Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize

Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications

Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

Background

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.

Results

We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.

Conclusions

Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication

BACKGROUND

Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.

RESULTS

We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.

CONCLUSIONS

Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.

The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

Gene duplication is a major driver of organismal evolution. Gene retroposition is a mechanism of gene duplication whereby a gene's transcript is used as a template to generate retroposed gene copies, or retrocopies. Intriguingly, the formation of retrocopies depends upon the enzymatic machinery encoded by retrotransposable elements, genomic parasites occurring in the majority of eukaryotes. Most retrocopies are depleted of the regulatory regions found upstream of their parental genes; therefore, they were initially considered transcriptionally incompetent gene copies, or retropseudogenes. However, examples of functional retrocopies, or retrogenes, have accumulated since the 1980s. Here, we review what we have learned about retrocopies in animals, plants and other eukaryotic organisms, with a particular emphasis on comparative and population genomic analyses complemented with transcriptomic datasets. In addition, these data have provided information about the dynamics of the different "life cycle" stages of retrocopies (i.e., polymorphic retrocopy number variants, fixed retropseudogenes and retrogenes) and have provided key insights into the retroduplication mechanisms, the patterns and evolutionary forces at work during the fixation process and the biological function of retrogenes. Functional genomic and transcriptomic data have also revealed that many retropseudogenes are transcriptionally active and a biological role has been experimentally determined for many. Finally, we have learned that not only non-long terminal repeat retroelements but also long terminal repeat retroelements play a role in the emergence of retrocopies across eukaryotes. This body of work has shown that mRNA-mediated duplication represents a widespread phenomenon that produces an array of new genes that contribute to organismal diversity and adaptation.

Protein-Coding Genes' Retrocopies and Their Functions

Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

In a broad range of taxa, genes can duplicate through an RNA intermediate in a process mediated by retrotransposons (retroposition). In mammals, L1 retrotransposons drive retroposition, but the elements responsible for retroposition in other animals have yet to be identified. Here, we examined young retrocopies from various animals that still retain the sequence features indicative of the underlying retroposition mechanism. In Drosophila melanogaster, we identified and de novo assembled 15 polymorphic retrocopies and found that all retroposed loci are chimeras of internal retrocopies flanked by discontinuous LTR retrotransposons. At the fusion points between the mRNAs and the LTR retrotransposons, we identified shared short similar sequences that suggest the involvement of microsimilarity-dependent template switches. By expanding our approach to mosquito, zebrafish, chicken, and mammals, we identified in all these species recently originated retrocopies with a similar chimeric structure and shared microsimilarities at the fusion points. We also identified several retrocopies that combine the sequences of two or more parental genes, demonstrating LTR-retroposition as a novel mechanism of exon shuffling. Finally, we found that LTR-mediated retrocopies are immediately cotranscribed with their flanking LTR retrotransposons. Transcriptional profiling coupled with sequence analyses revealed that the sense-strand transcription of the retrocopies often lead to the origination of in-frame proteins relative to the parental genes. Overall, our data show that LTR-mediated retroposition is highly conserved across a wide range of animal taxa; combined with previous work from plants and yeast, it represents an ancient and ongoing mechanism continuously shaping gene content evolution in eukaryotes.

LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

RNA-based duplicated genes or functional retrocopies (retrogenes) are known to drive phenotypic evolution. Retrogenes emerge via retroposition, which is mainly mediated by long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in mammals. By contrast, long terminal repeat (LTR) retrotransposons appear to be the major player in plants, although an L1-like mechanism has also been hypothesized to be involved in retroposition. We tested this hypothesis by searching for young retrocopies, as these still retain the sequence features associated with the underlying retroposition mechanism. Specifically, we identified polymorphic retrocopies (retroCNVs) by analyzing public Arabidopsis (Arabidopsis thaliana) resequencing data. Furthermore, we searched for recently originated retrocopies encoded by the reference genome of Arabidopsis and Manihot esculenta. Across these two datasets, we found cases with L1-like hallmarks, namely, the expected target site sequence, a polyA tail and target site duplications. Such data suggest that an L1-like mechanism could operate in plants, especially dicots.

The impact and origin of copy number variations in the Oryza species

Background

Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice.

Results

Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome ‘Nipponbare’. Using Oryza glaberrima as the outgroup, 80 % of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMADS56, BPH14, OsDCL2b and OsMADS30, implying that CNVs might have contributed to phenotypic variations in rice. Most CNV genes were found to be located in non-co-linear positions by comparison to O. glaberrima. One of the origins of these non-co-linear genes was genomic duplications caused by transposon activity or double-strand break repair. Comprehensive analysis of mutation mechanisms suggested an abundance of CNVs formed by non-homologous end-joining and mobile element insertion.

Conclusions

This study showed the impact and origin of copy number variations in rice on a genomic scale.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2589-2) contains supplementary material, which is available to authorized users.

Landscape and evolutionary dynamics of terminal repeat retrotransposons in miniature in plant genomes

Background

Terminal repeat retrotransposons in miniature (TRIMs) are a unique group of small long terminal repeat retrotransposons that are difficult to identify. Thus far, only a few TRIMs have been characterized in the euphyllophytes, and their evolutionary and biological significance as well as their transposition mechanisms are poorly understood.

Results

Using a combination of de novo and homology-based methods, we annotate TRIMs in 48 plant genome sequences, spanning land plants to algae. The TRIMs are grouped into 156 families including 145 that were previously undefined. Notably, we identify the first TRIMs in a lycophyte and non-vascular plants. The majority of the TRIM families are highly conserved and shared within and between plant families. Unlike other long terminal repeat retrotransposons, TRIMs are enriched in or near genes; they are also targeted by sRNAs between 21 and 24 nucleotides in length, and are frequently found in CG body-methylated genes. Importantly, we also identify putative autonomous retrotransposons and very recent transpositions of a TRIM element in Oryza sativa.

Conclusions

We perform the most comprehensive analysis of TRIM transposons thus far and report that TRIMs are ubiquitous across plant genomes. Our results show that TRIMs are more frequently associated with large and CG body-methylated genes that have undergone strong purifying selection. Our findings also indicate that TRIMs are likely derived from internal deletions of large long terminal repeat retrotransposons. Finally, our data and methodology are important resources for the characterization and evolutionary and genomic studies of long terminal repeat retrotransposons in other genomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0867-y) contains supplementary material, which is available to authorized users.

