The diversity of retroelements in diploid and allotetraploid Brassica species

The Genomic Shock Hypothesis: Genetic and Epigenetic Alterations of Transposable Elements after Interspecific Hybridization in Plants

Transposable elements (TEs) are major components of plant genomes with the ability to change their position in the genome or to create new copies of themselves in other positions in the genome. These can cause gene disruption and large-scale genomic alterations, including inversions, deletions, and duplications. Host organisms have evolved a set of mechanisms to suppress TE activity and counter the threat that they pose to genome integrity. These includes the epigenetic silencing of TEs mediated by a process of RNA-directed DNA methylation (RdDM). In most cases, the silencing machinery is very efficient for the vast majority of TEs. However, there are specific circumstances in which TEs can evade such silencing mechanisms, for example, a variety of biotic and abiotic stresses or in vitro culture. Hybridization is also proposed as an inductor of TE proliferation. In fact, the discoverer of the transposons, Barbara McClintock, first hypothesized that interspecific hybridization provides a "genomic shock" that inhibits the TE control mechanisms leading to the mobilization of TEs. However, the studies carried out on this topic have yielded diverse results, showing in some cases a total absence of mobilization or being limited to only some TE families. Here, we review the current knowledge about the impact of interspecific hybridization on TEs in plants and the possible implications of changes in the epigenetic mechanisms.

An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae)

Whole genome duplication, associated with the induction of widespread genetic changes, has played an important role in the evolution of many plant taxa. All extant angiosperm species have undergone at least one polyploidization event, forming either an auto- or allopolyploid organism. Compared with allopolyploidization, however, few studies have examined autopolyploidization, and few studies have focused on the response of genetic changes to autopolyploidy. In the present study, newly synthesized C. nankingense autotetraploids (Asteraceae) were employed to characterize the genome shock following autopolyploidization. Available evidence suggested that the genetic changes primarily involved the loss of old fragments and the gain of novel fragments, and some novel sequences were potential long terminal repeat (LTR) retrotransposons. As Ty1-copia and Ty3-gypsy elements represent the two main superfamilies of LTR retrotransposons, the dynamics of Ty1-copia and Ty3-gypsy were evaluated using RT-PCR, transcriptome sequencing, and LTR retrotransposon-based molecular marker techniques. Additionally, fluorescence in situ hybridization(FISH)results suggest that autopolyploidization might also be accompanied by perturbations of LTR retrotransposons, and emergence retrotransposon insertions might show more rapid divergence, resulting in diploid-like behaviour, potentially accelerating the evolutionary process among progenies. Our results strongly suggest a need to expand the current evolutionary framework to include a genetic dimension when seeking to understand genomic shock following autopolyploidization in Asteraceae.

Screening diversity and distribution of Copia retrotransposons reveals a specific amplification of BARE1 elements in genomes of the polyploid Hordeum murinum complex

We explored diversity, distribution and evolutionary dynamics of Ty1-Copia retrotransposons in the genomes of the Hordeum murinum polyploid complex and related taxa. Phylogenetic and fluorescent in situ hybridization (FISH) analyses of reverse transcriptase sequences identified four Copia families in these genomes: the predominant BARE1 (including three groups or subfamilies, A, B and C), and the less represented RIRE1, IKYA and TAR-1. Within the BARE1 family, BARE1-A elements and a subgroup of BARE1-B elements (named B1) have proliferated in the allopolyploid members of the H. murinum complex (H. murinum and H. leporinum), and in their extant diploid progenitor, subsp. glaucum. Moreover, we found a specific amplification of BARE1-B elements within each Hordeum species surveyed. The low occurrence of RIRE1, IKYA and TAR-1 elements in the allopolyploid cytotypes suggests that they are either weakly represented or highly degenerated in their diploid progenitors. The results demonstrate that BARE1-A and BARE1-B1 Copia elements are particularly well represented in the genomes of the H. murinum complex and constitute its genomic hallmark. No BARE1-A and -B1 homologs were detected in the reference barley genome. The similar distribution of RT-Copia probes across chromosomes of diploid, tetraploid and hexaploid taxa of the murinum complex shows no evidence of proliferation following polyploidization.

