Massive haplotypes underlie ecotypic differentiation in sunflowers.

Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.

Mutation Load in Sunflower Inversions Is Negatively Correlated with Inversion Heterozygosity.

Recombination is critical both for accelerating adaptation and purging deleterious mutations. Chromosomal inversions can act as recombination modifiers that suppress local recombination in heterozygotes and thus, under some conditions, are predicted to accumulate such mutations. In this study, we investigated patterns of recombination, transposable element abundance, and coding sequence evolution across the genomes of 1,445 individuals from three sunflower species, as well as within nine inversions segregating within species. We also analyzed the effects of inversion genotypes on 87 phenotypic traits to test for overdominance. We found significant negative correlations of long terminal repeat retrotransposon abundance and deleterious mutations with recombination rates across the genome in all three species. However, we failed to detect an increase in these features in the inversions, except for a modest increase in the proportion of stop codon mutations in several very large or rare inversions. Consistent with this finding, there was little evidence of overdominance of inversions in phenotypes that may relate to fitness. On the other hand, significantly greater load was observed for inversions in populations polymorphic for a given inversion compared to populations monomorphic for one of the arrangements, suggesting that the local state of inversion polymorphism affects deleterious load. These seemingly contradictory results can be explained by the low frequency of inversion heterozygotes in wild sunflower populations, apparently due to divergent selection and associated geographic structure. Inversions contributing to local adaptation represent ideal recombination modifiers, acting to facilitate adaptive divergence with gene flow, while largely escaping the accumulation of deleterious mutations.

Standing variation rather than recent adaptive introgression probably underlies differentiation of the texanus subspecies of Helianthus annuus.

The origins of geographic races in wide-ranging species are poorly understood. In Texas, the texanus subspecies of Helianthus annuus has long been thought to have acquired its defining phenotypic traits via introgression from a local congener, H. debilis, but previous tests of this hypothesis were inconclusive. Here, we explore the origins of H. a. texanus using whole genome sequencing data from across the entire range of H. annuus and possible donor species, as well as phenotypic data from a common garden study. We found that although it is morphologically convergent with H. debilis, H. a. texanus has conflicting signals of introgression. Genome wide tests (Patterson's D and TreeMix) only found evidence of introgression from H. argophyllus (sister species to H. annuus and also sympatric), but not H. debilis, with the exception of one individual of 109 analysed. We further scanned the genome for localized signals of introgression using PCAdmix and found minimal but nonzero introgression from H. debilis and significant introgression from H. argophyllus in some populations. Given the paucity of introgression from H. debilis, we argue that the morphological convergence observed in Texas is probably from standing genetic variation. We also found that genomic differentiation in H. a. texanus is mostly driven by large segregating inversions, several of which have signatures of natural selection based on haplotype frequencies.

The activation of the decapping enzyme DCP2 by DCP1 occurs on the EDC4 scaffold and involves a conserved loop in DCP1.

The removal of the 5'-cap structure by the decapping enzyme DCP2 and its coactivator DCP1 shuts down translation and exposes the mRNA to 5'-to-3' exonucleolytic degradation by XRN1. Although yeast DCP1 and DCP2 directly interact, an additional factor, EDC4, promotes DCP1-DCP2 association in metazoan. Here, we elucidate how the human proteins interact to assemble an active decapping complex and how decapped mRNAs are handed over to XRN1. We show that EDC4 serves as a scaffold for complex assembly, providing binding sites for DCP1, DCP2 and XRN1. DCP2 and XRN1 bind simultaneously to the EDC4 C-terminal domain through short linear motifs (SLiMs). Additionally, DCP1 and DCP2 form direct but weak interactions that are facilitated by EDC4. Mutational and functional studies indicate that the docking of DCP1 and DCP2 on the EDC4 scaffold is a critical step for mRNA decapping in vivo. They also revealed a crucial role for a conserved asparagine-arginine containing loop (the NR-loop) in the DCP1 EVH1 domain in DCP2 activation. Our data indicate that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5'-to-3' mRNA degradation by XRN1 in human cells.