Small-scale gene duplications played a major role in the recent evolution of wheat chromosome 3B

Background

Bread wheat is not only an important crop, but its large (17 Gb), highly repetitive, and hexaploid genome makes it a good model to study the organization and evolution of complex genomes. Recently, we produced a high quality reference sequence of wheat chromosome 3B (774 Mb), which provides an excellent opportunity to study the evolutionary dynamics of a large and polyploid genome, specifically the impact of single gene duplications.

Results

We find that 27 % of the 3B predicted genes are non-syntenic with the orthologous chromosomes of Brachypodium distachyon, Oryza sativa, and Sorghum bicolor, whereas, by applying the same criteria, non-syntenic genes represent on average only 10 % of the predicted genes in these three model grasses. These non-syntenic genes on 3B have high sequence similarity to at least one other gene in the wheat genome, indicating that hexaploid wheat has undergone massive small-scale interchromosomal gene duplications compared to other grasses. Insertions of non-syntenic genes occurred at a similar rate along the chromosome, but these genes tend to be retained at a higher frequency in the distal, recombinogenic regions. The ratio of non-synonymous to synonymous substitution rates showed a more relaxed selection pressure for non-syntenic genes compared to syntenic genes, and gene ontology analysis indicated that non-syntenic genes may be enriched in functions involved in disease resistance.

Conclusion

Our results highlight the major impact of single gene duplications on the wheat gene complement and confirm the accelerated evolution of the Triticeae lineage among grasses.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0754-6) contains supplementary material, which is available to authorized users.

The bright side of transposons in crop evolution

The past decades have revealed an unexpected yet prominent role of so-called 'junk DNA' in the regulation of gene expression, thereby challenging our view of the mechanisms underlying phenotypic evolution. In particular, several mechanisms through which transposable elements (TEs) participate in functional genome diversity have been depicted, bringing to light the 'TEs bright side'. However, the relative contribution of those mechanisms and, more generally, the importance of TE-based polymorphisms on past and present phenotypic variation in crops species remain poorly understood. Here, we review current knowledge on both issues, and discuss how analyses of massively parallel sequencing data combined with statistical methodologies and functional validations will help unravelling the impact of TEs on crop evolution in a near future.

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.

Young, intact and nested retrotransposons are abundant in the onion and asparagus genomes

BACKGROUND AND AIMS

Although monocotyledonous plants comprise one of the two major groups of angiosperms and include >65 000 species, comprehensive genome analysis has been focused mainly on the Poaceae (grass) family. Due to this bias, most of the conclusions that have been drawn for monocot genome evolution are based on grasses. It is not known whether these conclusions apply to many other monocots.

METHODS

To extend our understanding of genome evolution in the monocots, Asparagales genomic sequence data were acquired and the structural properties of asparagus and onion genomes were analysed. Specifically, several available onion and asparagus bacterial artificial chromosomes (BACs) with contig sizes >35 kb were annotated and analysed, with a particular focus on the characterization of long terminal repeat (LTR) retrotransposons.

KEY RESULTS

The results reveal that LTR retrotransposons are the major components of the onion and garden asparagus genomes. These elements are mostly intact (i.e. with two LTRs), have mainly inserted within the past 6 million years and are piled up into nested structures. Analysis of shotgun genomic sequence data and the observation of two copies for some transposable elements (TEs) in annotated BACs indicates that some families have become particularly abundant, as high as 4-5 % (asparagus) or 3-4 % (onion) of the genome for the most abundant families, as also seen in large grass genomes such as wheat and maize.

CONCLUSIONS

Although previous annotations of contiguous genomic sequences have suggested that LTR retrotransposons were highly fragmented in these two Asparagales genomes, the results presented here show that this was largely due to the methodology used. In contrast, this current work indicates an ensemble of genomic features similar to those observed in the Poaceae.

Lessons from natural and artificial polyploids in higher plants

Polyploidy in higher plants is a major source of genetic novelty upon which selection may act to drive evolution, as evidenced by the widespread success of polyploid species in the wild. However, research into the effects of polyploidy can be confounded by the entanglement of several processes: genome duplication, hybridisation (allopolyploidy is frequent in plants) and subsequent evolution. The discovery of the chemical agent colchicine, which can be used to produce artificial polyploids on demand, has enabled scientists to unravel these threads and understand the complex genomic changes involved in each. We present here an overview of lessons learnt from studies of natural and artificial polyploids, and from comparisons between the 2, covering basic cellular and metabolic consequences through to alterations in epigenetic gene regulation, together with 2 in-depth case studies in Senecio and Glycine. See also the sister article focusing on animals by Arai and Fujimoto in this themed issue.

Co-evolution of plant LTR-retrotransposons and their host genomes

Transposable elements (TEs), particularly, long terminal repeat retrotransposons (LTR-RTs), are the most abundant DNA components in all plant species that have been investigated, and are largely responsible for plant genome size variation. Although plant genomes have experienced periodic proliferation and/or recent burst of LTR-retrotransposons, the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms, and/or were deleted/truncated by unequal homologous recombination and illegitimate recombination, as suppression mechanisms that counteract genome expansion caused by LTR-RT amplification. LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes, which appears to be the outcomes of preferential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms. Potential functions of various TEs in their host genomes remain blurry; nevertheless, LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expressions in their host genomes.