Comparative analysis of cytokinin response factors in Brassica diploids and amphidiploids and insights into the evolution of Brassica species

Background

Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many genes, including cytokinin response factors (CRFs). Although CRFs take vital part in the growth of Arabidopsis thaliana and Solanum lycopersicum, little information of the CRFs in the Brassica U-triangle species has been known yet.

Results

We identified and compared 141 CRFs in the diploids and amphidiploids of Brassica species, including B. rapa, B. oleracea, B. nigra, B. napus, and B. juncea. For all the 141 CRFs, the sequence and structure analysis, physiological and biochemical characteristics analysis were performed. Meanwhile, the Ka/Ks ratios of orthologous and paralogous gene pairs were calculated, which indicated the natural selective pressure upon the overall length or a certain part of the CRFs. The expression profiles of CRFs in different tissues and under various stresses were analyzed in B. oleracea, B. nigra, and B. napus. The similarities and differences in gene sequences and expression profiles among the homologous genes of these species were discussed. In addition, AtCRF11 and its ortholog BrCRF11a were identified to be related to primary root growth in Arabidopsis.

Conclusion

This study performed a genome-wide comparative analysis of the CRFs in the diploids and amphidiploids of the Brassica U-triangle species. Many similarities and differences in gene sequences and expression profiles existed among the CRF homologous genes of these species. In the bioinformatics analysis, we found the close relativity of the CRF homologous genes in the Brassica A and C genomes and the distinctiveness of those in the B genome, and the CRF homologous genes in B subgenome were considerably influenced by the A subgenome of B. juncea. In addition, we identified a new function of the Clade V CRFs related to root growth, which also clarified the functional conservation between Arabidopsis and B. rapa. These results not only offer useful information on the functional analysis of CRFs but also provide new insights into the evolution of Brassica species.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5114-y) contains supplementary material, which is available to authorized users.

The landscape and structural diversity of LTR retrotransposons in Musa genome

Long terminal repeat retrotransposons represent a major component of plant genomes and act as drivers of genome evolution and diversity. Musa is an important fruit crop and also used as a starchy vegetable in many countries. BAC sequence analysis by dot plot was employed to investigate the LTR retrotransposons from Musa genomes. Fifty intact LTR retrotransposons from selected Musa BACs were identified by dot plot analysis and further BLASTN searches retrieved 153 intact copies, 61 truncated, and a great number of partial copies/remnants from GenBank database. LARD-like elements were also identified with several copies dispersed among the Musa genotypes. The predominant elements were the LTR retrotransposons Copia and Gypsy, while Caulimoviridae (pararetrovirus) were rare in the Musa genome. PCR amplification of reverse transcriptase (RT) sequences revealed their abundance in almost all tested Musa accessions and their ancient nature before the divergence of Musa species. The phylogenetic analysis based on RT sequences of Musa and other retrotransposons clustered them into Gypsy, Caulimoviridae, and Copia lineages. Most of the Musa-related elements clustered in their respective groups, while some grouped with other elements indicating homologous sequences. The present work will be helpful to understand the LTR retrotransposons landscape, giving a complete picture of the nature of the elements, their structural features, annotation, and evolutionary dynamics in the Musa genome.

