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Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol
The ribosomal RNA genes (rDNA) are universal genome components with a housekee** function, given the crucial role of ribosomal RNA in the synthesis...
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Characterization of repetitive DNA on the genome of the marsh rat Holochilus nanus (Cricetidae: Sigmodontinae)
Repetitive DNA are sequences repeated hundreds or thousands of times and an abundant part of eukaryotic genomes. SatDNA represents the majority of...
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Identification of 45S rDNA in Passiflora using low coverage sequencing: analysis of GC content and chromosomal localization
BackgroundThe 45S rDNA is considered the most useful chromosomal marker for cytogenetic analysis of Passiflora . Amplification of 45S rDNA sequence...
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Global analysis of repetitive DNA from unassembled sequence reads using RepeatExplorer2
RepeatExplorer2 is a novel version of a computational pipeline that uses graph-based clustering of next-generation sequencing reads for...
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A first genomic portrait of the deep-water azooxanthellate reef-building coral Madracis myriaster: genome size, repetitive elements, nuclear RNA gene operon, mitochondrial genome, and phylogenetic placement in the family Pocilloporidae
The coral Madracis myriaster is one of the most important reef builders in deep-water habitats of the Caribbean Sea, offering refuge to numerous...
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Interspecific cytogenomic comparison reveals a potential chromosomal centromeric marker in Proceratophrys frog species
Among the repetitive elements, satellite DNA (SatDNA) emerges as extensive arrays of highly similar tandemly repeated units, spanning megabases in...
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First genome survey and repeatome analysis of Chrysopogon zizanioides based on next-generation sequencing
Chrysopogon zizanioides is a perennial C4 grass that has been widely utilized for soil erosion control and ecological restoration. Nevertheless,...
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The holocentricity in the dioecious nutmeg (Myristica fragrans) is not based on major satellite repeats
Holocentric species are characterized by the presence of centromeres throughout the length of the chromosomes. We confirmed the holocentricity of the...
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Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus)
BackgroundSatellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome...
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Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses
BackgroundCultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the...
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Plant Cytogenetics: From Chromosomes to Cytogenomics
Chromosomes have been studied since the late nineteenth century in the disciplines of cytology and cytogenetics. Analyzing their numbers, features,...
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Diversity of the repetitive DNA fraction in Cestrum, the genus with the largest genomes within Solanaceae
BackgroundCestrum species present large genomes (2 C = ~ 24 pg), a high occurrence of B chromosomes and great diversity in heterochromatin bands....
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Comprehensive analysis of the Xya riparia genome uncovers the dominance of DNA transposons, LTR/Gypsy elements, and their evolutionary dynamics
Transposable elements (TEs) are DNA sequences that can move or replicate within a genome, and their study has become increasingly important in...
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Unveiling the distinctive traits of functional rye centromeres: minisatellites, retrotransposons, and R-loop formation
Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments. Despite their conserved...
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Identification of differential abundance of satellite DNA sequences in Asclepias (Apocynaceae): in-depth characterization of species-specific sequences
Satellite DNA is a class of tandemly repetitive sequences characterized by rapid evolution and high intra- and inter-specific diversification and is...
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Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species...
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Satellite DNA probes of Alstroemeria longistaminea (Alstroemeriaceae) paint the heterochromatin and the B chromosome, reveal a G-like banding pattern, and point to a strong structural karyotype conservation
Alstroemeria species present a well-conserved and asymmetric karyotype. The genus is divided into a Chilean clade, rich in heterochromatin, and a...
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Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species
Main conclusionOpposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the...
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The evolution and formation of centromeric repeats analysis in Vitis vinifera
Main conclusionSix grape centromere-specific markers for cytogenetics were mined by combining genetic and immunological assays, and the possible...
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Divergence of 10 satellite repeats in Artemisia (Asteraceae: Anthemideae) based on sequential fluorescence in situ hybridization analysis: evidence for species identification and evolution
Artemisia is a large genus encompassing about 400 diverse species, many of which have considerable medicinal and ecological value. However, complex...