Mendelian and non-Mendelian regulation of gene expression in maize

Transcriptome variation plays an important role in affecting the phenotype of an organism. However, an understanding of the underlying mechanisms regulating transcriptome variation in segregating populations is still largely unknown. We sought to assess and map variation in transcript abundance in maize shoot apices in the intermated B73×Mo17 recombinant inbred line population. RNA–based sequencing (RNA–seq) allowed for the detection and quantification of the transcript abundance derived from 28,603 genes. For a majority of these genes, the population mean, coefficient of variation, and segregation patterns could be predicted by the parental expression levels. Expression quantitative trait loci (eQTL) mapping identified 30,774 eQTL including 96 trans-eQTL “hotspots,” each of which regulates the expression of a large number of genes. Interestingly, genes regulated by a trans-eQTL hotspot tend to be enriched for a specific function or act in the same genetic pathway. Also, genomic structural variation appeared to contribute to cis-regulation of gene expression. Besides genes showing Mendelian inheritance in the RIL population, we also found genes whose expression level and variation in the progeny could not be predicted based on parental difference, indicating that non-Mendelian factors also contribute to expression variation. Specifically, we found 145 genes that show patterns of expression reminiscent of paramutation such that all the progeny had expression levels similar to one of the two parents. Furthermore, we identified another 210 genes that exhibited unexpected patterns of transcript presence/absence. Many of these genes are likely to be gene fragments resulting from transposition, and the presence/absence of their transcripts could influence expression levels of their ancestral syntenic genes. Overall, our results contribute to the identification of novel expression patterns and broaden the understanding of transcriptional variation in plants.

Phenotypes are determined by the expression of genes, the environment, and the interaction of gene expression and the environment. However, a complete understanding of the inheritance of and genome-wide regulation of gene expression is lacking. One approach, called expression quantitative trait locus (eQTL) mapping provides the opportunity to examine the genome-wide inheritance and regulation of gene expression. In this paper, we conducted high-throughput sequencing of gene transcripts to examine gene expression in the shoot apex of a maize biparental mapping population. We quantified expression levels from 28,603 genes in the population and showed that the vast majority of genes exhibited the expected pattern of Mendelian inheritance. We genetically mapped the expression patterns and identified genomic regions associated with gene expression. Notably, we detected gene expression patterns that exhibited non-Mendelian inheritance. These included 145 genes that exhibited expression patterns in the progeny that were similar to only one of the parents and 210 genes with unexpected presence/absence expression patterns. The findings of non-Mendelian inheritance underscore the complexity of gene expression and provide a framework for understanding these complexities.

Analysis of the bread wheat genome using whole-genome shotgun sequencing

Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.

A widespread occurrence of extra open reading frames in plant Ty3/gypsy retrotransposons

Long terminal repeat (LTR) retrotransposons make up substantial parts of most higher plant genomes where they accumulate due to their replicative mode of transposition. Although the transposition is facilitated by proteins encoded within the gag-pol region which is common to all autonomous elements, some LTR retrotransposons were found to potentially carry an additional protein coding capacity represented by extra open reading frames located upstream or downstream of gag-pol. In this study, we performed a comprehensive in silico survey and comparative analysis of these extra open reading frames (ORFs) in the group of Ty3/gypsy LTR retrotransposons as the first step towards our understanding of their origin and function. We found that extra ORFs occur in all three major lineages of plant Ty3/gypsy elements, being the most frequent in the Tat lineage where most (77 %) of identified elements contained extra ORFs. This lineage was also characterized by the highest diversity of extra ORF arrangement (position and orientation) within the elements. On the other hand, all of these ORFs could be classified into only two broad groups based on their mutual similarities or the presence of short conserved motifs in their inferred protein sequences. In the Athila lineage, the extra ORFs were confined to the element 3' regions but they displayed much higher sequence diversity compared to those found in Tat. In the lineage of Chromoviruses the extra ORFs were relatively rare, occurring only in 5' regions of a group of elements present in a single plant family (Poaceae). In all three lineages, most extra ORFs lacked sequence similarities to characterized gene sequences or functional protein domains, except for two Athila-like elements with similarities to LOGL4 gene and part of the Chromoviruses extra ORFs that displayed partial similarity to histone H3 gene. Thus, in these cases the extra ORFs most likely originated by transduction or recombination of cellular gene sequences. In addition, the protein domain which is otherwise associated with DNA transposons have been detected in part of the Tat-like extra ORFs, pointing to their origin from an insertion event of a mobile element.

Boty-like retrotransposons in the filamentous fungus Botrytis cinerea contain the additional antisense gene brtn

Long-terminal repeat (LTR) retrotransposons typically contain gag, pol, or gag-pol, and in some case env genes. In this work, we used data mining of the Botrytis cinerea genomic sequence and a molecular approach to identify Boty-like LTR retrotransposons in B. cinerea containing an antisense gene (brtn) between pol and the 3'-LTR. Reverse transcriptase PCR (RT-PCR) revealed that some brtn-like genes could be expressed, at least in B. cinerea T4. We conducted BLAST comparisons and conserved-domain analysis, but the function of putative BRTN is presently unknown. Boty-like LTR retrotransposons in Sclerotinia sclerotiorum, called ScscLRET and containing brtn homologs at positions similar to brtn, were detected by homology searches and data mining of the S. sclerotiorum 1980 genomic sequence. Thus, this study demonstrated that some fungal LTR retrotransposons contain additional antisense genes.

Evolutionary transients in the rice transcriptome

In the canonical version of evolution by gene duplication, one copy is kept unaltered while the other is free to evolve. This process of evolutionary experimentation can persist for millions of years. Since it is so short lived in comparison to the lifetime of the core genes that make up the majority of most genomes, a substantial fraction of the genome and the transcriptome may—in principle—be attributable to what we will refer to as “evolutionary transients”, referring here to both the process and the genes that have gone or are undergoing this process. Using the rice gene set as a test case, we argue that this phenomenon goes a long way towards explaining why there are so many more rice genes than Arabidopsis genes, and why most excess rice genes show low similarity to eudicots.

