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Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-re...
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... the available results argue against this hypothesis: (1) gel- Surprisingly, the Ty3/gypsy-related DNA sequences identified in the sorghum centromeres were detected in blot hybridization of sorghum and rice genomic DNA digested with numerous restriction enzymes suggests a much wider range of plant species than all previously reported retrotransposons. Positive gel-blot hybridiza- that the Ty3/gypsy-related centromeric sequences are not tandem repeats, but are dispersed in the centro- tion signals were detected in grass species across the three examined subfamilies of the Gramineae when meric regions; (2) clustered Fiber-FISH signals, charac- teristic of tandem repeats, were not observed when pSau3A9 and pHind22 were used as probes ( Figure 3). There are two possible explanations for this rare pHind22, pSau3A9, and pRCS1 were used as probes (S. A. Jackson and J. Jiang, unpublished results); (3) conservation. ...
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Citations
... Retrotransposons fall into 2 large groups including long terminal repeat (LTR) and non-LTR elements (Kumar and Bennetzen 1999). A Ty3-gypsy type of centromeric LTR retrotransposon (CR) was first discovered in grass species (Aragon-Alcaide et al. 1996;Jiang et al. 1996;Miller et al. 1998;Presting et al. 1998). CR elements were best characterized in rice (CRR, CR of rice) Cheng, Dong, et al. 2002;Nagaki et al. 2004;Nagaki et al. 2005) and maize (CRM, CR of maize) (Zhong et al. 2002;Jin et al. 2004;Wolfgruber et al. 2009). ...
Centromeres in most multicellular eukaryotes are composed of long arrays of repetitive DNA sequences. Interestingly, several transposable elements, including the well-known long terminal repeat (LTR) retrotransposon CRM (centromeric retrotransposon of maize), were found to be enriched in functional centromeres marked by the centromeric histone H3 (CENH3). Here we report a centromeric long interspersed nuclear element (LINE), Celine, in Populus species. Celine has colonized preferentially in the CENH3-associated chromatin of every poplar chromosome, with 84% of the Celine elements localized in the CENH3-binding domains. By contrast, only 51% of the CRM elements were bound to CENH3 domains in Populus trichocarpa. These results suggest different centromere targeting mechanisms employed by Celine and CRM elements. Nevertheless, the high target specificity seems to be detrimental to further amplification of the Celine elements, leading to a shorter life span and patchy distribution among plant species compared to the CRM elements. Using a phylogenetically guided approach we were able to identify Celine-like LINE elements in tea plant (Camellia sinensis) and green ash tree (Fraxinus pennsylvanica). The centromeric localization of these Celine-like LINEs was confirmed in both species. We demonstrate that the centromere targeting property of Celine-like LINEs is of primitive origin and has been conserved among distantly related plant species.
... Centromeres are also occupied by specific retrotransposons in some plants and animals. For example, the centromeric retrotransposon Ty3-gypsy is present and conserved within Gramineae (Miller et al., 1998). In maize, centromeric repeat for maize (CRM) elements are interspersed with satellite repeats (Ananiev et al., 1998). ...
Centromere positioning and organization are crucial for genome evolution; however, research on centromere biology is largely influenced by the quality of available genome assemblies. Here, we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum (TM-1) and Gossypium barbadense (3-79). Compared with previously published reference genomes, our assemblies show substantial improvements, with the contig N50 improved by 4.6-fold and 5.6-fold, respectively, and thus represent the most complete cotton genomes to date. These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G. hirsutum and G. barbadense, respectively. Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize (CRM) and Tekay long terminal repeat families, and the CRM family reshapes the centromere structure of the At subgenome after polyploidization. These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes, ensuring centromere function and genome stability. In addition, the repositioning and high sequence divergence of centromeres between G. hirsutum and G. barbadense have contributed to speciation and centromere diversity. This study sheds light on centromere evolution in a significant crop and provides an alternative approach for exploring the evolution of polyploid plants.
... In angiosperm genomes, the distribution of Copia retrotransposons is usually dispersed across chromosomes, while Gypsy LTR REs tend to concentrate in centromeric and telomeric regions (Jiang et al. 1996;Miller et al. 1998;Pereira 2004;Wang et al. 2006;Neumann et al. 2011;Domingues et al. 2012). Dispersed chromosomal distribution of several RLX was observed in conifers, where only one TE family was found to be clustered in telomeres (Friesen et al. 2001). ...