Polyploidy: Pitfalls and paths to a paradigm

Investigators have long searched for a polyploidy paradigm-rules or principles that might be common following polyploidization (whole-genome duplication, WGD). Here we attempt to integrate what is known across the more thoroughly investigated polyploid systems on topics ranging from genetics to ecology. We found that while certain rules may govern gene retention and loss, systems vary in the prevalence of gene silencing vs. homeolog loss, chromosomal change, the presence of a dominant genome (in allopolyploids), and the relative importance of hybridization vs. genome doubling per se. In some lineages, aspects of polyploidization are repeated across multiple origins, but in other species multiple origins behave more stochastically in terms of genetic and phenotypic change. Our investigation also reveals that the path to synthesis is hindered by numerous gaps in our knowledge of even the best-known systems. Particularly concerning is the absence of linkage between genotype and phenotype. Moreover, most recent studies have focused on the genetic and genomic attributes of polyploidy, but rarely is there an ecological or physiological context. To promote a path to a polyploidy paradigm (or paradigms), we propose a major community goal over the next 10-20 yr to fill the gaps in our knowledge of well-studied polyploids. Before a meaningful synthesis is possible, more complete data sets are needed for comparison-systems that include comparable genetic, genomic, chromosomal, proteomic, as well as morphological, physiological, and ecological data. Also needed are more natural evolutionary model systems, as most of what we know about polyploidy continues to come from a few crop and genetic models, systems that often lack the ecological context inherent in natural systems and necessary for understanding the drivers of biodiversity.

Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus

Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent.

First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species

Peanut is an allotetraploid (2n = 2x = 40, AABB) of recent origin. Arachis duranensis and A. ipaënsis, the most probable diploid ancestors of the cultigen, and several other wild diploid species with different genomes (A, B, D, F and K) are used in peanut breeding programs. However, the genomic relationships and the evolutionary pathways of genome differentiation of these species are poorly understood. We performed a sequence-based phylogenetic analysis of the L1 reverse transcriptase and estimated its representation and chromosome distribution in species of five genomes and three karyotype groups with the aim of contributing to the knowledge of the genomic structure and evolution of peanut and wild diploid relatives. All the isolated rt fragments were found to belong to plant L1 lineage and were named ALI. The best supported phylogenetic groups were not concordant with the genomes or karyotype groups. The copy number of ALI sequences was higher than the expected one for plants and directly related to genome size. FISH experiments revealed that ALI is mainly located on the euchromatin of interstitial and distal regions of most chromosome arms. Divergence of ALI sequences would have occurred before the differentiation of the genomes and karyotype groups of Arachis. The representation and chromosome distribution of ALI in peanut was almost additive of those of the parental species suggesting that the spontaneous hybridization of the two parental species of peanut followed by chromosome doubling would not have induced a significant burst of ALI transposition.

Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids

The role played by whole-genome duplication (WGD) in evolution and adaptation is particularly well illustrated in allopolyploids, where WGD is concomitant with interspecific hybridization. This 'Genome Shock', usually accompanied by structural and functional modifications, has been associated with the activation of transposable elements (TEs). However, the impact of allopolyploidy on TEs has been studied in only a few polyploid species, and not in Brassica, which has been marked by recurrent polyploidy events. Here, we developed sequence-specific amplification polymorphism (SSAP) markers for three contrasting TEs, and compared profiles between resynthesized Brassica napus allotetraploids and their diploid Brassica progenitors. To evaluate restructuring at TE insertion sites, we scored changes in SSAP profiles and analysed a large set of differentially amplified SSAP bands. No massive structural changes associated with the three TEs surveyed were detected. However, several transposition events, specific to the youngest TE originating from the B. oleracea genome, were identified. Our study supports the hypothesis that TE responses to allopolyploidy are highly specific. The changes observed in SSAP profiles lead us to hypothesize that they may partly result from changes in DNA methylation, questioning the role of epigenetics during the formation of a new allopolyploid genome.

Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence

Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita. Fluorescent in situ hybridization (FISH) experiments showed that Matita is mainly located on the distal regions of chromosome arms and is of approximately equal frequency on both A- and B-chromosomes. Its chromosome-specific hybridization pattern facilitates the identification of individual chromosomes, a useful cytogenetic tool considering that chromosomes in peanut are mostly metacentric and of similar size. Phylogenetic analysis of Matita elements, molecular dating of transposition events, and an estimation of the evolutionary divergence of the most probable A- and B-donor species suggest that Matita underwent its last major burst of transposition activity at around the same time of the A- and B-genome divergence about 3.5 million years ago. By probing BAC libraries with overgos probes for Matita, resistance gene analogues, and single- or low-copy genes, it was demonstrated that Matita is not randomly distributed in the genome but exhibits a significant tendency of being more abundant near resistance gene homologues than near single-copy genes. The described work is a further step towards broadening the knowledge on genomic and chromosomal structure of peanut and on its evolution.

BraSto, a Stowaway MITE from Brassica: recently active copies preferentially accumulate in the gene space

We characterized a Brassica miniature inverted repeat transposable element (MITE) from the Stowaway superfamily, designated BraSto (Bra ssica Sto waway). BraSto copy number was assessed using real-time quantitative PCR in the two diploid species B. rapa (genome A) and B. oleracea (genome C) and the corresponding allotetraploid species B. napus (genome AC). Phylogenetic relationships among a set of 131 BraSto copies were then analyzed. BraSto appears to have been only moderately amplified in the Brassica genome and was still active recently with marks of proliferation in both diploid Brassica species, which diverged 3.75 million years ago, but also in the allotetraploid species after reuniting of the two differentiated genomes. We characterized insertion sites for low-divergence BraSto copies among the gene space of the B. rapa genome using bioinformatics approaches. For BraSto copies localized nearby or within genes, we observed frequent associations of BraSto with putative promoters and regulatory regions of genes, but exclusion from coding regions. In addition, BraSto was significantly similar to several Brassica expressed sequence tags (ESTs), including stress-induced ESTs. We also demonstrated the enrichment of BraSto sequences in binding sites for transcription factors and other regulatory elements. Our results lead to the question of a role for BraSto in the regulation of gene expression: this putative role, if further confirmed experimentally, would help to obtain a new insight into the significance of MITEs in the functional plant genome.

iPBS: a universal method for DNA fingerprinting and retrotransposon isolation

Molecular markers are essential in plant and animal breeding and biodiversity applications, in human forensics, and for map-based cloning of genes. The long terminal repeat (LTR) retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their "copy and paste" life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Nevertheless, up to a year has been required to develop a retrotransposon marker system in a new species, involving cloning and sequencing steps as well as the development of custom primers. Here, we describe a novel PCR-based method useful both as a marker system in its own right and for the rapid isolation of retrotransposon termini and full-length elements, making it ideal for "orphan crops" and other species with underdeveloped marker systems. The method, iPBS amplification, is based on the virtually universal presence of a tRNA complement as a reverse transcriptase primer binding site (PBS) in LTR retrotransposons. The method differs from earlier retrotransposon isolation methods because it is applicable not only to endogenous retroviruses and retroviruses, but also to both Gypsy and Copia LTR retrotransposons, as well as to non-autonomous LARD and TRIM elements, throughout the plant kingdom and to animals. Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge.

Diversity and evolution of Ty1-copia retroelements in representative tribes of Bambusoideae subfamily

Ty1-copia retroelements have been found in all major plants and are largely responsible for the huge differences in the genome size. In this study we isolated and sequenced Ty1-copia reverse transcriptase (rt) gene fragments from 44 representative species of bamboo and nine cultivars or forms of Phyllostachys pubescens. Phylogenetic analysis of 72 distinct Ty1-copia rt sequences showed that Ty1-copia retroelements were widespread, diverse and abundant in these species of Bambusoideae subfamily. In addition, a molecular phylogeny of the species of the Bambusoideae subfamily was established by using the internal transcribed spacer sequences of nuclear ribosomal DNA (ITS) sequences. The comparison between ITS- and Ty1-copia rt- based trees is obviously incongruent. The results suggested either the existence of horizontal transfer events between phylogenetically distant species, or an ancestral Ty1-copia retroelement polymorphism followed by different evolution and stochastic losses.