Characterization of retrotransposon sequences expressed in inflorescences of apomictic and sexual Paspalum notatum plants

Apomixis, an asexual mode of reproduction through seeds, holds much promise for agricultural advances. However, the molecular mechanisms underlying this trait are still poorly understood. We previously isolated several transcripts representing novel sequences differentially expressed in reproductive tissues of sexual and apomictic plants. Here, we report the characterization of two of these unknown RNA transcripts (experimental codes N17 and N22). Since original fragments showed no significant homologies to sequences at databases, preliminary genomic PCR experiments were carried out to discard possible contaminations. RACE extension on flanking regions provided longer sequences for the candidates and additional related transcripts, which revealed similarity to LTR retrotransposons carrying short transduplicated segments of protein-coding genes. Interestingly, some transduplicated segments corresponded to genes previously associated with apomictic development. Gene copy number estimations revealed a moderate representation of the elements in the genome, with significantly increased numbers in a sexual genotype with respect to an apomictic one. Genetic mapping of N17 showed that a copy of this particular element was located onto Paspalum notatum linkage group F3c, at a central non-recombinant region resembling a centromere. Expression analysis showed an increased activity of N17 and N22 sense strands in ovules of the sexual genotypes. A retrotransposon-specific differential display analysis aimed at detecting related sequences allowed the identification of a complex family, with the majority of its members represented in the sexual genotype. Our results suggest that these elements could be participating in regulatory pathways related to apomixis and sexuality.

Bs1, a new chimeric gene formed by retrotransposon-mediated exon shuffling in maize

Transposons are major components of all eukaryotic genomes. Although traditionally regarded as causes of detrimental mutations, recent evidence suggests that transposons may play a role in host gene diversification and evolution. For example, host gene transduction by retroelements has been suggested to be both common and to have the potential to create new chimeric genes by the shuffling of existing sequences. We have previously shown that the maize (Zea mays subsp. mays) retrotransposon Bs1 has transduced sequences from three different host genes. Here, we provide evidence that these transduction events led to the generation of a chimeric new gene that is both transcribed and translated. Expression of Bs1 is tightly controlled and occurs during a narrow developmental window in early ear development. Although all Bs1-associated transduction events took place before Zea speciation, a full uninterrupted open reading frame encoding the BS1 protein may have arisen in domesticated maize or in the diverse populations of its progenitor Z. mays subsp. parviglumis. We discuss potential functions based on domain conservation and evidence for functional constraints between the transduced sequences and their host gene counterparts.

Patching gaps in plant genomes results in gene movement and erosion of colinearity

Colinearity of genes in plant genomes generally decreases with increasing evolutionary distance while the actual number of genes remains more or less constant. To characterize the molecular mechanisms of this "gene movement," we identified non-colinear genes by three-way comparison of the genomes of Brachypodium, rice, and sorghum. We found that genomic fragments of up to 50 kb containing the non-colinear genes are duplicated to acceptor sites elsewhere in the genome. Apparent movement of genes may usually be the result of subsequent deletions of genes in the donor region. Often, the duplicated fragments are precisely bordered by transposable elements (TEs) at the acceptor site. Highly diagnostic sequence motifs at these borders strongly suggest that these gene movements were the result of double-strand break (DSB) repair through synthesis-dependent strand annealing. In these cases, a copy of the foreign DNA fragment is used as filler DNA to repair the DSB linked with the transposition of TEs. Interestingly, most TEs we found associated with gene movement have a very low copy number in the genome and for several we did not find autonomous copies. This suggests that some of these elements spontaneously arose from unspecific interaction with TE proteins that are encoded by autonomous elements. Additionally, we found evidence that gene movements can also be caused when DSBs are repaired after template slippage or unequal crossing-over events. The observed frequency of gene movements can explain the erosion of gene colinearity between plant genomes during evolution.

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and ∼35,000 copies, respectively, or a combined ∼1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.

Although TEs are a major component of all studied plant genomes, and are the most significant contributors to genome structure and evolution in almost all eukaryotes that have been investigated, their properties and reasons for existence are not well understood in any eukaryotic genome. In order to begin a comprehensive study of TE contributions to the structure, function, and evolution of both genes and genomes, we first identified all of the TEs in maize and then investigated whether there were non-random patterns in their dispersal. We used homology and TE structure criteria in an effort to discover all of the retroelements in the recently sequenced genome from maize inbred B73. We found that the retroelements are incredibly diverse in maize, with many hundreds of families that show different insertion and/or retention specificities across the maize chromosomes. Most of these element families are present in low copy numbers and had been missed by previous searches that relied on a high-copy-number criterion. Different element families exhibited very different biases for accumulation across the chromosomes, indicating that they can detect and utilize many different chromatin environments.

Detailed analysis of a contiguous 22-Mb region of the maize genome

Most of our understanding of plant genome structure and evolution has come from the careful annotation of small (e.g., 100 kb) sequenced genomic regions or from automated annotation of complete genome sequences. Here, we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an improved pseudomolecule for annotation. The sequence segment was comprehensively ordered, oriented, and confirmed using the maize optical map. Nearly 84% of the sequence is composed of transposable elements (TEs) that are mostly nested within each other, of which most families are low-copy. We identified 544 gene models using multiple levels of evidence, as well as five miRNA genes. Gene fragments, many captured by TEs, are prevalent within this region. Elimination of gene redundancy from a tetraploid maize ancestor that originated a few million years ago is responsible in this region for most disruptions of synteny with sorghum and rice. Consistent with other sub-genomic analyses in maize, small RNA mapping showed that many small RNAs match TEs and that most TEs match small RNAs. These results, performed on approximately 1% of the maize genome, demonstrate the feasibility of refining the B73 RefGen_v1 genome assembly by incorporating optical map, high-resolution genetic map, and comparative genomic data sets. Such improvements, along with those of gene and repeat annotation, will serve to promote future functional genomic and phylogenomic research in maize and other grasses.

Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider

DNA sequences provide useful insights into genome structure and organization as well as evolution of species. We report on a detailed analysis of the locus surrounding the tomato (Solanum lycopersicum) fruit-shape gene SUN to determine the driving force and genome environment that foster the appearance of novel phenotypes. The gene density at the sun locus is similar to that described in other euchromatic portions of the tomato genome despite the relatively high number of transposable elements. Genes at the sun locus include protein-coding as well as RNA genes, are small in size, and belong to families that were duplicated at the locus an estimated 5-74 million years ago. In general, the DNA transposons at the sun locus are older than the RNA transposons, and their insertion pre-dates the speciation of S. lycopersicum and S. pimpinellifolium. Gene redundancy and large intergenic regions may explain the tolerance of the sun locus to frequent rearrangements and transpositions. The most recent transposition event at the sun locus involved Rider, a recently discovered high-copy retrotransposon. Rider probably arose early during the speciation of tomato. The element inserts into or near to genes and may still be active, which are unusual features for a high-copy element. Rider full-length and read-through transcripts past the typical transcription termination stop are detected, and the latter are required for mobilizing nearby sequences. Rider activity has resulted in an altered phenotype in three known cases, and may therefore have played an important role in tomato evolution and domestication.