Repeatability of adaptation in sunflowers reveals that genomic regions harbouring inversions also drive adaptation in species lacking an inversion.

Local adaptation commonly involves alleles of large effect, which experience fitness advantages when in positive linkage disequilibrium (LD). Because segregating inversions suppress recombination and facilitate the maintenance of LD between locally adapted loci, they are also commonly found to be associated with adaptive divergence. However, it is unclear what fraction of an adaptive response can be attributed to inversions and alleles of large effect, and whether the loci within an inversion could still drive adaptation in the absence of its recombination-suppressing effect. Here, we use genome-wide association studies to explore patterns of local adaptation in three species of sunflower: Helianthus annuus, Helianthus argophyllus, and Helianthus petiolaris, which each harbour a large number of species-specific inversions. We find evidence of significant genome-wide repeatability in signatures of association to phenotypes and environments, which are particularly enriched within regions of the genome harbouring an inversion in one species. This shows that while inversions may facilitate local adaptation, at least some of the loci can still harbour mutations that make substantial contributions without the benefit of recombination suppression in species lacking a segregating inversion. While a large number of genomic regions show evidence of repeated adaptation, most of the strongest signatures of association still tend to be species-specific, indicating substantial genotypic redundancy for local adaptation in these species.

In plants, like in humans, DNA is arranged into sections known as genes that are in turn organised into structures called chromosomes. Mutations that modify the activity of these genes can help plant species to adapt to a new environment or to extreme conditions such as drought. However, successful adaptation often requires changes in many different genes. If these sets of genes are located close to each other on the same chromosome, any mutations will likely be passed onto the next generation together. If the genes are located further away, or even on different chromosomes, they may instead be inherited separately so that the next generation does not benefit as much from the adaptation. A chromosome inversion ­ when a segment of chromosome breaks off and reattaches the other way around ­ can increase the likelihood that sets of mutations on the same chromosome will be inherited together. Many previous studies have found that chromosome inversions tend to drive the ability of species to adapt to different environments by keeping together mutations that affect the same characteristics. However, it is not clear how inversions affect the repeatability of the adaptation, that is, if another group of closely related plants faced the same challenge in their environment would they evolve in the same way, or would they evolve a new response? To address this question, Soudi, Jahani et al. used a genetics approach known as a genome wide association study to explore how three closely related species of sunflower have adapted to their respective environments. Two of the species grow in various environments across the centre and west of the USA that are often hot and dry, whereas the third species is restricted to the more humid coastal plain of Texas, USA. The experiments found that a few key genes had changed in all three sunflower species. However, each species also had mutations in a larger set of unique genes that were not changed in the other species. Regions of chromosomes harbouring inversions in one of the species tended to have more of the key genes within them, compared to other genomic regions. This was also true for species that did not have inversions in those regions. This demonstrates that genes in regions affected by chromosome inversions can still help plants adapt to changes in the environment even in the absence of inversions. Sunflowers are widely grown for their edible oily seeds. In the future, some of the key genes identified in this work may be useful candidates for plant breeding to improve the resilience of sunflowers to drought, high temperatures and other environmental challenges.

HeliantHOME, a public and centralized database of phenotypic sunflower data.

Genomic studies often attempt to link natural genetic variation with important phenotypic variation. To succeed, robust and reliable phenotypic data, as well as curated genomic assemblies, are required. Wild sunflowers, originally from North America, are adapted to diverse and often extreme environments and have historically been a widely used model plant system for the study of population genomics, adaptation, and speciation. Moreover, cultivated sunflower, domesticated from a wild relative (Helianthus annuus) is a global oil crop, ranking fourth in production of vegetable oils worldwide. Public availability of data resources both for the plant research community and for the associated agricultural sector, are extremely valuable. We have created HeliantHOME ( http://www.helianthome.org ), a curated, public, and interactive database of phenotypes including developmental, structural and environmental ones, obtained from a large collection of both wild and cultivated sunflower individuals. Additionally, the database is enriched with external genomic data and results of genome-wide association studies. Finally, being a community open-source platform, HeliantHOME is expected to expand as new knowledge and resources become available.