Impact of transposable elements on the organization and function of allopolyploid genomes

Transposable elements (TEs) represent an important fraction of plant genomes and are likely to play a pivotal role in fuelling genome reorganization and functional changes following allopolyploidization. Various processes associated with allopolyploidy (i.e. genetic redundancy, bottlenecks during the formation of allopolyploids or genome shock following genome merging) may allow accumulation of TE insertions. Our objective in carrying out a survey of the literature and a comparative analysis across different allopolyploid systems is to shed light on the structural, epigenetic and functional modifications driven by TEs during allopolyploidization and subsequent diploidization. The available evidence indicates that TE proliferation in the short or the long term after allopolyploidization may be restricted to a few TEs, in specific polyploid systems. By contrast, data indicate major structural changes in the TE genome fraction immediately after allopolyploidization, mainly through losses of TE sequences as a result of recombination. Emerging evidence also suggests that TEs are targeted by substantial epigenetic changes, which may impact gene expression and genome stability. Furthermore, TEs may directly or indirectly support the evolution of new functionalities in allopolyploids during diploidization. All data stress allopolyploidization as a shock associated with drastic genome reorganization. Mechanisms controlling TEs during allopolyploidization as well as their impact on diploidization are discussed.

Mobilization of retrotransposons in synthetic allotetraploid tobacco

Allopolyploidy is a major driving force in plant evolution and can induce rapid structural changes in the hybrid genome. As major components of plant genomes, transposable elements are involved in these changes. In a previous work, we observed turnover of retrotransposon insertions in natural allotretraploid tobacco (Nicotiana tabacum). Here, we studied the early stages of allopolyploid formation by monitoring changes at retrotransposon insertion sites in the Th37 synthetic tobacco. We used sequence-specific amplification polymorphism (SSAP) to study insertion patterns of two populations of the Tnt1 retrotransposon in Th37 S4 generation plants, and characterized the nature of polymorphic insertion sites. We observed significant amplification of young Tnt1 populations. Newly transposed copies were amplified from maternal elements and were highly similar to Tnt1A tobacco copies amplified in response to microbial factors. A high proportion of paternal SSAP bands were not transmitted to the hybrid, corresponding to various rearrangements at paternal insertion sites, including indels or the complete loss of the Tnt1/flanking junction. These data indicate that major changes, such as retrotransposon amplification and molecular restructuring in or around insertion sites, occur rapidly in response to allopolyploidy.

The identification of candidate genes associated with Pch2 eyespot resistance in wheat using cDNA-AFLP

Eyespot is a fungal disease of the stem base of cereal crops and causes lodging and the premature ripening of grain. Wheat cultivar Cappelle Desprez contains a highly durable eyespot resistance gene, Pch2 on the long arm of chromosome 7A. A cDNA-amplified fragment length polymorphism (AFLP) platform was used to identify genes differentially expressed between the eyespot susceptible variety Chinese Spring (CS) and the CS chromosome substitution line Cappelle Desprez 7A (CS/CD7A) which contains Pch2. Induced and constitutive gene expression was examined to compare differences between non-infected and plants infected with Oculimacula acuformis. Only 34 of approximately 4,700 cDNA-AFLP fragments were differentially expressed between CS and CS/CD7A. Clones were obtained for 29 fragments, of which four had homology to proteins involved with plant defence responses. Fourteen clones mapped to chromosome 7A and three of these mapped in the region of Pch2 making them putative candidates for involvement in eyespot resistance. Of particular importance are two fragments; 4CD7A8 and 19CD7A4, which have homology to an Oryza sativa putative callose synthase protein and a putative cereal cyst nematode NBS-LRR disease resistance protein (RCCN) respectively. Differential expression associated with Pch2 was examined by semi-quantitative RT-PCR. Of those genes tested, only four were differentially expressed at 14 days post inoculation. We therefore suggest that a majority of the differences in the cDNA-AFLP profiles are due to allelic polymorphisms between CS and CD alleles rather than differences in expression.

