Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat

Weed competitive ability in wheat: a peek through in its functional significance, present status and future prospects

Weed competitive ability of a crop is one of the most widely explored aspects in the current scenario of aftermaths of synthetic herbicides such as herbicide resistant weeds emergence, residue accumulation in trophic levels; increased demands of organic produce, global climatic shifts, and other environmental issues. Further weed infestations are known to cause much more economic losses relative to crop attacks by pests. To understand the basic characteristics and underlying processes governing the competitive ability of a crop is therefore prudent, particularly in staples such as wheat. We discuss here an overview of the existing attributes of wheat-weed environment, the significance of crop competitiveness and various associated above-ground and below-ground traits (pertaining to early seed vigor and early seedling germination) discerned through biological, classical genetics and high throughput omics toolbox to provide numerous resources in terms of genome and transcriptome sequences, potential QTLs, genetic variation, molecular markers, association mapping studies, and others. Competitiveness is a cumulative response manifested as morphological, physiological, biochemical or allelochemical response ultimately driven through genetic architecture of a crop and its interaction with environment. Development of wheat competitive cultivar thus requires interdisciplinary approaches and germplasm screening to identify potential donors for competitiveness is an attractive and feasible alternative. For which utilization of landraces and other wild species, already proven to house sufficient genetic heterogeneity, thus poses a competitive advantage. Further, the availability of novel breeding techniques such as rapid generation advance could speed up the development of competitive wheat ideotype.

Chromosome restructuring among hybridizing wild wheats

The wheat group offers an outstanding system to address the interplay between hybridization, chromosomal evolution and biological diversification. Most diploid wild wheats originated following hybridization between the A-genome lineage and the B-genome lineage some 4 Myr ago, resulting in an admixed D-genome lineage that presented dramatic radiation accompanied by considerable changes in genome size and chromosomal rearrangements. Comparative profiling of low-copy genes, repeated sequences and transposable elements among those divergent species characterized by different karyotypes highlights high genome dynamics and sheds new light on the processes underlying chromosomal evolution in wild wheats. One of the hybrid clades presents upsizing of metacentric chromosomes going along with the proliferation of specific repeats (i.e. 'genomic obesity'), whereas other species show stable genome size associated with increasing chromosomal asymmetry. Genetic and ecological variation in those specialized species suggest that genome restructuring was coupled with adaptive processes to support the evolution of a majority of acrocentric chromosomes. This synthesis of current knowledge on genome restructuring across the diversity of wild wheats paves the way towards surveys based on latest sequencing technologies to characterize valuable resources and address the significance of chromosomal evolution in species with complex genomes.

Genomic Clues for Crop-Weed Interactions and Evolution

Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.

Major structural genomic alterations can be associated with hybrid speciation in Aegilops markgrafii (Triticeae)

During evolutionary history many grasses from the tribe Triticeae have undergone interspecific hybridization, resulting in allopolyploidy; whereas homoploid hybrid speciation was found only in rye. Homoeologous chromosomes within the Triticeae preserved cross-species macrocolinearity, except for a few species with rearranged genomes. Aegilops markgrafii, a diploid wild relative of wheat (2n = 2x = 14), has a highly asymmetrical karyotype that is indicative of chromosome rearrangements. Molecular cytogenetics and next-generation sequencing were used to explore the genome organization. Fluorescence in situ hybridization with a set of wheat cDNAs allowed the macrostructure and cross-genome homoeology of the Ae. markgrafii chromosomes to be established. Two chromosomes maintained colinearity, whereas the remaining were highly rearranged as a result of inversions and inter- and intrachromosomal translocations. We used sets of barley and wheat orthologous gene sequences to compare discrete parts of the Ae. markgrafii genome involved in the rearrangements. Analysis of sequence identity profiles and phylogenic relationships grouped chromosome blocks into two distinct clusters. Chromosome painting revealed the distribution of transposable elements and differentiated chromosome blocks into two groups consistent with the sequence analyses. These data suggest that introgressive hybridization accompanied by gross chromosome rearrangements might have had an impact on karyotype evolution and homoploid speciation in Ae. markgrafii.