Genetic basis and dual adaptive role of floral pigmentation in sunflowers.

Variation in floral displays, both between and within species, has been long known to be shaped by the mutualistic interactions that plants establish with their pollinators. However, increasing evidence suggests that abiotic selection pressures influence floral diversity as well. Here, we analyse the genetic and environmental factors that underlie patterns of floral pigmentation in wild sunflowers. While sunflower inflorescences appear invariably yellow to the human eye, they display extreme diversity for patterns of ultraviolet pigmentation, which are visible to most pollinators. We show that this diversity is largely controlled by cis-regulatory variation affecting a single MYB transcription factor, HaMYB111, through accumulation of ultraviolet (UV)-absorbing flavonol glycosides in ligules (the 'petals' of sunflower inflorescences). Different patterns of ultraviolet pigments in flowers are strongly correlated with pollinator preferences. Furthermore, variation for floral ultraviolet patterns is associated with environmental variables, especially relative humidity, across populations of wild sunflowers. Ligules with larger ultraviolet patterns, which are found in drier environments, show increased resistance to desiccation, suggesting a role in reducing water loss. The dual role of floral UV patterns in pollinator attraction and abiotic response reveals the complex adaptive balance underlying the evolution of floral traits.

Flowers are an important part of how many plants reproduce. Their distinctive colours, shapes and patterns attract specific pollinators, but they can also help to protect the plant from predators and environmental stresses. Many flowers contain pigments that absorb ultraviolet (UV) light to display distinct UV patterns ­ although invisible to the human eye, most pollinators are able to see them. For example, when seen in UV, sunflowers feature a 'bullseye' with a dark centre surrounded by a reflective outer ring. The sizes and thicknesses of these rings vary a lot within and between flower species, and so far, it has been unclear what causes this variation and how it affects the plants. To find out more, Todesco et al. studied the UV patterns in various wild sunflowers across North America by considering the ecology and molecular biology of different plants. This revealed great variation between the UV patterns of the different sunflower populations. Moreover, Todesco et al. found that a gene called HaMYB111 is responsible for the diverse UV patterns in the sunflowers. This gene controls how plants make chemicals called flavonols that absorb UV light. Flavonols also help to protect plants from damage caused by droughts and extreme temperatures. Todesco et al. showed that plants with larger bullseyes had more flavonols, attracted more pollinators, and were better at conserving water. Accordingly, these plants were found in drier locations. This study suggests that, at least in sunflowers, UV patterns help both to attract pollinators and to control water loss. These insights could help to improve pollination ­ and consequently yield ­ in cultivated plants, and to develop plants with better resistance to extreme weather. This work also highlights the importance of combining biology on small and large scales to understand complex processes, such as adaptation and evolution.

The role of deadenylation in the degradation of unstable mRNAs in trypanosomes.

Removal of the poly(A) tail is the first step in the degradation of many eukaryotic mRNAs. In metazoans and yeast, the Ccr4/Caf1/Not complex has the predominant deadenylase activity, while the Pan2/Pan3 complex may trim poly(A) tails to the correct size, or initiate deadenylation. In trypanosomes, turnover of several constitutively-expressed or long-lived mRNAs is not affected by depletion of the 5'-3' exoribonuclease XRNA, but is almost completely inhibited by depletion of the deadenylase CAF1. In contrast, two highly unstable mRNAs, encoding EP procyclin and a phosphoglycerate kinase, PGKB, accumulate when XRNA levels are reduced. We here show that degradation of EP mRNA was partially inhibited after CAF1 depletion. RNAi-targeting trypanosome PAN2 had a mild effect on global deadenylation, and on degradation of a few mRNAs including EP. By amplifying and sequencing degradation intermediates, we demonstrated that a reduction in XRNA had no effect on degradation of a stable mRNA encoding a ribosomal protein, but caused accumulation of EP mRNA fragments that had lost substantial portions of the 5' and 3' ends. The results support a model in which trypanosome mRNAs can be degraded by at least two different, partially independent, cytoplasmic degradation pathways attacking both ends of the mRNA.