... Monophyletic grouping of reverse transcriptase domain sequences suggested a common ancestry with subsequent speciesspecific proliferation of certain conifer TE lineages (Friesen et al. 2001). Currently, in plant genomes, a number of retrotransposons have been described with prevalence in pericentromeric, subtelomeric and in constitutive heterochromatin regions (Miller et al. 1998;Lippman et al. 2004;Dai et al. 2007;Gao et al. 2008;Neumann et al. 2011;Kejnovský et al. 2012;de Castro Nunes et al. 2018). Integrase genes of centromere associated retrotransposons contain chromodomains, which could regulate specific targeting of element transposition to centromeres (Kordiš 2005;Gao et al. 2008). ...
The importance of mobile genetic elements or transposons in genome evolution and adaptation is being increasingly recognized. Transposons were shown to be involved in gene regulation, shaping chromosome structures, reshuffling coding sequences and generating genetic diversity. Transposable elements constitute the largest fraction of plant genomes and are diverse by structure and distribution. There are still unanswered questions, with regard to their interaction with the environment, regulation mechanisms and convenience of horizontal transfer, but involvement in the epigenetic mechanisms could explain a fraction of missing heritability. Due to their repetitive nature and ubiquity throughout genomes, the study of transposons requires distinctly developed methods and assays. Even with the rapid development of sequencing technologies, genomic assembly and annotation of transposable elements in large genomes are still problematic, and therefore they are routinely excluded from analysis. In this chapter, we aim to summarize the main directions of transposable element research and basic findings in plants with an emphasis on more complex pine genomes providing further perspectives in this area. Although, compared to model species, transposon research in conifers is currently at an initial stage, further studies could uncover additional aspects of their role in genome architecture, adaptive responses and environment–genome interactions.KeywordsMobile genetic elementsTransposonsRetrotransposonsGene networksPine genomeDiversityNon-coding RNAGene regulation
... In angiosperm genomes, the distribution of Copia retrotransposons is usually dispersed across chromosomes, while Gypsy LTR REs tend to concentrate in centromeric and telomeric regions (Jiang et al. 1996;Miller et al. 1998;Pereira 2004;Wang et al. 2006;Neumann et al. 2011;Domingues et al. 2012). Dispersed chromosomal distribution of several RLX was observed in conifers, where only one TE family was found to be clustered in telomeres (Friesen et al. 2001). ...
... Monophyletic grouping of reverse transcriptase domain sequences suggested a common ancestry with subsequent speciesspecific proliferation of certain conifer TE lineages (Friesen et al. 2001). Currently, in plant genomes, a number of retrotransposons have been described with prevalence in pericentromeric, subtelomeric and constitutive heterochromatin regions (Miller et al. 1998;Lippman et al. 2004;Dai et al. 2007;Gao et al. 2008;Neumann et al. 2011;Kejnovský et al. 2012;de Castro Nunes et al. 2018). Integrase genes of centromereassociated retrotransposons contain chromodomains, which could regulate specific targeting of element transposition to centromeres (Kordiš 2005;Gao et al. 2008). ...
Pinus species are highly suitable for monitoring anthropogenic pollutants, including air contaminants, heavy metals and radionuclides. Scots pine (Pinus sylvestris L.) is one of the most widely distributed conifers in the world, and is characterized by a high sensitivity to environmental pollutants and an increased ability to accumulate pollutants in tissues. Because of its large genome size, this species is extremely sensitive to ionizing radiation, thus considered by the International Commission on Radiological Protection as a reference plant for radiation protection of biota. Current approaches in functional genomics and bioinformatics allow studying the transcriptional profiles of P. sylvestris in radioactively contaminated areas, revealing adaptive responses at a previously unattainable level. In the Chernobyl exclusion zone, where natural populations are under low-dose chronic radiation stress, such responses include direct structural protection of DNA integrity from radiation damage and modulation of reactive oxygen species production. Chronically irradiated pine populations have increased expression of genes encoding heat shock proteins and histones. However, no differential expression of genes related to DNA repair was revealed, while the transcriptional responses pointed to modulation of redox cellular homeostasis. These observations suggest that the response patterns to chronic low-dose and acute high-dose ionizing radiation exposure are partially different. Biomonitoring properties of P. sylvestris and a pipeline for assembling the transcriptome of this non-model species are also discussed.
