates seed development. We examined the expression of FIS2, MEA, and their paralogs, compared their cytosine and histone methylation patterns, and analyzed the sequence evolution of the genes. We found that FIS2 and MEA have reproductive-specific expression patterns that are correlated and derived from the broadly expressed VRN2 and SWN in outgroup species. In vegetative tissues of Arabidopsis (Arabidopsis thaliana), repressive methylation marks are enriched in FIS2 and MEA, whereas active marks are associated with their paralogs. We detected comparable accelerated amino acid substitution rates in FIS2 and MEA but not in their paralogs. We also show divergence patterns of the PRC2-associated VERNALIZATION5/VIN3-LIKE2 that are similar to FIS2 and MEA. These lines of evidence indicate that FIS2 and MEA have diverged in concert, resulting in functional divergence of the PRC2 complexes in Brassicaceae. This type of concerted divergence is a previously unreported fate of duplicated genes. In addition, the Brassicaceae-specific FIS-PRC2 complex modified the regulatory pathways in female gametophyte and seed development.

a b s t r a c tTransfer of mitochondrial genes to the nucleus, and subsequent gain of regulatory elements for expression, is an ongoing evolutionary process in plants. Many examples have been characterized, which in some cases have revealed sources of mitochondrial targeting sequences and cis-regulatory elements. In contrast, there have been no reports of a nuclear gene that has undergone intracellular transfer to the mitochondrial genome and become expressed. Here we show that the orf164 gene in the mitochondrial genome of several Brassicaceae species, including Arabidopsis, is derived from the nuclear ARF17 gene that codes for an auxin responsive protein and is present across flowering plants. Orf164 corresponds to a portion of ARF17, and the nucleotide and amino acid sequences are 79% and 81% identical, respectively. Orf164 is transcribed in several organ types of Arabidopsis thaliana, as detected by RT-PCR. In addition, orf164 is transcribed in five other Brassicaceae within the tribes Camelineae, Erysimeae and Cardamineae, but the gene is not present in Brassica or Raphanus. This study shows that nuclear genes can be transferred to the mitochondrial genome and become expressed, providing a new perspective on the movement of genes between the genomes of subcellular compartments.

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