Widespread interspecific divergence in cis-regulation of transposable elements in the Arabidopsis genus

Biased allelic expression in tissues of F1 hybrids between tropical and temperate lotus (Nelumbo nuicfera)

The genome-wide allele-specific expression in F1 hybrids from the cross of tropical and temperate lotus unveils how cis-regulatory divergences affect genes in key pathways related to ecotypic divergence. Genetic variation, particularly cis-regulatory variation, plays a crucial role in phenotypic variation and adaptive evolution in plants. Temperate and tropical lotus, the two ecotypes of Nelumbo nucifera, show distinction in the degree of rhizome enlargement, which is associated with winter dormancy. To understand the roles of genome-wide cis-regulatory divergences on adaptive evolution of temperate and tropical lotus (Nelumbo nucifera), here we performed allele-specific expression (ASE) analyses on the tissues including flowers, leaves and rhizome from F1 hybrids of tropical and temperate lotus. For all investigated tissues in F1s, about 36% of genes showed ASE and about 3% of genes showed strong consistent ASE. Most of ASEs were biased towards the tropical parent in all surveyed samples, indicating that the tropical genome might be dominant over the temperate genome in gene expression of tissues from their F1 hybrids. We found that promoter sequences with similar allelic expression are more conserved than genes with significant or conditional ASE, suggesting the cis-regulatory sequence divergence underlie the allelic expression bias. We further uncovered biased genes being related to phenotypic differentiation between two lotus ecotypes, especially metabolic and phytohormone-related pathways in the rhizome. Overall, our study provides a global landscape of cis-regulatory variations between two lotus ecotypes and highlights their roles in rhizome growth variation for the climatic adaptation.

Leaf chlorosis in Arabidopsis thaliana hybrids is associated with transgenerational decline and imbalanced ribosome number

The interaction of two parental genomes can result in negative outcomes in offspring, also known as hybrid incompatibility. We have previously reported a case in which two recessively interacting alleles result in hybrid chlorosis in Arabidopsis thaliana. A DEAD-box RNA helicase 18 (AtRH18) was identified to be necessary for chlorosis. In this study, we use a sophisticated genetic approach to investigate genes underlying hybrid chlorosis. Sequence comparisons, DNA methylation inhibitor drug treatment and segregation analysis were used to investigate the epigenetic regulation of hybrid chlorosis. Relative rRNA numbers were quantified using real-time quantitative PCR. We confirmed the causality of AtRH18 and provided evidence for the involvement of the promoter region of AtRH18 in the hybrid chlorosis. Furthermore, AtMOM1 from the second parent was identified as the likely candidate gene on chromosome 1. Chlorotic hybrids displayed transgenerational decline in chlorosis, and DNA demethylation experiment restored chlorophyll levels in chlorotic hybrids. Quantification of rRNA indicated that hybrid chlorosis was associated with an imbalance in the ratio of cytosolic and plastid ribosomes. Our findings highlight that the epigenetic regulation of AtRH18 causes hybrid breakdown and provide novel information about the role of AtRH18 in plant development.

Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids

Mitochondrial DNA (mtDNA) in yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, thus becoming homoplasmic. Therefore, hybrids between the yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Saccharomyces cerevisiae/S. uvarum hybrids preferentially retained S. uvarum mtDNA when formed on rich media at colder temperatures, while S. cerevisiae mtDNA was primarily retained on non-fermentable carbon source, at any temperature. Transcriptome data for hybrids harbouring different mtDNA showed a strong environmentally dependent allele preference, which was more important in respiratory conditions. Co-expression analysis for specific biological functions revealed a clear pattern of concerted allelic transcription within the same allele type, which supports the notion that the hybrid cell works preferentially with one set of parental alleles (or the other) for different cellular functions. Given that the type of mtDNA retained in hybrids affects both nuclear expression and fitness, it might play a role in driving hybrid genome evolution in terms of gene retention and loss.

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

Background

Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri.

Results

Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes.

Conclusion

Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.

