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Cladogram showing the relationships between Ty1-copia and Ty3-gypsy retrotransposable element superfamilies identified in the transcriptome of B. decumbens within contigs/unigenes (black names) or as characteristic domains (red). Arrows indicate the gypsy LTR-RTs sequences used to design primers for in situ hybridization (Table 1)
Source publication
Like other eukaryotes, the nuclear genome of plants consists of DNA with a small proportion of low- copy DNA (genes and regulatory sequences) and very abundant DNA sequence motifs that are repeated thou- sands up to millions of times in the genomes including transposable elements (TEs) and satellite DNA. Retrotransposons, one class of TEs, are sequ...
Similar publications
Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within tribe Phaseoleae (Fabaceae), some genera, such as Phaseolus, Vigna, and Cajanus, show small genome and mostly stable chromosome number. Here, we applied a combined computational and cytological approach...
Citations
... Additionally, differences in the ratio between Gypsy and Copia have been observed in different groups. Gypsy was the most abundant retrotransposon in Helianthus and Brachiaria [37,38], whereas Copia was the most abundant in Rhynchospora [39]. ...
The species Passiflora alata, P. cincinnata, and P. edulis have great economic value due to the use of their fruits for human consumption. In this study, we compared the repetitive genome fractions of these three species. The compositions of the repetitive DNA of these three species’ genomes were analyzed using clustering and identification of the repetitive sequences with RepeatExplorer. It was found that repetitive DNA content represents 74.70%, 66.86%, and 62.24% of the genome of P. alata, P. edulis, and P. cincinnata, respectively. LTR Ty3/Gypsy retrotransposons represent the highest genome proportions in P. alata and P. edulis, while Ty1/Copia comprises the largest proportion of P. cincinnata genome. Chromosomal mapping by Fluorescent In Situ Hybridization (FISH) showed that LTR retrotransposons have a dispersed distribution along chromosomes. The subtelomeric region of chromosomes is where 145 bp satellite DNA is located, suggesting that these elements may play important roles in genome structure and organization in these species. In this work, we obtained the first global characterization of the composition of repetitive DNA in Passiflora, showing that an increase in genome size is related to an increase in repetitive DNA, which represents an important evolutionary route for these species.
... In this study, we used both specific probes developed using graph-based sequence clustering compared with "universal" conserved regions of Ty1-copia and Ty3-gypsy retroelements. Similar to Urochloa tropical forage grasses, where genomic DNA and retroelements used as probes showed no substantial differences between the genomes (Santos et al., 2015;Tomaszewska et al., 2021b), parallel universal retroelement repeats used in this study were relatively equally abundant over the whole Cenchrus ciliaris genome (see Supplementary Figure 1). The Gy105 probe (see Figure 1D) labeled some chromosomes as more weaker. ...
Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.
... The karyotype organization that has been observed suggests an allopolyploid origin for U. brizantha, corroborating the results from a study of the physical mapping of rDNA genes in this species (Nielen et al., 2009). In another study, the occurrence, mapping, and distribution of gypsy retrotransposons in U. decumbens, U. brizantha, U. ruziziensis and U. humidicola showed that mobile elements, in addition to the chromosome number variation, contributed to karyotype evolution (Santos et al., 2015b;Worthington et al., 2021). ...
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
... The karyotype organization that has been observed suggests an allopolyploid origin for U. brizantha, corroborating the results from a study of the physical mapping of rDNA genes in this species (Nielen et al., 2009). In another study, the occurrence, mapping, and distribution of gypsy retrotransposons in U. decumbens, U. brizantha, U. ruziziensis and U. humidicola showed that mobile elements, in addition to the chromosome number variation, contributed to karyotype evolution (Santos et al., 2015b;Worthington et al., 2021). ...
Pastures based on perennial monocotyledonous plants are the principal source of nutrition for ruminant livestock in tropical and subtropical areas across the globe. The Urochloa genus comprises important species used in pastures, and these mainly include Urochloa brizantha, Urochloa decumbens, Urochloa humidicola, and Urochloa ruziziensis. Despite their economic relevance, there is an absence of genomic-level information for these species, and this lack is mainly due to genomic complexity, including polyploidy, high heterozygosity, and genomes with a high repeat content, which hinders advances in molecular approaches to genetic improvement. Next-generation sequencing techniques have enabled the recent release of reference genomes, genetic linkage maps, and transcriptome sequences, and this information helps improve our understanding of the genetic architecture and molecular mechanisms involved in relevant traits, such as the apomictic reproductive mode. However, more concerted research efforts are still needed to characterize germplasm resources and identify molecular markers and genes associated with target traits. In addition, the implementation of genomic selection and gene editing is needed to reduce the breeding time and expenditure. In this review, we highlight the importance and characteristics of the four main species of Urochloa used in pastures and discuss the current findings from genetic and genomic studies and research gaps that should be addressed in future research.