Structure-based discovery and description of plant and animal Helitrons

Helitrons are recently discovered eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. They are present in most plant and animal species investigated, but were previously overlooked partly because they lack terminal repeats and do not create target site duplications. Helitrons are particularly abundant in flowering plants, where they frequently acquire, and sometimes express, 1 or more gene fragments. A structure-based search protocol was developed to find Helitrons and was used to analyze several plant and animal genomes, leading to the discovery of hundreds of new Helitrons. Analysis of these Helitrons has uncovered mechanisms of element evolution, including end creation and sequence acquisition. Preferential accumulation in gene-poor regions and target site specificities were also identified. Overall, these studies provide insights into the transposition and evolution of Helitrons and their contributions to evolved gene content and genome structure.

RNA-based gene duplication: mechanistic and evolutionary insights

Gene copies that stem from the mRNAs of parental source genes have long been viewed as evolutionary dead-ends with little biological relevance. Here we review a range of recent studies that have unveiled a significant number of functional retroposed gene copies in both mammalian and some non-mammalian genomes. These studies have not only revealed previously unknown mechanisms for the emergence of new genes and their functions but have also provided fascinating general insights into molecular and evolutionary processes that have shaped genomes. For example, analyses of chromosomal gene movement patterns via RNA-based gene duplication have shed fresh light on the evolutionary origin and biology of our sex chromosomes.

A new family of Ty1-copia-like retrotransposons originated in the tomato genome by a recent horizontal transfer event

Rider is a novel and recently active Ty1-copia-like retrotransposon isolated from the T3238fer mutant of tomato. Structurally, it is delimited by a duplication of target sites and contains two long terminal direct repeats and an internal open reading frame, which encodes a Ty1-copia-type polyprotein with characteristic protein domains required for retrotransposition. The family of Rider elements has an intermediate copy number and is scattered in the chromosomes of tomato. Rider family members in the tomato genome share high sequence similarity, but different structural groups were identified (full-size elements, deletion derivatives, and solo LTRs). Southern blot analysis in Solanaceae species showed that Rider was a Lycopersicon-specific element. Sequence analysis revealed that among other plants, two Arabidopsis elements (named as Rider-like 1 and Rider-like 2) are most similar to Rider in both the coding and noncoding regions. RT-PCR analysis indicates that Rider is constitutively expressed in tomato plants. The phylogeny-based parsimony analysis and the sequence substitution analyses of these data suggest that these Rider-like elements originated from a recent introgression of Rider into the tomato genome by horizontal transfer 1-6 million years ago. Considering its transcriptional activity and the recent insertion of the element into at least two genes, Rider is a recently active retrotransposon in the tomato genome.

The functional role of pack-MULEs in rice inferred from purifying selection and expression profile

Gene duplication is an important mechanism for evolution of new genes. In plants, a special group of transposable elements, called Pack-MULEs or transduplicates, is able to duplicate and amplify genes or gene fragments on a large scale. Despite the abundance of Pack-MULEs, the functionality of these duplicates is not clear. Here, we present a comprehensive analysis of expression and purifying selection on 2809 Pack-MULEs in rice (Oryza sativa), which are derived from 1501 parental genes. At least 22% of the Pack-MULEs are transcribed, and 28 Pack-MULEs have direct evidence of translation. Chimeric Pack-MULEs, which contain gene fragments from multiple genes, are much more frequently expressed than those derived only from a single gene. In addition, Pack-MULEs are frequently associated with small RNAs. The presence of these small RNAs is associated with a reduction in expression of both the Pack-MULEs and their parental genes. Furthermore, an assessment of the selection pressure on the Pack-MULEs using the ratio of nonsynonymous (Ka) and synonymous (Ks) substitution rates indicates that a considerable number of Pack-MULEs likely have been under selective constraint. The Ka/Ks values of Pack-MULE and parental gene pairs are lower among Pack-MULEs that are expressed in sense orientations. Taken together, our analysis suggests that a significant number of Pack-MULEs are expressed and subjected to purifying selection, and some are associated with small RNAs. Therefore, at least a subset of Pack-MULEs are likely functional and have great potential in regulating gene expression as well as providing novel coding capacities.

Replication of nonautonomous retroelements in soybean appears to be both recent and common

Retrotransposons and their remnants often constitute more than 50% of higher plant genomes. Although extensively studied in monocot crops such as maize (Zea mays) and rice (Oryza sativa), the impact of retrotransposons on dicot crop genomes is not well documented. Here, we present an analysis of retrotransposons in soybean (Glycine max). Analysis of approximately 3.7 megabases (Mb) of genomic sequence, including 0.87 Mb of pericentromeric sequence, uncovered 45 intact long terminal repeat (LTR)-retrotransposons. The ratio of intact elements to solo LTRs was 8:1, one of the highest reported to date in plants, suggesting that removal of retrotransposons by homologous recombination between LTRs is occurring more slowly in soybean than in previously characterized plant species. Analysis of paired LTR sequences uncovered a low frequency of deletions relative to base substitutions, indicating that removal of retrotransposon sequences by illegitimate recombination is also operating more slowly. Significantly, we identified three subfamilies of nonautonomous elements that have replicated in the recent past, suggesting that retrotransposition can be catalyzed in trans by autonomous elements elsewhere in the genome. Analysis of 1.6 Mb of sequence from Glycine tomentella, a wild perennial relative of soybean, uncovered 23 intact retroelements, two of which had accumulated no mutations in their LTRs, indicating very recent insertion. A similar pattern was found in 0.94 Mb of sequence from Phaseolus vulgaris (common bean). Thus, autonomous and nonautonomous retrotransposons appear to be both abundant and active in Glycine and Phaseolus. The impact of nonautonomous retrotransposon replication on genome size appears to be much greater than previously appreciated.

Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies in Senecio

Interspecific hybridization is an important mechanism of speciation in higher plants. In flowering plants, hybrid speciation is usually associated with polyploidy (allopolyploidy), but hybrid speciation without genome duplication (homoploid hybrid speciation) is also possible, although it is more difficult to detect. The combination of divergent genomes within a hybrid can result in profound changes to both genome and transcriptome. Recent transcriptomic studies of wild and resynthesized homoploid and allopolyploid hybrids have revealed widespread changes to gene expression in hybrids relative to expression levels in their parents. Many of these changes to gene expression are 'non-additive', i.e. not simply the sum of the combined expression levels of parental genes. Some gene expression changes are far outside the range of gene expression in either parent, and can therefore be viewed as 'transgressive'. Such profound changes to gene expression may enable new hybrids to survive in novel habitats not accessible to their parent species. Here, we give a brief overview of hybrid speciation in plants, with an emphasis on genomic change, before focusing discussion on findings from recent transcriptomic studies. We then discuss our current work on gene expression change associated with hybrid speciation in the genus Senecio (ragworts and groundsels) focusing on the findings from a reanalysis of gene expression data obtained from recent microarray studies of wild and resynthesized allopolyploid Senecio cambrensis. These data, showing extensive non-additive and transgressive gene expression changes in Senecio hybrids, are discussed in the light of findings from other model systems, and in the context of the potential importance of gene expression change to hybrid speciation in plants.

Diversity of a complex centromeric satellite and molecular characterization of dispersed sequence families in sugar beet (Beta vulgaris)

BACKGROUND AND AIMS

The aim of this work was the identification and molecular characterization of novel sugar beet (Beta vulgaris) repetitive sequences to unravel the impact of repetitive DNA on size and evolution of Beta genomes via amplification and diversification.

METHODS

Genomic DNA and a pool of B. vulgaris repetitive sequences were separately used as probes for a screening of high-density filters from a B. vulgaris plasmid library. Novel repetitive motifs were identified by sequencing and further used as probes for Southern analyses in the genus Beta. Chromosomal localization of the repeats was analysed by fluorescent in situ hybridization on chromosomes of B. vulgaris and two other species of the section Beta.

KEY RESULTS

Two dispersed repetitive families pDvul1 and pDvul2 and the tandemly arranged repeat family pRv1 were isolated from a sugar beet plasmid library. The dispersed repetitive families pDvul1 and pDvul2 were identified in all four sections of the genus Beta. The members of the pDvul1 and pDvul2 family are scattered over all B. vulgaris chromosomes, although amplified to a different extent. The pRv1 satellite repeat is exclusively present in species of the section Beta. The centromeric satellite pBV1 by structural variations of the monomer and interspersion of pRv1 units forms complex satellite structures, which are amplified in different degrees on the centromeres of 12 chromosomes of the three species of the Beta section.

CONCLUSIONS

The complexity of the pBV1 satellite family observed in the section Beta of the genus Beta and, in particular, the strong amplification of the pBV1/pRv1 satellite in the domesticated B. vulgaris indicates the dynamics of centromeric satellite evolution during species radiation within the genus. The dispersed repeat families pDvul1 and pDvul2 might represent derivatives of transposable elements.

Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize

The mass movement of gene sequences by Helitrons has significantly contributed to the lack of gene collinearity reported between different maize inbred lines. However, Helitron captured-genes reported to date represent truncated versions of their progenitor genes. In this report, we provide evidence that maize CYP72A27-Zm gene represents a cytochrome P450 monooxygenase (P450) gene recently captured by a Helitron and transposed into an Opie-2 retroposon. The four exons of the CYP72A27 gene contained within the element contain a putative open reading frame (ORF) for 428 amino acid residues. We provide evidence that Helitron captured CYP72A27-Zm is transcribed. To identify the progenitor gene and the evolutionary time of capture, we searched the plant genome database and discovered other closely related CYP72A27-Zm genes in maize and grasses. Our analysis indicates that CYP72A27-Zm represents an almost complete copy of maize CYP72A26-Zm gene captured by a Helitron about 3.1 million years ago (mya). The Helitron-captured gene then duplicated twice, approximately 1.5-1.6 mya giving rise to CYP72A36-Zm and CYP72A37-Zm. These data provide evidence that Helitrons can capture and mobilize intact genes that are transcribed and potentially encode biologically relevant proteins.

Retrosequence formation restructures the yeast genome

Retrosequences generated by reverse transcription of mRNA transcripts have a substantial influence on gene expression patterns, generation of novel gene functions, and genome organization. The Ty1 retrotransposon is a major source of RT activity in the yeast, Saccharomyces cerevisiae, and Ty1 retromobility is greatly elevated in strains lacking telomerase. We report that Ty1-dependent formation of retrosequences derived from single-copy gene transcripts is progressively elevated as yeast cells senesce in the absence of telomerase. Retrosequences are frequently fused to Ty1 sequences, and occasionally to sequences from other mRNA transcripts, forming chimeric pseudogenes. Efficient retrosequence formation requires the homologous recombination gene RAD52. Selection for retrosequence formation is correlated with a high frequency of chromosome rearrangements in telomerase-negative yeast. Ty1-associated retrosequences were present at the breakpoint junctions of four chromosomes analyzed in detail. Our results support a role for reverse transcripts in promoting chromosome rearrangements.

Analysis of genes associated with retrotransposons in the rice genome

Retrotransposons comprise a significant fraction of the rice genome. Despite their prevalence, the effects of retrotransposon insertions are not well understood, especially with regard to how they affect the expression of genes. In this study, we identified one-sixth of rice genes as being associated with retrotransposons, with insertions either in the gene itself or within its putative promoter region. Among genes with insertions in the promoter region, the likelihood of the gene being expressed was shown to be directly proportional to the distance of the retrotransposon from the translation start site. In addition, retrotransposon insertions in the transcribed region of the gene were found to be positively correlated with the presence of alternative splicing forms. Furthermore, preferential association of retrotransposon insertions with genes in several functional classes was identified. Some of the retrotransposons that are part of full-length cDNA (fl-cDNA) contribute splice sites and give rise to novel exons. Several interesting trends concerning the effects of retrotransposon insertions on gene expression were identified. Taken together, our data suggests that retrotransposon association with genes have a role in gene regulation. The data presented in this study provides a foundation for experimental studies to determine the role of retrotransposons in gene regulation.

