The Evolutionary Dynamics of Repetitive DNA and Its Impact on the Genome Diversification in the Genus Sorghum

Contrasting distributions and expression characteristics of transcribing repeats in Setaria viridis

Repetitive DNA contributes significantly to plant genome size, adaptation, and evolution. However, little is understood about the transcription of repeats. This is addressed here in the plant green foxtail millet (Setaria viridis). First, we used RepeatExplorer2 to calculate the genome proportion (GP) of all repeat types and compared the GP of long terminal repeat (LTR) retroelements against annotated complete and incomplete LTR retroelements (Ty1/copia and Ty3/gypsy) identified by DANTE in a whole genome assembly. We show that DANTE-identified LTR retroelements can comprise ∼0.75% of the inflorescence poly-A transcriptome and ∼0.24% of the stem ribo-depleted transcriptome. In the RNA libraries from inflorescence tissue, both LTR retroelements and DNA transposons identified by RepeatExplorer2 were highly abundant, where they may be taking advantage of the reduced epigenetic silencing in the germ line to amplify. Typically, there was a higher representation of DANTE-identified LTR retroelements in the transcriptome than RepeatExplorer2-identified LTR retroelements, potentially reflecting the transcription of elements that have insufficient genomic copy numbers to be detected by RepeatExplorer2. In contrast, for ribo-depleted libraries of stem tissues, the reverse was observed, with a higher transcriptome representation of RepeatExplorer2-identified LTR retroelements. For RepeatExplorer2-identified repeats, we show that the GP of most Ty1/copia and Ty3/gypsy families were positively correlated with their transcript proportion. In addition, guanine- and cytosine-rich repeats with high sequence similarity were also the most abundant in the transcriptome, and these likely represent young elements that are most capable of amplification due to their ability to evade epigenetic silencing.

Repeatome landscapes and cytogenetics of hortensias provide a framework to trace Hydrangea evolution and domestication

BACKGROUND AND AIMS

Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analysed six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias' evolutionary paths and can guide breeding initiatives.

METHODS

We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as the evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole-genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multicolour FISH.

KEY RESULTS

The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes.

CONCLUSIONS

Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and guiding future hortensia breeding.

Chromosome-specific barcode system with centromeric repeat in cultivated soybean and wild progenitor

Wild soybean Glycine soja is the progenitor of cultivated soybean Glycine max Information on soybean functional centromeres is limited despite extensive genome analysis. These species are an ideal model for studying centromere dynamics for domestication and breeding. We performed a detailed chromatin immunoprecipitation analysis using centromere-specific histone H3 protein to delineate two distinct centromeric DNA sequences with unusual repeating units with monomer sizes of 90-92 bp (CentGm-1) and 413-bp (CentGm-4) shorter and longer than standard nucleosomes. These two unrelated DNA sequences with no sequence similarity are part of functional centromeres in both species. Our results provide a comparison of centromere properties between a cultivated and a wild species under the effect of the same kinetochore protein. Possible sequence homogenization specific to each chromosome could highlight the mechanism for evolutionary conservation of centromeric properties independent of domestication and breeding. Moreover, a unique barcode system to track each chromosome is developed using CentGm-4 units. Our results with a unifying centromere composition model using CentGm-1 and CentGm-4 superfamilies could have far-reaching implications for comparative and evolutionary genome research.

A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study

BACKGROUND

The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.

MAIN BODY

In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.

CONCLUSION

Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.

Plant kinetochore complex: composition, function, and regulation

The kinetochore complex, an important protein assembly situated on the centromere, plays a pivotal role in chromosome segregation during cell division. Like in animals and fungi, the plant kinetochore complex is important for maintaining chromosome stability, regulating microtubule attachment, executing error correction mechanisms, and participating in signaling pathways to ensure accurate chromosome segregation. This review summarizes the composition, function, and regulation of the plant kinetochore complex, emphasizing the interactions of kinetochore proteins with centromeric DNAs (cenDNAs) and RNAs (cenRNAs). Additionally, the applications of the centromeric histone H3 variant (the core kinetochore protein CENH3, first identified as CENP-A in mammals) in the generation of ploidy-variable plants and synthesis of plant artificial chromosomes (PACs) are discussed. The review serves as a comprehensive roadmap for researchers delving into plant kinetochore exploration, highlighting the potential of kinetochore proteins in driving technological innovations in synthetic genomics and plant biotechnology.

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.

Aegilops crassa Boiss. repeatome characterized using low-coverage NGS as a source of new FISH markers: Application in phylogenetic studies of the Triticeae

Aegilops crassa Boiss. is polyploid grass species that grows in the eastern part of the Fertile Crescent, Afghanistan, and Middle Asia. It consists of tetraploid (4x) and hexaploid (6x) cytotypes (2n = 4x = 28, D¹D (Abdolmalaki et al., 2019) X^crX^cr and 2n = 6x = 42, D¹D (Abdolmalaki et al., 2019) X^crX^crD²D (Adams and Wendel, 2005), respectively) that are similar morphologically. Although many Aegilops species were used in wheat breeding, the genetic potential of Ae. crassa has not yet been exploited due to its uncertain origin and significant genome modifications. Tetraploid Ae. crassa is thought to be the oldest polyploid Aegilops species, the subgenomes of which still retain some features of its ancient diploid progenitors. The D¹ and D² subgenomes of Ae. crassa were contributed by Aegilops tauschii (2n = 2x = 14, DD), while the X^cr subgenome donor is still unknown. Owing to its ancient origin, Ae. crassa can serve as model for studying genome evolution. Despite this, Ae. crassa is poorly studied genetically and no genome sequences were available for this species. We performed low-coverage genome sequencing of 4x and 6x cytotypes of Ae. crassa, and four Ae. tauschii accessions belonging to different subspecies; diploid wheatgrass Thinopyrum bessarabicum (J^b genome), which is phylogenetically close to D (sub)genome species, was taken as an outgroup. Subsequent data analysis using the pipeline RepeatExplorer2 allowed us to characterize the repeatomes of these species and identify several satellite sequences. Some of these sequences are novel, while others are found to be homologous to already known satellite sequences of Triticeae species. The copy number of satellite repeats in genomes of different species and their subgenome (D¹ or X^cr) affinity in Ae. crassa were assessed by means of comparative bioinformatic analysis combined with quantitative PCR (qPCR). Fluorescence in situ hybridization (FISH) was performed to map newly identified satellite repeats on chromosomes of common wheat, Triticum aestivum, 4x and 6x Ae. crassa, Ae. tauschii, and Th. bessarabicum. The new FISH markers can be used in phylogenetic analyses of the Triticeae for chromosome identification and the assessment of their subgenome affinities and for evaluation of genome/chromosome constitution of wide hybrids or polyploid species.