Robustness of Transposable Element Regulation but No Genomic Shock Observed in Interspecific Arabidopsis Hybrids

The merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. Although our study did not examine TE transposition activity in hybrids, the examination of the transcriptome shows that TE expression is globally robust to hybridization. The term “genomic shock” is perhaps not appropriate to describe transcriptional modification in a viable hybrid merging divergent genomes.

Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus

Background

The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species.

Results

Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome.

Conclusion

These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2060-9) contains supplementary material, which is available to authorized users.

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of Two Oryza Species

Ecological speciation is a common mechanism by which new species arise. Despite great efforts, the role of gene expression in ecological divergence and speciation is poorly understood. Here, we conducted a genome-wide gene expression investigation of two Oryza species that are evolutionarily young and distinct in ecology and morphology. Using digital gene expression technology and the paired-end RNA sequencing method, we obtained 21,415 expressed genes across three reproduction-related tissues. Of them, approximately 8% (1,717) differed significantly in expression levels between the two species and these differentially expressed genes are randomly distributed across the genome. Moreover, 62% (1,064) of the differentially expressed genes exhibited a signature of directional selection in at least one species. Importantly, the genes with differential expression between species evolved more rapidly at the 5' flanking sequences than the genes without differential expression relative to coding sequences, suggesting that cis-regulatory changes are likely adaptive and play an important role in the ecological divergence of the two species. Finally, we showed evidence of significant differentiation between species in phenotype traits and observed that genes with differential expression were overrepresented with functional terms involving phenotypic and ecological differentiation between the two species, including reproduction- and stress-related characteristics. Our findings demonstrate that ecological speciation is associated with widespread and adaptive alterations in genome-wide gene expression and provide new insights into the importance of regulatory evolution in ecological speciation in plants.

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella

The selfing syndrome constitutes a suite of floral and reproductive trait changes that have evolved repeatedly across many evolutionary lineages in response to the shift to selfing. Convergent evolution of the selfing syndrome suggests that these changes are adaptive, yet our understanding of the detailed molecular genetic basis of the selfing syndrome remains limited. Here, we investigate the role of cis-regulatory changes during the recent evolution of the selfing syndrome in Capsella rubella, which split from the outcrosser Capsella grandiflora less than 200 ka. We assess allele-specific expression (ASE) in leaves and flower buds at a total of 18,452 genes in three interspecific F1 C. grandiflora x C. rubella hybrids. Using a hierarchical Bayesian approach that accounts for technical variation using genomic reads, we find evidence for extensive cis-regulatory changes. On average, 44% of the assayed genes show evidence of ASE; however, only 6% show strong allelic expression biases. Flower buds, but not leaves, show an enrichment of cis-regulatory changes in genomic regions responsible for floral and reproductive trait divergence between C. rubella and C. grandiflora. We further detected an excess of heterozygous transposable element (TE) insertions near genes with ASE, and TE insertions targeted by uniquely mapping 24-nt small RNAs were associated with reduced expression of nearby genes. Our results suggest that cis-regulatory changes have been important during the recent adaptive floral evolution in Capsella and that differences in TE dynamics between selfing and outcrossing species could be important for rapid regulatory divergence in association with mating system shifts.

Genome size shifts: karyotype evolution in Crepis section Neglectoides (Asteraceae)

Plant genome size evolution is a very dynamic process: the ancestral genome of angiosperms was initially most likely small, which led to a tendency towards genome increase during evolution. However, findings in several angiosperm lineages demonstrate mechanisms that also led to genome size contraction. Recent molecular investigations on the Asteraceae genus Crepis suggest that several genomic reduction events have occurred during the evolution of the genus. This study focuses on the Mediterranean Crepis sect. Neglectoides, which includes three species with some of the smallest genomes within the whole genus. Crepis neglecta has the largest genome in sect. Neglectoides, approximately twice the size of the two species Crepis cretica and Crepis hellenica. Whereas C. cretica and C. hellencia are more closely related to each other than to C. neglecta the karyotypes of the latter species and C. cretica are similar, while that of C. hellenica differs considerably. Here, the karyotypic organisation of the three species is investigated with fluorescence in-situ hybridisation and studied in a molecular phylogenetic framework based on the nuclear markers Actin, CHR12, CPN60B, GPCR1 and XTH23. Our findings further corroborate the occurrence of genome size contraction in Crepis, and suggest that the difference in genome size between C. neglecta and C. cretica is mostly due to elimination of dispersed repetitive elements, whereas chromosomal reorganisation was involved in the karyotype formation of C. hellenica.

