Repetitive DNAs are ubiquitous in plant genomes and play crucial roles such as structural backbones of the genome, regulators of gene expression, and motors of evolution. Still, their unique biology is far from being fully understood and appreciated. One reason for this knowledge gap is the vast underrepresentation of repetitive DNAs in reference genome sequences and, if present, their often imprecise assembly and annotation. As current long and short read data reveals unprecedented insights into the evolution and small-scale organization of repetitive DNAs, integration of visual techniques can offer the additional insight into the large-scale organization of repeats along the chromosomes. With progressing innovation, the once clear-cut border between cytogenetics and genomics is further blurring enabling us to more fully capture the dynamic nature and evolution of chromosomes. For example, newer –omics technologies also allow the investigation of the genome’s spatial structure, whereas bulked oligonucleotides transfer information from a genome assembly directly onto the physical chromosomes.
In this Research Topic, we want to focus on the opportunities, challenges, and limitations of integrating genomics with visual techniques, especially for the investigation of repetitive DNAs, including satellite DNAs, ribosomal DNAs, telomeres, and transposable elements in model and non-model plant genomes. We would like to tackle fundamental questions arising from these evolutionarily dynamic regions in relation to genomic plasticity and speciation. We also welcome comparative studies, focusing on several repeat types or plant genomes in order to better understand any genomic restructuring that may have occurred between species. Similarly, investigations dealing with genetic and epigenetic consequences of different repeat dynamics are invited, especially if their impact on the ecology and distribution of plant species is targeted. For all studies, we wish to highlight findings that are supported by a combination of techniques that broadly fit within the scope of “genomics meets cytogenetics”.
The aim of the current Research Topic is to cover promising, recent, and novel research trends for the investigation of repetitive DNA regions in plant genomes, especially those that combine the use of genomics and cytogenetics techniques. We encourage to submit articles targeting both model and non-model plants. Specifically, we will receive Original Research, Review, and Methodology articles. Regarding the future of this research field, we also encourage the submission of Opinions and Perspectives. Areas to be covered in this Research Topic may include, but are not limited to:
? The composition of plant centromeres and telomeres.
? The role of more rapidly evolving regions, such as centromeres and subtelomeres, in genomic plasticity.
? Satellite DNA evolution and their impact on plant genomes.
? Karyotype evolution and role of chromosome rearrangements in meiosis and speciation, especially in relation to the repetitive regions of the genome.
? Transposable element dynamics.
? (Cyto)genomic studies of the repetitive landscape of plant genomes.
? (Cyto)genomics of plant ribosomal DNAs.
? Methodical approaches and pipelines that allow the integration of genomics and cytogenetics for the analysis of repetitive DNA regions.
Repetitive DNAs are ubiquitous in plant genomes and play crucial roles such as structural backbones of the genome, regulators of gene expression, and motors of evolution. Still, their unique biology is far from being fully understood and appreciated. One reason for this knowledge gap is the vast underrepresentation of repetitive DNAs in reference genome sequences and, if present, their often imprecise assembly and annotation. As current long and short read data reveals unprecedented insights into the evolution and small-scale organization of repetitive DNAs, integration of visual techniques can offer the additional insight into the large-scale organization of repeats along the chromosomes. With progressing innovation, the once clear-cut border between cytogenetics and genomics is further blurring enabling us to more fully capture the dynamic nature and evolution of chromosomes. For example, newer –omics technologies also allow the investigation of the genome’s spatial structure, whereas bulked oligonucleotides transfer information from a genome assembly directly onto the physical chromosomes.
In this Research Topic, we want to focus on the opportunities, challenges, and limitations of integrating genomics with visual techniques, especially for the investigation of repetitive DNAs, including satellite DNAs, ribosomal DNAs, telomeres, and transposable elements in model and non-model plant genomes. We would like to tackle fundamental questions arising from these evolutionarily dynamic regions in relation to genomic plasticity and speciation. We also welcome comparative studies, focusing on several repeat types or plant genomes in order to better understand any genomic restructuring that may have occurred between species. Similarly, investigations dealing with genetic and epigenetic consequences of different repeat dynamics are invited, especially if their impact on the ecology and distribution of plant species is targeted. For all studies, we wish to highlight findings that are supported by a combination of techniques that broadly fit within the scope of “genomics meets cytogenetics”.
The aim of the current Research Topic is to cover promising, recent, and novel research trends for the investigation of repetitive DNA regions in plant genomes, especially those that combine the use of genomics and cytogenetics techniques. We encourage to submit articles targeting both model and non-model plants. Specifically, we will receive Original Research, Review, and Methodology articles. Regarding the future of this research field, we also encourage the submission of Opinions and Perspectives. Areas to be covered in this Research Topic may include, but are not limited to:
? The composition of plant centromeres and telomeres.
? The role of more rapidly evolving regions, such as centromeres and subtelomeres, in genomic plasticity.
? Satellite DNA evolution and their impact on plant genomes.
? Karyotype evolution and role of chromosome rearrangements in meiosis and speciation, especially in relation to the repetitive regions of the genome.
? Transposable element dynamics.
? (Cyto)genomic studies of the repetitive landscape of plant genomes.
? (Cyto)genomics of plant ribosomal DNAs.
? Methodical approaches and pipelines that allow the integration of genomics and cytogenetics for the analysis of repetitive DNA regions.