... PHRE2 was, however, predominantly expressed in roots associated with xylem and xylem parenchyma cells and in the guard cells of matured leaves. Our findings in moso bamboo draw parallels to the earlier reports of Gypsy retroelements in Brachiaria forage grasses [66]. Several LTR retrotransposons of the Ty3/Gypsy and Ty1/Copia family have been reported to Fig. 7 The yeast one-hybrid assay showing TCP20, DOF2, and GATA transcription factors (TFs) interactions with PHRE1 and PHRE2 LTR. ...
Background
LTR retrotransposons play a significant role in plant growth, genome evolution, and environmental stress response, but their regulatory response to heat stress remains unclear. We have investigated the activities of two LTR retrotransposons, PHRE1 and PHRE2, of moso bamboo (Phyllostachys edulis) in response to heat stress.
Results
The differential overexpression of PHRE1 and PHRE2 with or without CaMV35s promoter showed enhanced expression under heat stress in transgenic plants. The transcriptional activity studies showed an increase in transposition activity and copy number among moso bamboo wild type and Arabidopsis transgenic plants under heat stress. Comparison of promoter activity in transgenic plants indicated that 5’LTR promoter activity was higher than CaMV35s promoter. Additionally, yeast one-hybrid (Y1H) system and in planta biomolecular fluorescence complementation (BiFC) assay revealed interactions of heat-dependent transcription factors (TFs) with 5’LTR sequence and direct interactions of TFs with pol and gag.
Conclusions
Our results conclude that the 5’LTR acts as a promoter and could regulate the LTR retrotransposons in moso bamboo under heat stress.
... Despite the agronomic importance of Urochloa, and the need to make crosses for breeding, genomes are not clearly defined (Boldrini et al., 2009a), although some ploidy measurements have been made (Penteado et al., 2010;Jungmann et al., 2010). The use of transposable element probes against Urochloa chromosomes indicates that many species are allopolyploid with differentiation in their transposable element composition (Santos et al., 2015). Allopolyploidy is also shown by genetic analysis in apomicts (Worthington et al., 2016) and genomic in situ hybridization (Corrêa et al., 2020). ...
... Physical mapping of 5S and 18S-5.8S-25S rDNA locations provides a chromosome marker, but the mostly similar patterns in the 'brizantha' complex did not assist in identification of genome composition (see Fig. 2; Akiyama et al., 2010;Nielen et al., 2010;Santos et al., 2015;Nani et al., 2018). In the three accessions with desirable agronomic characteristics that could not be assigned to species based on morphology, the number of rDNA sites did not correspond to ploidy, with only one pair of 45S rDNA sites in the two tetraploids (two pairs of sites expected), and four 45S sites in a pentaploid (expectation five), suggesting a more complex origin involving processes such as karyotype reorganization, aneuploidy or segmental allopolyploidy and introgression. ...
... The autopolyploid origin of U. maxima and its facultative apomixis type of reproduction have been proved by different authors (Toledo-Silva et al., 2013;Lara et al., 2019), meaning that gDNA probes here showing both terminal and pericentromeric signals are informative. Santos et al. (2015) revealed some differentiation of candidate genome-specific Ty3-gypsy retrotransposons in pericentromeric regions of Urochloa chromosomes. Urochloa contrasts with another Poaceae, Avena, where GISH can characterize individual genomes (Katsiotis et al., 2000;Tomaszewska and Kosina, 2021), 'painting' most of the chromosomal lengths. ...
Background and Aims
Diploid and polyploid Urochloa (including Brachiaria, Panicum and Megathyrsus species) C4 tropical forage grasses originating from Africa are important for food security and the environment , often being planted in marginal lands worldwide. We aimed to characterize the nature of their genomes, the repetitive DNA, and the genome composition of polyploids, leading to a model of the evolutionary pathways within the group including many apomictic species.
Methods
Some 362 forage grass accessions from international germplasm collections were studied, and ploidy determined using an optimized flow cytometry method. Whole-genome survey sequencing and molecular cytogenetic analysis were used to identify chromosomes and genomes in Urochloa accessions belonging to the 'brizantha' and 'humidicola' agamic complexes and U. maxima.