The FIP-1 like polyadenylation factor in trypanosomes and the structural basis for its interaction with CPSF30.

In trypanosomes transcription is polycistronic and individual mRNAs are generated by a trans-splicing/polyadenylation coupled reaction. We identified a divergent trypanosome FIP1-like, a factor required for mRNA 3' end formation from yeasts to human. Here we showed that it is a nuclear protein with a speckled distribution essential for trypanosome viability. A strong interaction was found between TcFIP1-like and TcCPSF30, a component of the polyadenylation complex. We determined the specific amino acids in each protein involved in the interaction. Significant differences were found between the trypanosome interaction surface and its human counterpart. Although CPSF30/FIP1 interaction is known in other organisms, this is the first report mapping the interaction surface at the amino acid level.

Functional characterization and protein-protein interactions of trypanosome splicing factors U2AF35, U2AF65 and SF1.

Early in the assembly of eukaryotes the branch-point binding protein (BBP, also called SF1) recognizes the branch point sequence, whereas the heterodimer U2AF, consisting of a 65 and a 35 kDa subunit, contacts the polypyrimidine tract and the AG splice site, respectively. Herein, we identified, cloned and expressed the Trypanosoma cruzi and Trypanosoma brucei U2AF35, U2AF65 and SF1. Trypanosomatid U2AF65 strongly diverged from yeast and human homologues. On the contrary, trypanosomatid SF1 was conserved but lacked the C-terminal sequence present in the mammalian protein. Yeast two hybrid approaches were used to assess their interactions. The interaction between U2AF35 and U2AF65 was very weak or not detectable. However, as in other eukaryotes, the interaction between U2AF65 and SF1 was strong. At the cellular level, these results were confirmed by fractionation and affinity-selection experiments in which SF1 and U2AF65 were affinity-selected with TAP tagged SF1, but not with TAP tagged U2AF35. Silencing one of the three factors affected growth and trans-splicing in the first step of this reaction. Trypanosomes are the first described example of eukaryotic cells in which the interaction of two expressed U2AF factors seemed to be very weak, or not detectable.

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.

Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

Mapping of the protein-binding interface between splicing factors SF3b155 and p14 of Trypanosoma cruzi.

SF3b155 and p14 are essential components of spliceosome core that recognize the branch point adenosine, a critical step in splicing in eukaryotes. Trypanosomes are unusual since every transcribed gene is processed by trans-splicing instead of cis-splicing. Thus, the trans-spliceosome emerges as an interesting anti-parasitic drug target since this process is not present in mammalian hosts. Here, we present the orthologues of these proteins in Trypanosoma cruzi that interact strongly with each other. To define similarities and differences with the human pair, we performed a detailed alanine scan analysis that allowed us to identify the regions and the critical amino acids of T. cruzi SF3b155 involved in interaction with p14. We demonstrate that the T. cruzi SF3b155 interface is larger and contains more complex elements than its human counterpart. Additionally, our results provide the first insights into the core of the putative mRNA processing complex of trypanosomes.

Protein-protein interaction map of the Trypanosoma cruzi ribosomal P protein complex.

The large subunit of the eukaryotic ribosome possesses a long and protruding stalk formed by the ribosomal P proteins. Four out of five ribosomal P proteins of Trypanosoma cruzi, TcP0, TcP1alpha, TcP2alpha, and TcP2beta had been previously characterized. Data mining of the T. cruzi genome data base allowed the identification of the fifth member of this protein group, a novel P1 protein, named P1beta. To gain insight into the assembly of the stalk, a yeast two-hybrid based protein interaction map was generated. A parasite specific profile of interactions amongst the ribosomal P proteins of T. cruzi was evident. The TcP0 protein was able to interact with all both P1 and both P2 proteins. Moreover, the interactions between P2beta with P1alpha as well as with P2alpha were detected, as well as the ability of TcP2beta to homodimerize. A quantitative evaluation of the interactions established that the strongest interacting pair was TcP0-TcP1beta.