... In angiosperm genomes, the distribution of Copia retrotransposons is usually dispersed across chromosomes, while Gypsy LTR REs tend to concentrate in centromeric and telomeric regions (Jiang et al. 1996;Miller et al. 1998;Pereira 2004;Wang et al. 2006;Neumann et al. 2011;Domingues et al. 2012). Dispersed chromosomal distribution of several RLX was observed in conifers, where only one TE family was found to be clustered in telomeres (Friesen et al. 2001). ...
... Monophyletic grouping of reverse transcriptase domain sequences suggested a common ancestry with subsequent speciesspecific proliferation of certain conifer TE lineages (Friesen et al. 2001). Currently, in plant genomes, a number of retrotransposons have been described with prevalence in pericentromeric, subtelomeric and constitutive heterochromatin regions (Miller et al. 1998;Lippman et al. 2004;Dai et al. 2007;Gao et al. 2008;Neumann et al. 2011;Kejnovský et al. 2012;de Castro Nunes et al. 2018). Integrase genes of centromereassociated retrotransposons contain chromodomains, which could regulate specific targeting of element transposition to centromeres (Kordiš 2005;Gao et al. 2008). ...
The largest pine tree in the world, sugar pine, also has one the largest genomes ever sequenced in any plant species. The reference genome, transcriptome, and SNP markers developed for the species have been used to support breeding disease resistant trees and answer questions related to genome obesity. These resources also create an opportunity to explore associations between genetic variation and environmental variables. By combining ordination and association techniques such as PCA, MLM, and RDA, we identified markers and genes associated with environmental variation across the Sugar Pine species range. Most of the genes identified by our analysis were associated with precipitation though temperature and continentality were also found to be associated with putatively adaptive genes. The results of the PCA and environmental correlations demonstrated explicit groupings among the environmental variables. Functional annotations for these genes were primarily related to signal transduction and disease resistance, but annotations related to biotic and abiotic stress were also identified. Results further provide insight into the geographic pattern of environmentally correlated genetic variation in the species. These findings may provide important insights to guide management strategies looking to maintain the species through ongoing changes in climate and fire regimes.KeywordsGenotype-environment associationRedundancy analysisSugar pineClimate adaptationgenomics
... Moreover, the centromeric locus as well as the pericentromeric region may bear TEs in addition to satDNA sequences . Centromeric-specific retrotransposons (CR) form a clade of chromoviruses, a lineage of Ty3/gypsy retrotransposons that have been found in centromeres of banana (Čížková et al. 2013) and grasses such as barley (Presting et al. 1998;Hudakova et al. 2001), maize (Ananiev et al. 1998b;Zhong et al. 2002;Nagaki et al. 2003a;Sharma and Presting 2014), sorghum (Jiang et al. 1996;Miller et al. 1998;Presting et al. 1998), wheat (Liu et al. 2008;Li et al. 2013), goatgrass , rice Miller et al. 1998;Bao et al. 2006;Cheng et al. 2002;, rye (Francki 2001), and sugarcane (Nagaki and Murata 2005) among others Sharma and Presting 2014). They have also been found in dicotyledonous species such as Arabidopsis (Brandes et al. 1997;Fransz et al. 1998), radish , and Beta (Gindullis et al. 2001;Weber and Schmidt 2009) among others . ...
... Moreover, the centromeric locus as well as the pericentromeric region may bear TEs in addition to satDNA sequences . Centromeric-specific retrotransposons (CR) form a clade of chromoviruses, a lineage of Ty3/gypsy retrotransposons that have been found in centromeres of banana (Čížková et al. 2013) and grasses such as barley (Presting et al. 1998;Hudakova et al. 2001), maize (Ananiev et al. 1998b;Zhong et al. 2002;Nagaki et al. 2003a;Sharma and Presting 2014), sorghum (Jiang et al. 1996;Miller et al. 1998;Presting et al. 1998), wheat (Liu et al. 2008;Li et al. 2013), goatgrass , rice Miller et al. 1998;Bao et al. 2006;Cheng et al. 2002;, rye (Francki 2001), and sugarcane (Nagaki and Murata 2005) among others Sharma and Presting 2014). They have also been found in dicotyledonous species such as Arabidopsis (Brandes et al. 1997;Fransz et al. 1998), radish , and Beta (Gindullis et al. 2001;Weber and Schmidt 2009) among others . ...