Novel exon combinations generated by alternative splicing of gene fragments mobilized by a CACTA transposon in Glycine max

BACKGROUND

The recent discoveries of transposable elements carrying host gene fragments such as the Pack-MULEs (Mutator-like transposable elements) of maize (Zea mays), rice (Oryza sativa) and Arabidopsis thaliana, the Helitrons of maize and the Tgm-Express of soybeans, revealed a widespread genetic mechanism with the potential to rearrange genomes and create novel chimeric genes affecting genomic and proteomic diversity. Not much is known with regard to the mechanisms of gene fragment capture by those transposon elements or the expression of the captured host gene fragments. There is some evidence that chimeric transcripts can be assembled and exist in EST collections.

RESULTS

We report results obtained from analysis of RT-PCR derived cDNAs of the Glycine max mutant flower color gene, wp, that contains a 5.7-kb transposon (Tgm-Express1) in Intron 2 of the flavanone 3-hydroxylase gene (F3H) and is composed of five unrelated host gene fragments. The collection of cDNAs derived from the wp allele represents a multiplicity of processed RNAs varying in length and sequence that includes some identical to the correctly processed mature F3H transcript with three properly spliced exons. Surprisingly, the five gene fragments carried by the Tgm-Express1 were processed through complex alternative splicing as additional exons of the wp transcript.

CONCLUSION

The gene fragments carried by the Tgm inverted repeat ends appear to be retained as functional exons/introns within the element. The spliceosomes then select indiscriminately the canonical intron splice sites from a pre-mRNA to assemble diverse chimeric transcripts from the exons contained in the wp allele. The multiplicity and randomness of these events provide some insights into the origin and mechanism of alternatively spliced genes.

ROSINA (RSI) is part of a CACTA transposable element, TamRSI, and links flower development to transposon activity

ROSINA (RSI) was isolated as a DNA binding factor able to bind to the CArG-box present in the promoter of the MADS-box gene DEFICIENS of Antirrhinum majus. The mosaic nature of RSI and its multi-copy presence in the A. majus genome indicated that RSI could be a part of a mobile genetic element. Here we show that RSI is a part of a CACTA transposable element system of A. majus, named TamRSI, which has evolved and is still evolving within the terminal inverted repeats (TIRs) of this CACTA transposon. Interestingly, RSI is always found in opposite orientation with respect to the transcription of a second gene present within the CACTA transposon, which encodes a putative TRANSPOSASE (TNP). This structural configuration has not yet been described for any member of the CACTA transposons superfamily. Internal deletion derivatives of the TamRSI produce aberrant RSI transcripts (RSI-ATs) that carry parts of the RSI RNA fused to parts of the TNP RNA. In addition, an intriguing seed phenotype shown by RNAi transgenic lines generated to silence RSI, relate TamRSI to epigenetic mechanisms and associate the control of flower development to transposon activity.

Allelic variation and heterosis in maize: how do two halves make more than a whole?

In this review, we discuss the recent research on allelic variation in maize and possible implications of this work toward our understanding of heterosis. Heterosis, or hybrid vigor, is the increased performance of a hybrid relative to the parents, and is a result of the variation that is present within a species. Intraspecific comparisons of sequence and expression levels in maize have documented a surprisingly high level of allelic variation, which includes variation for the content of genic fragments, variation in repetitive elements surrounding genes, and variation in gene expression levels. There is evidence that transposons and repetitive DNA play a major role in the generation of this allelic diversity. The combination of allelic variants provides a more comprehensive suite of alleles in the hybrid that may be involved in novel allelic interactions. A major unresolved question is how the combined allelic variation and interactions in a hybrid give rise to heterotic phenotypes. An understanding of allelic variation present in maize provides an opportunity to speculate on mechanisms that might lead to heterosis. Variation for the presence of genes, the presence of novel beneficial alleles, and modified levels of gene expression in hybrids may all contribute to the heterotic phenotypes.

Modification of nitrogen remobilization, grain fill and leaf senescence in maize (Zea mays) by transposon insertional mutagenesis in a protease gene

A maize (Zea mays) senescence-associated legumain gene, See2beta, was characterized at the physiological and molecular levels to determine its role in senescence and resource allocation. A reverse-genetics screen of a maize Mutator (Mu) population identified a Mu insertion in See2beta. Maize plants homozygous for the insertion were produced. These See2 mutant and sibling wild-type plants were grown under high or low quantities of nitrogen (N). The early development of both genotypes was similar; however, tassel tip and collar emergence occurred earlier in the mutant. Senescence of the mutant leaves followed a similar pattern to that of wild-type leaves, but at later sampling points mutant plants contained more chlorophyll than wild-type plants and showed a small extension in photosynthetic activity. Total plant weight was higher in the wild-type than in the mutant, and there was a genotype x N interaction. Mutant plants under low N maintained cob weight, in contrast to wild-type plants under the same treatment. It is concluded, on the basis of transposon mutagenesis, that See2beta has an important role in N-use and resource allocation under N-limited conditions, and a minor but significant function in the later stages of senescence.

Ogre elements--a distinct group of plant Ty3/gypsy-like retrotransposons

Ogre elements are a group of LTR retrotransposons recently discovered in legume plants, where they constitute almost 40% of the genome in some species. They are exceptional in their size (reaching 25 kb) and possess several specific features, including an intron within a polyprotein-coding region, and an extra open reading frame (ORF1) encoding a protein of unknown function located upstream of the gag gene. Although these features make Ogres interesting for further research, identification of additional elements from a broader range of plant taxa has been complicated by the divergence of their sequences, preventing their detection using similarity-based searches. Here we report the results of structure-based computational searches for Ogre elements in available plant genomic sequences, which proved to be more efficient and revealed occurrences of Ogres in three families of dicot plants (Leguminosae, Solanaceae and Salicaceae). In addition, a representative set of 85 elements was retrieved from a model legume species Medicago truncatula. All identified full-length elements were used for comparative analysis, which showed that in spite of only little conservation of their nucleotide sequences, their protein domains were highly conserved, including several regions within ORF1. Further, the elements shared the same functional regions, including a primer binding site complementary to tRNA(arg), a conserved motif within a polypurine tract, and a putative intron between the pro and rt/rh coding domains. These findings, together with analysis of their phylogenetic relationship to other retrotransposons based on similarities of rt domains suggest that Ogre elements from different plant taxa have a common origin and thus constitute a distinct group of Ty3/gypsy retrotransposons.