Key Results
Genome structures are complex and variable, with multiple ploidies and genome compositions within the species, and no clear geographical patterns. Sequence analysis of nine diploid and polyploid accessions enabled identification of abundant genome-specific repetitive DNA motifs . In situ hybridization with a combination of repetitive DNA and genomic DNA probes, identified evolutionary divergence and allowed us to discriminate the different genomes present in polyploids.
Conclusions
We suggest a new coherent nomenclature for the genomes present . We develop a model of evolution at the whole-genome level in diploid and polyploid accessions showing processes of grass evolution. We support the retention of narrow species concepts for U. brizantha, U. decumbens, and U. ruziziensis, and do not consider diploids and polyploids of single species as cytotypes. The results and model will be valuable in making rational choices of parents for new hybrids, assist in use of the germplasm for breeding and selection of Urochloa with improved sustainability and agronomic potential, and will assist in measuring and conserving biodiversity in grasslands.
... Previous studies reported variation in the richness and predominant lineages of TEs within the Poaceae family (Křivánková et al., 2017). Other grasses, such as Brachiaria decumbens Stapf, present a genome Ty3-Gypsy profile similar to that of D. antarctica (Santos et al., 2015). However, in other cases, as in the F. pratensis genome, the most abundant retroelement observed belongs to the Athila family (Křivánková et al., 2017). ...
... The results obtained for Ty3-Gypsy families, Tekay and TatV, showed their distribution throughout all the chromosomes in both localities, presenting an increase of hybridization signals in the proximal and centromeric regions. This observation agrees with the general distribution of retrotransposon sequences of the order LTR belonging to the Ty3-Gypsy superfamily in most grasses, such as Brachiaria (Santos et al., 2015), Triticeae (Belyayev et al., 2005), F. pratensis (Křivánková et al., 2017), Oryza, and Z. mays (Li et al., 2017) and in other groups, such as Arabidopsis thaliana (L.) Heynh. (Li et al., 2017). ...
Deschampsia antarctica is one of the two native vascular plants present in the Antarctic continent. More than half of its genome is composed of repetitive DNA. The present work aims to study the amount, composition and chromosomal localization of the main retroelements in the genome of D. antarctica, via a bioinformatic analysis and cytogenetic approach in two Antarctic localities. The retroelements are the largest fraction of genomic repetitive DNA. Ty3-Gypsy superfamily was more abundant than Ty1-Copia in D. antarctica´s genome. However, Ty1-Copia was more diverse. Angela, SIRE, TatV and Tekay families were the most abundant in the studied genome. The hybridization signals showed that the four retrotransposon families have dispersal distributions in both Antarctic localities studied. However, some differences in the chromosomal distribution were observed among families and between localities. This study contributes to the understanding of the diversity and distribution of repetitive DNA in D. antarctica.
... Several studies (reviewed in Vicient and Casacuberta, 2017) have reported transcriptional reactivation of some TE lineages in hybrids and allopolyploids or new insertions as found in tobacco, sunflower, wheat, or Brachiaria sp. (Ungerer et al., 2006;Petit et al., 2010;Yaakov and Kashkush, 2012;Santos et al., 2015). As TE expression is controlled by epigenetic regulation (e.g., DNA hypermethylation and siRNAs), new TE regulation following polyploid speciation may result in altered neighbor gene expression including gene silencing and novel gene expression patterns (Kashkush et al., 2003;Hollister and Gaut, 2009;Parisod et al., 2010a;Zhang et al., 2015;Lerat et al., 2019). ...