Genomic variation in Arabidopsis: tools and insights from next-generation sequencing

The release of a reference genome for Arabidopsis thaliana in 2000 has been an enormous boon for the study of plant genetics. Less than a decade later, however, a revolution in sequencing technology had enabled rapid and inexpensive re-sequencing of whole A. thaliana genomes. Large-scale efforts to characterize natural genomic variation in A. thaliana have revealed remarkable intra-specific variation in this species, ranging from single-nucleotide differences to large structural rearrangements. The partitioning of this variation by geography and local adaptation has been described using powerful new methods and tools. Simultaneously, an ambitious research agenda has emerged to sequence 1001 A. thaliana lines from around the world, while sequencing of related species is enabling powerful evolutionary genomic analyses. In this review, I summarize recent progress in genomic analysis of natural variation in A. thaliana and its close relatives. This progress has set the stage for the emergence of Arabidopsis as a model genus for evolutionary and functional genomics.

The Arabidopsis genus: An emerging model to elucidate the molecular basis of interspecific differences in transposable element activity

Arabidopsis thaliana is a model plant species and its molecular dissection has greatly contributed to our understanding of the systems preventing genome invasion by transposable elements (TE). Recent advances suggest that A. thaliana may be more efficient than its congener A. lyrata at controlling TE expression and proliferation. The comparative analysis of TE transcription in A. thaliana and A. lyrata, which differ by 40% in genome size, may help understand how silencing mechanisms contribute to the evolution of transposition rate, an important factor controlling genome size variation in plants and animals.

Transgenerational phenotypic and epigenetic changes in response to heat stress in Arabidopsis thaliana

Exposure to heat stress causes physiological and epigenetic changes in plants, which may also be altered in the progeny. We compared the progeny of stressed and control Arabidopsis thaliana wild type and Dicer-like mutant dcl2, dcl3, and dcl4 plants for variations in physiology and molecular profile, including global genome methylation, mRNA levels, and histone modifications in the subset of differentially expressed genes at normal conditions and in response to heat stress. We found that the immediate progeny of heat-stressed plants had fewer, but larger leaves, and tended to bolt earlier. Transposon expression was elevated in the progeny of heat-stressed plants, and heat stress in the same generation tended to decrease global genome methylation. Progeny of stressed plants had increased expression of HSFA2, and reduction in MSH2, ROS1, and several SUVH genes. Gene expression positively correlated with permissive histone marks and negatively correlated with repressive marks. Overall, the progeny of heat stressed plants varied in both their physiology and epigenome and dcl2 and dcl3 mutants were partially deficient for these changes.

The contributions of transposable elements to the structure, function, and evolution of plant genomes

Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.

Understanding desiccation tolerance using the resurrection plant Boea hygrometrica as a model system

Vegetative tissues of Boea hygrometrica, a member of the Gesneriaceae family, can tolerate severe water loss to desiccated state and fully recover upon rehydration. Unlike many other so called "resurrection plants," the detached leaves of B. hygrometrica also possess the same level of capacity for desiccation tolerance (DT) as that of whole plant. B. hygrometrica is distributed widely from the tropics to northern temperate regions in East Asia and grows vigorously in areas around limestone rocks, where dehydration occurs frequently, rapidly, and profoundly. The properties of detached B. hygrometrica leaves and relative ease of culture have made it a useful system to study the adaptive mechanisms of DT. Extensive studies have been conducted to identify the physiological, cellular, and molecular mechanisms underlying DT in the last decade, including specific responses to water stress, such as cell wall folding and pigment-protein complex stabilizing in desiccated leaves. In this review, the insight into the structural, physiological, and biochemical, and molecular alterations that accompany the acquisition of DT in B. hygrometrica is described. Finally a future perspective is proposed, with an emphasis on the emerging regulatory roles of retroelements and histone modifications in the acquisition of DT, and the need of establishment of genome sequence database and high throughput techniques to identify novel regulators for fully understanding of the matrix of DT.