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana

We sequenced five BAC clones of Brassica oleracea doubled haploid 'Early Big' broccoli containing major genes in the aliphatic glucosinolate pathway, and comparatively analyzed them with similar sequences in A. thaliana and B. rapa. Additionally, we included in the analysis published sequences from three other B. oleracea BAC clones and a contig of this species corresponding to segments in A. thaliana chromosomes IV and V. A total of 2,946 kb of B. oleracea, 1,069 kb of B. rapa sequence and 2,607 kb of A. thaliana sequence were compared and analyzed. We found conserved collinearity for gene order and content restricted to specific chromosomal segments, but breaks in collinearity were frequent resulting in gene absence likely not due to gene loss but rearrangements. B. oleracea has the lowest gene density of the three species, followed by B. rapa. The genome expansion of the Brassica species, B. oleracea in particular, is due to larger introns and gene spacers resulting from frequent insertion of DNA transposons and retrotransposons. These findings are discussed in relation to the possible origin and evolution of the Brassica genomes.

The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation

We isolated and characterized a Brassica C genome-specific CACTA element, which was designated Bot1 (Brassica oleracea transposon 1). After analysing phylogenetic relationships, copy numbers and sequence similarity of Bot1 and Bot1 analogues in B. oleracea (C genome) versus Brassica rapa (A genome), we concluded that Bot1 has encountered several rounds of amplification in the oleracea genome only, and has played a major role in the recent rapa and oleracea genome divergence. We performed in silico analyses of the genomic organization and internal structure of Bot1, and established which segment of Bot1 is C-genome specific. Our work reports a fully characterized Brassica repetitive sequence that can distinguish the Brassica A and C chromosomes in the allotetraploid Brassica napus, by fluorescent in situ hybridization. We demonstrated that Bot1 carries a host S locus-associated SLL3 gene copy. We speculate that Bot1 was involved in the proliferation of SLL3 around the Brassica genome. The present study reinforces the assumption that transposons are a major driver of genome and gene evolution in higher plants.

A and C genome distinction and chromosome identification in brassica napus by sequential fluorescence in situ hybridization and genomic in situ hybridization

The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)-with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes-followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.

Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus

Centromeres and telomeres are obvious markers on chromosomes but their location on genetic maps is difficult to determine, which hampers many basic and applied research programmes. In this study, we used the characteristic distribution of five Brassica repeated sequences to generate physically anchored molecular markers tentatively tagging Brassica centromeres (84 markers) and telomeres (31 markers). These markers were mapped to the existing oilseed rape genetic map. Clusters of centromere-related loci were observed on 14 linkage groups; in addition to previous reports, we could thus provide information about the most likely position of centromeres on 17 of the 19 B. napus linkage groups. The location of centromeres on linkage groups usually matches their position on chromosomes and coincides with sites of evolutionary breakage between chromosomes. Most telomere sequence-derived markers mapped interstitially or in the proximity of centromeres; this result echoes previous reports on many eukaryote genomes and may reflect different forms of chromosome evolution. Seven telomere sequence-derived markers were located at the outermost positions of seven linkage groups and therefore probably tagged telomeres.