Gene expression dynamics is a key component of polyploid evolution, varying in nature, intensity, and temporal scales, most particularly in allopolyploids, where two or more sub-genomes from differentiated parental species and different repeat contents are merged. Here, we investigated transcriptome evolution at different evolutionary time scales among tetraploid, hexaploid, and neododecaploid Spartina species (Poaceae, Chloridoideae) that successively diverged in the last 6–10 my, at the origin of differential phenotypic and ecological traits. Of particular interest are the recent (19th century) hybridizations between the two hexaploids Spartina alterniflora (2n = 6x = 62) and S. maritima (2n = 6x = 60) that resulted in two sterile F1 hybrids: Spartina × townsendii (2n = 6x = 62) in England and Spartina × neyrautii (2n = 6x = 62) in France. Whole genome duplication of S. × townsendii gave rise to the invasive neo-allododecaploid species Spartina anglica (2n = 12x = 124). New transcriptome assemblies and annotations for tetraploids and the enrichment of previously published reference transcriptomes for hexaploids and the allododecaploid allowed identifying 42,423 clusters of orthologs and distinguishing 21 transcribed transposable element (TE) lineages across the seven investigated Spartina species. In 4x and 6x mesopolyploids, gene and TE expression changes were consistent with phylogenetic relationships and divergence, revealing weak expression differences in the tetraploid sister species Spartina bakeri and Spartina versicolor (<2 my divergence time) compared to marked transcriptome divergence between the hexaploids S. alterniflora and S. maritima that diverged 2–4 mya. Differentially expressed genes were involved in glycolysis, post-transcriptional protein modifications, epidermis development, biosynthesis of carotenoids. Most detected TE lineages (except SINE elements) were found more expressed in hexaploids than in tetraploids, in line with their abundance in the corresponding genomes. Comparatively, an astonishing (52%) expression repatterning and deviation from parental additivity were observed following recent reticulate evolution (involving the F1 hybrids and the neo-allododecaploid S. anglica), with various patterns of biased homoeologous gene expression, including genes involved in epigenetic regulation. Downregulation of TEs was observed in both hybrids and accentuated in the neo-allopolyploid. Our results reinforce the view that allopolyploidy represents springboards to new regulatory patterns, offering to worldwide invasive species, such as S. anglica, the opportunity to colonize stressful and fluctuating environments on saltmarshes.
... possesses various polyploid species with different basic chromosome number (× = 6 to × = 9). The occurence, mapping and distribution of gypsy retrotransposons in the karyotype of Brachiaria decumbens (Mez) Davidse, B. brizantha (Mez) Davidse, B. ruziziensis (Mez) Davidse and B. humidicola (Mez) Davidse evidenced that, besides the chromosome number variation, mobile elements also contributed to karyotype evolution [68]. In addition, genetic variation was showed in polyploid Paspalum species from SSR markers developed for this genus. ...
Polyploidy means having more than two basic sets of chromosomes. Polyploid plants may be artificially obtained through chemical, physical and biological (2n gametes) methods. This approach allows an increased gene scope and expression, thus resulting in phenotypic changes such as yield and product quality. Nonetheless, breeding new cultivars through induced polyploidy should overcome deleterious effects that are partly contributed by genome and epigenome instability after polyploidization. Furthermore, shortening the time required from early chromosome set doubling to the final selection of high yielding superior polyploids is a must. Despite these hurdles, plant breeders have successfully obtained polyploid bred-germplasm in broad range of forages after optimizing methods, concentration and time, particularly when using colchicine. These experimental polyploids are a valuable tool for understanding gene expression, which seems to be driven by dosage dependent gene expression, altered gene regulation and epigenetic changes. Isozymes and DNA-based markers facilitated the identification of rare alleles for particular loci when compared with diploids, and also explained their heterozygosity, phenotypic plasticity and adaptability to diverse environments. Experimentally induced polyploid germplasm could enhance fresh herb-age yield and quality, e.g., leaf protein content, leaf total soluble solids, water soluble carbohydrates and sucrose content. Offspring of experimentally obtained hybrids should undergo selection for several generations to improve their performance and stability.
... The occurence, mapping and distribution of gypsy retrotransposons in the karyotype of Brachiaria decumbens, B. brizantha, B. ruziziensis and B. humidicola evidenced that, besides the chromosome number variation, mobile elements also contributed to karyotype evolution [56]. In addition, genetic variation was showed in polyploid Paspalum species from SSR markers developed for this genus. ...
Polyploidy means having more than two basic sets of chromosomes. Polyploid plants may be artificially obtained through chemical, physical and biological (2n gametes) methods. This approach allows an increased gene scope and expression, thus resulting in phenotypic changes such as yield and product quality. Nonetheless, breeding new cultivars through induced polyploidy should overcome deleterious effects that are partly contributed by genome and epigenome instability after polyploidization. Furthermore, shortening the time required from early chromosome set doubling to the final selection of high yielding superior polyploids is a must. Despite these hurdles, plant breeders have successfully obtained polyploid bred-germplasm in broad range of forages after optimizing methods, concentration and time, particularly when using colchicine. These experimental polyploids are a valuable tool for understanding gene expression, which seems to be driven by dosage dependent gene expression, altered gene regulation and epigenetic changes. Isozymes and DNA-based markers facilitated the identification of rare alleles for particular loci when compared with diploids, and also explained their heterozygosity, phenotypic plasticity and adaptability to diverse environments. Experimentally induced polyploid germplasm could enhance fresh herbage yield and quality, e.g. leaf protein content, leaf total soluble solids, water soluble carbohydrates and sucrose content. Offspring of experimentally obtained hybrids should undergo selection for several generations to improve their performance and stability.