Hidden genetic nature of epigenetic natural variation in plants

Transcriptional gene silencing (TGS) is an epigenetic mechanism that suppresses the activity of repetitive DNA elements via accumulation of repressive chromatin marks. We discuss natural variation in TGS, with a particular focus on cases that affect the function of protein-coding genes and lead to developmental or physiological changes. Comparison of the examples described has revealed that most natural variation is associated with genetic determinants, such as gene rearrangements, inverted repeats, and transposon insertions that triggered TGS. Recent technical advances have enabled the study of epigenetic natural variation at a whole-genome scale and revealed patterns of inter- and intraspecific epigenetic variation. Future studies exploring non-model species may reveal species-specific evolutionary adaptations at the level of chromatin configuration.

A comparison of transcriptome and epigenetic status between closely related species in the genus Arabidopsis

Difference in the level of expression of genes is one of the factors contributing to plant phenotype. As well as being under genetic control, gene expression is regulated by epigenetic processes such as DNA methylation and histone modifications. We compared genome-wide gene expression between Arabidopsis thaliana and the related species Arabidopsis lyrata subsp. lyrata and Arabidopsis halleri subsp. gemmifera to understand which genes might contribute to species differences. Genes categorized into response to stress tended to show differential expression between species, suggesting that divergence of expression in these genes contributes to adaptation to environmental conditions following the divergence of species. Regions methylated in A. lyrata were identified from Methylated-DNA immunoprecipitation, and this DNA methylation profile together with transcriptome data revealed that gene body methylation was not associated with differential gene expression between A. thaliana and A. lyrata. The DNA methylation status of four putative imprinted genes of A. lyrata was examined and found to be conserved in vegetative tissues between A. thaliana and A. lyrata in FIS2, HDG3, and HDG9, but not in HDG8.

Genome-wide analysis of cis-regulatory divergence between species in the Arabidopsis genus

Cis-regulatory DNA has been suspected to play a preeminent role in adaptive evolution, but understanding the role of cis-regulatory mutations in gene expression divergence first requires an accurate analysis of the functional differences associated with these regions. We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species Arabidopsis thaliana and A. lyrata with a whole-genome SNP (single nucleotide polymorphism) tiling array. We observed 2,205 genes showing ASE pattern in at least one tissue. Nearly 90% of genes displaying ASE preferentially expressed the allele of A. lyrata. Genome-wide comparison of sequence divergence revealed that genes displaying ASE had a higher ratio of nonsynonymous to synonymous substitutions in coding regions. We further observe that the epigenetic landscape of histone methylation in A. thaliana genome associate with ASE. The asymmetry in the direction of allele-specific expression suggests interspecific differences in the efficiency of gene silencing in F1 hybrids.

Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica)

In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual elements. Our analyses uncover three strong trends: long LTR-RTs are more highly methylated, the insertion times of LTR-RTs are negatively correlated with methylation, and young LTR-RTs tend to be closer to genes than older insertions. Additionally, a phylogenetic examination of the gypsy-like LTR-RT superfamily revealed that methylation is phylogenetically correlated. Given these observations, we present a model suggesting that the phylogenetic correlation among related LTR-RTs is a primary mechanism driving methylation. In this model, bursts of transposition produce new elements with high sequence similarity. The host machinery identifies proliferating elements as well as closely related LTR-RTs through cross-homology. In addition, our data are consistent with previous hypotheses that methylated LTR-RT elements are removed preferentially from regions near genes, explaining some of the observed age distribution.