... It should also be taken into account that the abundance of CentC has decreased after domestication (Albert et al. 2010;Bilinski et al. 2015;Schneider et al. 2016). Similarly, rice centromeres are composed mainly of 155-bp CentO tandem repeats Nonomura and Kurata 2001;Cheng et al. 2002) and interspersed centromerespecific CRR retrotransposons Miller et al. 1998;Cheng et al. 2002;. CentC and CentO repeats are homologous and have certain regions of high sequence identity though these species have diverged during more than 50 my (Lee et al. 2005;Cheng et al. 2002). ...
Next-Generation Sequencing (NGS) has revealed that B chromosomes in several species are enriched in repetitive DNA, mostly satellite DNA (satDNA). This raises the question of whether satDNA is important to B chromosomes for functional reasons or else its abundance on Bs is simply a consequence of properties of B chromosomes such as their dispensability and late replication. Here we review current knowledge in this respect and contextualize it within the frame of practical difficulties to perform this kind of research, the most important being the absence of good full genome sequencing for B-carrying species, which is an essential requisite to ascertain the intragenomic origin of B chromosomes. Our review analysis on 16 species revealed that 38% of them showed B-specific satDNAs whereas only one of them (6%) carried an inter-specifically originated B chromosome. This shows that B-specific satDNA families can eventually evolve in intraspecifically arisen B chromosomes. Finally, the possibility of satDNA accumulation on B chromosomes for functional reasons is exemplified by B chromosomes in rye, as they contain B-specific satDNAs which are transcribed and occupy chromosome locations where they might facilitate the kind of drive shown by this B chromosome during pollen grain mitosis.
... Genome assemblies demonstrated that the heterochromatic, pericentromeric regions of S. bicolor are enriched in repetitive elements (Kim et al., 2005;Paterson et al., 2009;McCormick et al., 2018). The satellite repeat CEN38 (Miller et al., 1998b;Zwick et al., 2000) and the retrotransposon-related DNA element Sau3A9 (Miller et al., 1998a) were found to be associated with the centromeres. Nevertheless, variation in the repeat composition and distribution among different Sorghum species remain largely unknown. ...
... The centromeric Ty3_gypsy-CRM retroelements were also identified in the wild Saccharum species, S. spontaneum (Zhang et al., 2017). While Ty3_gypsy-CRM retroelements are commonly found in plant centromeres (Miller et al., 1998a;Neumann et al., 2011), Ty3_gypsy-Athila elements are less frequently detected in centromeric regions except in the centromere core of Arabidopsis (Kumekawa et al., 2000), Festuca, and Lolium species (Zwyrtkova et al., 2020). ...
Polyploidization is an evolutionary event leading to structural changes of the genome(s), particularly allopolyploidization, which combines different genomes of distinct species. The tetraploid species, Sorghum halepense, is assumed an allopolyploid species formed by hybridization between diploid S. bicolor and S. propinquum. The repeat profiles of S. bicolor, S. halepense, and their relatives were compared to elucidate the repeats’ role in shaping their genomes. The repeat frequencies and profiles of the three diploid accessions (S. bicolor, S. bicolor ssp. verticilliflorum, and S. bicolor var. technicum) and two tetraploid accessions (S. halepense) are similar. However, the polymorphic distribution of the subtelomeric satellites preferentially enriched in the tetraploid S. halepense indicates drastic genome rearrangements after the allopolyploidization event. Verified by CENH3 chromatin immunoprecipitation (ChIP)-sequencing and fluorescence in situ hybridization (FISH) analysis the centromeres of S. bicolor are mainly composed of the abundant satellite SorSat137 (CEN38) and diverse CRMs, Athila of Ty3_gypsy and Ty1_copia-SIRE long terminal repeat (LTR) retroelements. A similar centromere composition was found in S. halepense. The potential contribution of S. bicolor in the formation of tetraploid S. halepense is discussed.