Resolving fine-grained dynamics of retrotransposons: comparative analysis of inferential methods and genomic resources

Transposable elements support genome diversification, but comparison of their proliferation and genomic distribution within and among species is necessary to characterize their role in evolution. Such inferences are challenging because of potential bias with incomplete sampling of repetitive genome regions. Here, using the assembled genome as well as genome skimming datasets in Arabis alpina, we assessed the limits of current approaches inferring the biology of transposable elements. Long terminal repeat retrotransposons (LTR-RTs) identified in the assembled genome were classified into monophyletic lineages (here called tribes), including families of similar copies in Arabis along with elements from related Brassicaceae. Inference of their dynamics using divergence of LTRs in full-length copies and mismatch distribution of genetic variation among all copies congruently highlighted recent transposition bursts, although ancient proliferation events were apparent only with mismatch distribution. Similar inferences of LTR-RT dynamics based on random sequences from genome skimming were highly correlated with assembly-based estimates, supporting accurate analyses from shallow sequencing. Proportions of LTR-RT copies next to genes from both assembled genomes and genome skimming were congruent, pointing to tribes being over- or under-represented in the vicinity of genes. Finally, genome skimming at low coverage revealed accurate inferences of LTR-RT dynamics and distribution, although only the most abundant families appeared robustly analysed at 0.1X. Examining the pitfalls and benefits of approaches relying on different genomic resources, we highlight that random sequencing reads represent adequate data suitably complementing biased samples of LTR-RT copies retrieved from assembled genomes towards comprehensive surveys of the biology of transposable elements.

Profiling Transposable Elements and Their Epigenetic Effects in Non-model Species

Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences.

Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification

RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.

Chromosome Specific Substitution Lines of Aegilops geniculata Alter Parameters of Bread Making Quality of Wheat

Wheat cultivars with wide introgression have strongly impacted global wheat production. Aegilops geniculata (M^gU^g) is an important wild relative with several useful traits that can be exploited for wheat improvement. Screening of Ae. geniculata addition lines indicated a negative effect of 1U^g and the positive effect of 1M^g chromosome on wheat dough strength. Negative effect of 1U^g is probably associated with variation in number and position of the tripeptide repeat motif in the high molecular weight glutenin (HMW-G) gene. To utilize the positive potential of 1M^g chromosome, three disomic substitution lines (DSLs) 1M^g(1A), 1M^g(1B) and 1M^g(1D) were created. These lines were characterized for morphological, cytogenetic properties and biochemical signatures using FISH, 1D-, 2D-PAGE and RP-HPLC. Contribution of wheat 1A, 1B and 1D chromosomes towards dough mixing and baking parameters, chapatti quality, Fe/Zn content and glume color were identified. Observed order of variation in the dough mixing and baking parameters {1M^g(1D) ≤wheat ≤1M^g(1B) ≤1M^g(1A)} indicated that chromosome specific introgression is desirable for best utilization of wild species’ potential.

New molecular markers and cytogenetic probes enable chromosome identification of wheat-Thinopyrum intermedium introgression lines for improving protein and gluten contents