Analysis of a nuclear localization signal in the p14 splicing factor in Trypanosoma cruzi.

There are only a few reported nuclear localization signals (NLS) in trypanosomes despite intensive research on nuclear metabolic processes such as mRNA processing and transcription during the recent past. Moreover, there are only two reports for a monopartite (La protein) and bipartite (H2B histone, ESAG8) NLS in Trypanosoma brucei. We decided to investigate a NLS in Trypanosoma cruzi by selecting p14, a small RNA recognition motif (RRM) containing protein involved in the splicing process in the nucleus. Its small size (117 amino acids), and an optimized streamlined workflow for analysis in T. cruzi, allowed us to define a region of basic amino acids (RRKRRR) located at the C-terminus that is necessary for nuclear localization. However, the NLS for p14 appeared to be more complex since the signature RRKRRR alone is necessary but not sufficient to direct heterologous proteins, such as GFP, to the nucleus. Since p14 interacts strongly with splicing factor SF3b155, a much larger protein, we designed a p14 variant unable to interact with it. The results allowed us to discard the notion that p14 is entering the nucleus, or is retained within, as the sole consequence of being part of a larger complex. Extensive mapping showed that all of the information for nuclear import resides within the small p14 protein in a bipartite NLS composed of the signature RRKRRR and a region of the RRM domain. Thus, NLS definition in T. cruzi is more complex than previously described.

Identification of core components of the exon junction complex in trypanosomes.

In animal cells, the exon junction complex (EJC) is deposited onto mRNAs during the second step of splicing, 20-24 nt upstream of the exon-exon junction. The EJC core contains four proteins: Mago, Y14, eIF4AIII and Btz. In trypanosomes, cis-splicing is very rare but all mRNAs are subject to 5'trans-splicing of a 39-nt RNA sequence. Here we show that trypanosomes have a conserved Mago and a divergent Y14 protein, but we were unable to identify a Btz orthologue. We demonstrate that Mago and Y14 form a stable heterodimer using yeast two hybrid analyses. We also show that this complex co-purifies in vivo in trypanosomes with a protein containing an NTF2 domain, typically involved in mRNA transport.

Trypanosoma cruzi: analysis of the complete PUF RNA-binding protein family.

The members of the PUF family of RNA-binding proteins regulate the fate of mRNAs by binding to their 3'UTR sequence elements in eukaryotes. In trypanosomes, for which gene expression is polycistronic and controlled almost exclusively by post-transcriptional processes, PUF proteins could play a crucial role. We report here the complete analysis of the PUF protein family of Trypanosoma cruzi composed of 10 members. In silico analysis predicts the existence of at least three major groups within the T. cruzi family, based on their putative binding specificity. Using yeast three hybrid assays, we tested some of these predictions for TcPUF1, TcPUF3, TcPUF5, and TcPUF8 as representatives of these groups. Data mining of the T. cruzi genome led us to describe putative binding targets for the TcPUFs of the most conserved group, TcPUF1 and TcPUF2. The targets include genes for mitochondrial proteins and protein kinases. Finally, immunolocalization experiments showed that TcPUF1 is localized in multiple discrete foci in the cytoplasm supporting its proposed function.

Protein interactions within the TcZFP zinc finger family members of Trypanosoma cruzi: implications for their functions.

The small zinc finger proteins tbZFP1 and tbZFP2 have been implicated in the control of Trypanosoma brucei differentiation to the procyclic form. Here, we report that the complete ZFP family in Trypanosoma cruzi is composed by four members, ZFP1A and B, and ZFP2A and B. ZFP1B is a paralog specific gene restricted to T. cruzi, while the ZFP2A and B paralogs diverged prior to the trypanosomatid lineage separation. Moreover, we demonstrate that TcZFP1 and TcZFP2 members interact with each other and that this interaction is mediated by a WW domain in TcZFP2. Also, TcZFP2B strongly homodimerizes by a glycine rich region absent in TcZFP2A. We propose a model to discuss the relevance of these protein-protein interactions in terms of the functions of these proteins.