... Moreover, the centromeric locus as well as the pericentromeric region may bear TEs in addition to satDNA sequences . Centromeric-specific retrotransposons (CR) form a clade of chromoviruses, a lineage of Ty3/gypsy retrotransposons ) that have been found in centromeres of banana (Čížková et al. 2013) and grasses such as barley (Presting et al. 1998;Hudakova et al. 2001), maize (Ananiev et al. 1998b;Zhong et al. 2002;Nagaki et al. 2003a;Sharma and Presting 2014), sorghum (Jiang et al. 1996;Miller et al. 1998;Presting et al. 1998), wheat (Liu et al. 2008;Li et al. 2013), goatgrass , rice Miller et al. 1998;Bao et al. 2006;Cheng et al. 2002;, rye (Francki 2001), and sugarcane (Nagaki and Murata 2005) among others Sharma and Presting 2014). They have also been found in dicotyledonous species such as Arabidopsis (Brandes et al. 1997;Fransz et al. 1998), radish (He et al. 2015), and Beta (Gindullis et al. 2001;Weber and Schmidt 2009) among others . ...
... Moreover, the centromeric locus as well as the pericentromeric region may bear TEs in addition to satDNA sequences . Centromeric-specific retrotransposons (CR) form a clade of chromoviruses, a lineage of Ty3/gypsy retrotransposons ) that have been found in centromeres of banana (Čížková et al. 2013) and grasses such as barley (Presting et al. 1998;Hudakova et al. 2001), maize (Ananiev et al. 1998b;Zhong et al. 2002;Nagaki et al. 2003a;Sharma and Presting 2014), sorghum (Jiang et al. 1996;Miller et al. 1998;Presting et al. 1998), wheat (Liu et al. 2008;Li et al. 2013), goatgrass , rice Miller et al. 1998;Bao et al. 2006;Cheng et al. 2002;, rye (Francki 2001), and sugarcane (Nagaki and Murata 2005) among others Sharma and Presting 2014). They have also been found in dicotyledonous species such as Arabidopsis (Brandes et al. 1997;Fransz et al. 1998), radish (He et al. 2015), and Beta (Gindullis et al. 2001;Weber and Schmidt 2009) among others . ...
... It should also be taken into account that the abundance of CentC has decreased after domestication (Albert et al. 2010;Bilinski et al. 2015;Schneider et al. 2016). Similarly, rice centromeres are composed mainly of 155-bp CentO tandem repeats Nonomura and Kurata 2001;Cheng et al. 2002) and interspersed centromerespecific CRR retrotransposons Miller et al. 1998;Cheng et al. 2002;. CentC and CentO repeats are homologous and have certain regions of high sequence identity though these species have diverged during more than 50 my (Lee et al. 2005;Cheng et al. 2002). ...
The twenty-first century began with a certain indifference to the research of satellite DNA (satDNA). Neither genome sequencing projects were able to accurately encompass the study of satDNA nor classic methodologies were able to go further in undertaking a better comprehensive study of the whole set of satDNA sequences of a genome. Nonetheless, knowledge of satDNA has progressively advanced during this century with the advent of new analytical techniques. The enormous advantages that genome-wide approaches have brought to its analysis have now stimulated a renewed interest in the study of satDNA. At this point, we can look back and try to assess more accurately many of the key questions that were left unsolved in the past about this enigmatic and important component of the genome. I review here the understanding gathered on plant satDNAs over the last few decades with an eye on the near future.
... In situ localisation of the retrotransposons dispersed throughout the chromosomes is a common feature of large plant genomes, while small genomes tend to have them at pericentromeric regions (Miller et al. 1998;Cheng and Murata 2003;Nagaki 2004;Neumann et al. 2011). Unlike retrotransposons, satellite DNAs usually form blocks on heterochromatic chromosome regions (Heslop-Harrison and Schwarzacher 2011;Heslop-Harrison and Schmidt 2012;Ribeiro et al. 2017). ...
Main conclusions
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed.
AbstractRepetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
... Analyzed sequences included the knob repeats knob180 and TR-1 [38,39], 5S and 45S rDNA repeats [40], and centromere-associated CentC satellite repeats [41]. We also queried consensus sequences for centromere retrotransposons of maize (CRM) families 1-4 [42][43][44][45]. In all cases, we found the percentages to be similar in the 2C, 4C and 8C samples (S2D and S2E Fig), further suggesting that there is little or no over-or under-replication. ...
Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed.