High rate of chimeric gene origination by retroposition in plant genomes

Retroposition is widely found to play essential roles in origination of new mammalian and other animal genes. However, the scarcity of retrogenes in plants has led to the assumption that plant genomes rarely evolve new gene duplicates by retroposition, despite abundant retrotransposons in plants and a reported long terminal repeat (LTR) retrotransposon-mediated mechanism of retroposing cellular genes in maize (Zea mays). We show extensive retropositions in the rice (Oryza sativa) genome, with 1235 identified primary retrogenes. We identified 27 of these primary retrogenes within LTR retrotransposons, confirming a previously observed role of retroelements in generating plant retrogenes. Substitution analyses revealed that the vast majority are subject to negative selection, suggesting, along with expression data and evidence of age, that they are likely functional retrogenes. In addition, 42% of these retrosequences have recruited new exons from flanking regions, generating a large number of chimerical genes. We also identified young chimerical genes, suggesting that gene origination through retroposition is ongoing, with a rate an order of magnitude higher than the rate in primates. Finally, we observed that retropositions have followed an unexpected spatial pattern in which functional retrogenes avoid centromeric regions, while retropseudogenes are randomly distributed. These observations suggest that retroposition is an important mechanism that governs gene evolution in rice and other grass species.

Microarray analysis reveals differential gene expression in hybrid sunflower species

This paper describes the creation of a cDNA microarray for annual sunflowers and its use to elucidate patterns of gene expression in Helianthus annuus, Helianthus petiolaris, and the homoploid hybrid species Helianthus deserticola. The array comprises 3743 ESTs (expressed sequence tags) representing approximately 2897 unique genes. It has an average clone/EST identity rate of 91%, is applicable across species boundaries within the annual sunflowers, and shows patterns of gene expression that are highly reproducible according to real-time RT-PCR (reverse transcription-polymerase chain reaction) results. Overall, 12.8% of genes on the array showed statistically significant differential expression across the three species. Helianthus deserticola displayed transgressive, or extreme, expression for 58 genes, with roughly equal numbers exhibiting up- or down-regulation relative to both parental species. Transport-related proteins were strongly over-represented among the transgressively expressed genes, which makes functional sense given the extreme desert floor habitat of H. deserticola. The potential adaptive value of differential gene expression was evaluated for five genes in two populations of early generation (BC2) hybrids between the parental species grown in the H. deserticola habitat. One gene (a G protein-coupled receptor) had a significant association with fitness and maps close to a QTL controlling traits that may be adaptive in the desert habitat.

Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize

Helitron transposable elements carrying gene fragments were recently discovered in maize. These elements are frequently specific to certain maize lineages. Here we report evidence supporting the involvement of helitrons in the rapid evolution of the maize genome, in particular in the multiplication of related genic fragments across the genome. We describe a family of four closely related, non-autonomous maize helitrons and their insertion sites at four non-allelic genetic loci across the maize genome: two specific to the B73 inbred, and two to the Mo17 inbred. We propose the phylogeny of this helitron family and provide an approximate timeline of their genomic insertions. One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. Significantly, it produces an alternatively spliced and chimeric transcript joining together genic segments of different chromosomal origin contained within the helitron. This transcript potentially encodes up to four open reading frames. During the course of evolution, transcribed helitrons containing multiple gene fragments may occasionally give rise to new genes with novel biochemical functions by a combinatorial assembly of exons. Thus helitrons not only constantly reshape the genomic organization of maize and profoundly affect its genetic diversity, but also may be involved in the evolution of gene function.

Gene movement by Helitron transposons contributes to the haplotype variability of maize

Different maize inbred lines are polymorphic for the presence or absence of genic sequences at various allelic chromosomal locations. In the bz genomic region, located in 9S, sequences homologous to four different genes from rice and Arabidopsis are present in line McC but absent from line B73. It is shown here that this apparent intraspecific violation of genetic colinearity arises from the movement of genes or gene fragments by Helitrons, a recently discovered class of eukaryotic transposons. Two Helitrons, HelA and HelB, account for all of the genic differences distinguishing the two bz locus haplotypes. HelA is 5.9 kb long and contains sequences for three of the four genes found only in the McC bz genomic region. A nearly identical copy of HelA was isolated from a 5S chromosomal location in B73. Both the 9S and 5S sites appear to be polymorphic in maize, suggesting that these Helitrons have been active recently. Helitrons lack the strong predictive terminal features of other transposons, so the definition of their ends is greatly facilitated by the identification of their vacant sites in Helitron-minus lines. The ends of the 2.7-kb HelB Helitron were discerned from a comparison of the McC haplotype sequence with that of yet a third line, Mo17, because the HelB vacant site is deleted in B73. Maize Helitrons resemble rice Pack-MULEs in their ability to capture genes or gene fragments from several loci and move them around the genome, features that confer on them a potential role in gene evolution.

Hybrid speciation in plants: new insights from molecular studies

Abrupt speciation through interspecific hybridisation is an important mechanism in angiosperm evolution. Flowering plants therefore offer excellent opportunities for studying genetic processes associated with hybrid speciation. Novel molecular approaches are now available to examine these processes at the level of both genome organization and gene expression - transcriptomics. Here, we present an overview of the molecular technologies currently used to study hybrid speciation and how they are providing new insights into this mode of speciation in flowering plants. We begin with an introduction to hybrid speciation in plants, followed by a review of techniques, such as isozymes and other markers, which have been used to study hybrid species in the past. We then review advances in molecular techniques that have the potential to be applied to studies of hybrid species, followed by an overview of the main genomic and transcriptomic changes suspected, or known, to occur in newly formed hybrids, together with commentary on the application of advanced molecular tools to studying these changes.