Phylogenetic determination of the pace of transposable element proliferation in plants: copia and LINE-like elements in Gossypium

Transposable elements contribute significantly to plant genome evolution in myriad ways, ranging from local insertional mutations to global effects exerted on genome size through accumulation. Differential accumulation and deletion of transposable elements may profoundly affect genome size, even among members of the same genus. One example is that of Gossypium (cotton), where much of the 3-fold genome size variation is due to differential accumulation of one gypsy-like LTR retrotransposon, Gorge3. Copia and non-LTR LINE retrotransposons are also major components of the Gossypium genome, but unlike Gorge3, their extant copy numbers do not correlate with genome size. In the present study, we describe the nature and timing of transposition for copia and LINE retrotransposons in Gossypium. Our findings indicate that copia retrotransposons have been active in each lineage since divergence from a common ancestor, and that they have proliferated in a punctuated manner. However, the evolutionary history of LINEs contrasts markedly with that of the copia retrotransposons. Although LINEs have also been active in each lineage, they have accumulated in a stochastically regular manner, and phylogenetic analysis suggests that extant LINE populations in Gossypium are dominated by ancient insertions. Interestingly, the magnitude of transpositional bursts in each lineage corresponds directly with extant estimated copy number.

Cytogenetics and genome analysis in Brassica crops

The genus Brassica contains a wide range of diploid and amphipolyploid species including some of the most important vegetable, condiment and oilseed crops worldwide. As members of the Brassicaceae family the brassicas are the closest crop relatives to the model plant Arabidopsis thaliana, and hence are major beneficiaries from the vast array of Arabidopsis molecular genetic and genomic tools and the increasingly good annotation to major Brassica crop genomes. In this review examples are shown from recent studies that demonstrate the potential for intergenome navigation from model to crop plant and for comparisons among genetic and cytogenetic maps between the model and crop species and among different crop brassicas. The use of interspecific and intergeneric hybridization for introgression of novel traits into Brassica genomes from the secondary and tertiary crucifer genepools is described. In this context the use of the Brassica triangle of three diploid species and their corresponding amphiploids as an excellent model system for studying the mechanisms and control of homeologous recombination and polyploidization is discussed from a crop breeding perspective.

Diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in the non-photosynthetic flowering plants Orobanche and Phelipanche (Orobanchaceae)

We present the first study on the diversity and evolution of Ty1-copia and Ty3-gypsy retroelements in a group of non-photosynthetic flowering plants. To this end partial sequences of the reverse transcriptase (rt) gene were obtained from 20 clones for each retroelement type from seven and six accessions of Orobanche and Phelipanche (Orobanchaceae), respectively. Overall sequence similarity is higher in Ty3-gypsy elements than in Ty1-copia elements in agreement with the results from other angiosperm groups. Higher sequence diversity and stronger phylogenetic structure, especially of Ty1-copia sequences, in Orobanche species compared to Phelipanche species support the previously suggested hypothesis (based on karyological and cytological data) that genomes of Orobanche species are more dynamic than those of Phelipanche species. No evidence was found for intraspecific differences of retroelement diversity nor for differences between pest taxa and their putative wild relatives, e.g., O. crenata and O. owerini. The occurrence of a few sequences from Phelipanche species in clades otherwise comprising sequences from Orobanche species might be due to horizontal gene transfer, but the alternative of vertical transmission cannot be rejected unambiguously.

The genomic organization of retrotransposons in Brassica oleracea

We have investigated the copy numbers and genomic organization of five representative reverse transcriptase domains from retrotransposons in Brassica oleracea. Two non-homologous Pseudoviridae (Ty1/copia-like) elements, two Metaviridae (Ty3/gypsy-like) elements (one related to the Athila family) and one Retroposinae (LINE) element were hybridized to a gridded BAC library, "BoB". The results indicated that the individual LTR retrotransposons (copia and gypsy-like) were represented by between 90 and 320 copies in the haploid genome, with only evidence of a single location for the LINE. Sequence analysis of the same elements against genome survey sequence gave estimates of between 60 and 570, but no LINE was found. There was minimal evidence for clustering between any of these retroelements: only half the randomly expected number of BACs hybridized to both LTR-retrotransposon families. Fluorescent in situ hybridization showed that each of the retroelements had a characteristic genomic distribution. Our results suggest there are preferential sites and perhaps control mechanisms for the insertion or excision of different retrotransposon groups.