New molecular markers were developed for targeting Thinopyrum intermedium 1St#2 chromosome, and novel FISH probe representing the terminal repeats was produced for identification of Thinopyrum chromosomes. Thinopyrum intermedium has been used as a valuable resource for improving the disease resistance and yield potential of wheat. A wheat-Th. intermedium ssp. trichophorum chromosome 1St#2 substitution and translocation has displayed superior grain protein and wet gluten content. With the aim to develop a number of chromosome 1St#2 specific molecular and cytogenetic markers, a high throughput, low-cost specific-locus amplified fragment sequencing (SLAF-seq) technology was used to compare the sequences between a wheat-Thinopyrum 1St#2 (1D) substitution and the related species Pseudoroegneria spicata (St genome, 2n = 14). A total of 5142 polymorphic fragments were analyzed and 359 different SLAF markers for 1St#2 were predicted. Thirty-seven specific molecular markers were validated by PCR from 50 randomly selected SLAFs. Meanwhile, the distribution of transposable elements (TEs) at the family level between wheat and St genomes was compared using the SLAFs. A new oligo-nucleotide probe named Oligo-pSt122 from high SLAF reads was produced for fluorescence in situ hybridization (FISH), and was observed to hybridize to the terminal region of 1St#L and also onto the terminal heterochromatic region of Th. intermedium genomes. The genome-wide markers and repetitive based probe Oligo-pSt122 will be valuable for identifying Thinopyrum chromosome segments in wheat backgrounds.

Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification

Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.

Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum

Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference Sorghum bicolor genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of S. bicolor and its close relative S. propinquum. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of S. propinquum reads to the S. bicolor database failed to fully describe TE content in S. propinquum, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons.

Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation

Interspecific hybridization leads to new interactions among divergent genomes, revealing the nature of genetic incompatibilities having accumulated during and after the origin of species. Conflicts associated with misregulation of transposable elements (TEs) in hybrids expectedly result in their activation and genome-wide changes that may be key to species boundaries. Repetitive genomes of wild wheats have diverged under differential dynamics of specific long terminal repeat retrotransposons (LTR-RTs), offering unparalleled opportunities to address the underpinnings of plant genome reorganization by selfish sequences. Using reciprocal F1 hybrids between three Aegilops species, restructuring and epigenetic repatterning was assessed at random and LTR-RT sequences with amplified fragment length polymorphism and sequence-specific amplified polymorphisms as well as their methylation-sensitive counterparts, respectively. Asymmetrical reorganization of LTR-RT families predicted to cause conflicting interactions matched differential survival of F1 hybrids. Consistent with the genome shock model, increasing divergence of merged LTR-RTs yielded higher levels of changes in corresponding genome fractions and lead to repeated reorganization of LTR-RT sequences in F1 hybrids. Such non-random reorganization of hybrid genomes is coherent with the necessary repression of incompatible TE loci in support of hybrid viability and indicates that TE-driven genomic conflicts may represent an overlooked factor supporting reproductive isolation.

Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex

Long terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR-RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR-RT families revealed contrasted dynamics during species diversification. Quiescent LTR-RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of LTR-RT proliferation. Although reputed stable, autopolyploid genomes show LTR-RT fractions presenting analogies with polyploids between widely divergent genomes.

Transposable element dynamics among asymbiotic and ectomycorrhizal Amanita fungi

Transposable elements (TEs) are ubiquitous inhabitants of eukaryotic genomes and their proliferation and dispersal shape genome architectures and diversity. Nevertheless, TE dynamics are often explored for one species at a time and are rarely considered in ecological contexts. Recent work with plant pathogens suggests a link between symbiosis and TE abundance. The genomes of pathogenic fungi appear to house an increased abundance of TEs, and TEs are frequently associated with the genes involved in symbiosis. To investigate whether this pattern is general, and relevant to mutualistic plant-fungal symbioses, we sequenced the genomes of related asymbiotic (AS) and ectomycorrhizal (ECM) Amanita fungi. Using methods developed to interrogate both assembled and unassembled sequences, we characterized and quantified TEs across three AS and three ECM species, including the AS outgroup Volvariella volvacea. The ECM genomes are characterized by abundant numbers of TEs, an especially prominent feature of unassembled sequencing libraries. Increased TE activity in ECM species is also supported by phylogenetic analysis of the three most abundant TE superfamilies; phylogenies revealed many radiations within contemporary ECM species. However, the AS species Amanita thiersii also houses extensive amplifications of elements, highlighting the influence of additional evolutionary parameters on TE abundance. Our analyses provide further evidence for a link between symbiotic associations among plants and fungi, and increased TE activity, while highlighting the importance individual species’ natural histories may have in shaping genome architecture.

Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats

Transposable elements (TEs) are expectedly central to genome evolution. To assess the impact of TEs in driving genome turnover, we used allopolyploid genomes, showing considerable deviation from the predicted additivity of their diploid progenitors and thus having undergone major restructuring. Genome survey sequencing was used to select 17 putatively active families of long terminal repeat retrotransposons. Genome-wide TE insertions were genotyped with sequence-specific amplified polymorphism (SSAP) in diploid progenitors and their derived polyploids, and compared with changes in random sequences to assess restructuring of four independent Aegilops allotetraploid genomes. Generally, TEs with different evolutionary trajectories from those of random sequences were identified. Thus, TEs presented family-specific and species-specific dynamics following polyploidy, as illustrated by Sabine showing proliferation in particular polyploids, but massive elimination in others. Contrasting with that, only a few families (BARE1 and Romani) showed proliferation in all polyploids. Overall, TE divergence between progenitors was strongly correlated with the degree of restructuring in polyploid TE fractions. TE families present evolutionary trajectories that are decoupled from genome-wide changes after allopolyploidy and have a pervasive impact on their restructuring.

Sequencing of chloroplast genomes from wheat, barley, rye and their relatives provides a detailed insight into the evolution of the Triticeae tribe

Using Roche/454 technology, we sequenced the chloroplast genomes of 12 Triticeae species, including bread wheat, barley and rye, as well as the diploid progenitors and relatives of bread wheat Triticum urartu, Aegilops speltoides and Ae. tauschii. Two wild tetraploid taxa, Ae. cylindrica and Ae. geniculata, were also included. Additionally, we incorporated wild Einkorn wheat Triticum boeoticum and its domesticated form T. monococcum and two Hordeum spontaneum (wild barley) genotypes. Chloroplast genomes were used for overall sequence comparison, phylogenetic analysis and dating of divergence times. We estimate that barley diverged from rye and wheat approximately 8–9 million years ago (MYA). The genome donors of hexaploid wheat diverged between 2.1–2.9 MYA, while rye diverged from Triticum aestivum approximately 3–4 MYA, more recently than previously estimated. Interestingly, the A genome taxa T. boeoticum and T. urartu were estimated to have diverged approximately 570,000 years ago. As these two have a reproductive barrier, the divergence time estimate also provides an upper limit for the time required for the formation of a species boundary between the two. Furthermore, we conclusively show that the chloroplast genome of hexaploid wheat was contributed by the B genome donor and that this unknown species diverged from Ae. speltoides about 980,000 years ago. Additionally, sequence alignments identified a translocation of a chloroplast segment to the nuclear genome which is specific to the rye/wheat lineage. We propose the presented phylogeny and divergence time estimates as a reference framework for future studies on Triticeae.

Copy number variation of transposable elements in Triticum-Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization

Here, we report on copy number variation of transposable elements and on the genome-specific proliferation in wheat. In addition, we report on revolutionary and evolutionary dynamics of transposons. Wheat is a valuable model for understanding the involvement of transposable elements (TEs) in speciation as wheat species (Triticum-Aegilops group) have diverged from a common ancestor, have undergone two events of speciation through allopolyploidy, and contain a very high fraction of TEs. However, an unbiased genome-wide examination of TE variation among these species has not been conducted. Our research utilized quantitative real time PCR to assess the relative copy numbers of 16 TE families in various Triticum and Aegilops species. We found (1) high variation and genome-specificity of TEs in wheat species, suggesting they were active throughout the evolution of wheat, (2) neither Ae. searsii nor Ae. speltoides by themselves can be the only contributors of the B genome to wheat, and (3) nonadditive changes in TE quantities in polyploid wheat. This study indicates the apparent involvement of large TEs in creating genetic variation in revolutionary and evolutionary scales following allopolyploidization events, presumably assisting in the diploidization of homeologous chromosomes.