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1. ModDotPlot—rapid and interactive visualization of tandem repeats

   https://doi.org/10.1093/bioinformatics/btae493  

   Sweeten, Alexander P; Schatz, Michael C; Phillippy, Adam M (August 2024, Bioinformatics)

   Ponty, Yann (Ed.)

   Motivation: A common method for analyzing genomic repeats is to produce a sequence similarity matrix visualized via a dot plot. Innovative approaches such as StainedGlass have improved upon this classic visualization by rendering dot plots as a heatmap of sequence identity, enabling researchers to better visualize multi-megabase tandem repeat arrays within centromeres and other heterochromatic regions of the genome. However, computing the similarity estimates for heatmaps requires high computational overhead and can suffer from decreasing accuracy. Results: In this work, we introduce ModDotPlot, an interactive and alignment-free dot plot viewer. By approximating average nucleotide identity via a k-mer-based containment index, ModDotPlot produces accurate plots orders of magnitude faster than StainedGlass. We accomplish this through the use of a hierarchical modimizer scheme that can visualize the full 128 Mb genome of Arabidopsis thaliana in under 5 min on a laptop. ModDotPlot is bundled with a graphical user interface supporting real-time interactive navigation of entire chromosomes. Availability and implementation: ModDotPlot is available at https://github.com/marbl/ModDotPlot. 

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2. Diagrammatic approaches to RNA structures with trinucleotide repeats

   https://doi.org/10.1016/j.bpj.2021.04.010  

   Mak, Chi H.; Phan, Ethan N.H. (June 2021, Biophysical Journal)

   null (Ed.)
3. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

   https://doi.org/10.1186/s13059-021-02336-9  

   Formenti, Giulio; Rhie, Arang; Balacco, Jennifer; Haase, Bettina; Mountcastle, Jacquelyn; Fedrigo, Olivier; Brown, Samara; Capodiferro, Marco Rosario; Al-Ajli, Farooq O.; Ambrosini, Roberto; et al (December 2021, Genome Biology)

   Abstract Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone. 

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4. Structure-forming repeats and their impact on genome stability

   https://doi.org/10.1016/j.gde.2020.10.006  

   Brown, Rebecca E; Freudenreich, Catherine H (April 2021, Current Opinion in Genetics & Development)

   null (Ed.)
5. Natural variation in C. elegans short tandem repeats

   https://doi.org/10.1101/gr.277067.122  

   Zhang, Gaotian; Wang, Ye; Andersen, Erik C. (October 2022, Genome Research)

   Short tandem repeats (STRs) represent an important class of genetic variation that can contribute to phenotypic differences. Although millions of single nucleotide variants (SNVs) and short indels have been identified among wild Caenorhabditis elegans strains, the natural diversity in STRs remains unknown. Here, we characterized the distribution of 31,991 STRs with motif lengths of 1–6 bp in the reference genome of C. elegans . Of these STRs, 27,667 harbored polymorphisms across 540 wild strains and only 9691 polymorphic STRs (pSTRs) had complete genotype data for more than 90% of the strains. Compared with the reference genome, the pSTRs showed more contraction than expansion. We found that STRs with different motif lengths were enriched in different genomic features, among which coding regions showed the lowest STR diversity and constrained STR mutations. STR diversity also showed similar genetic divergence and selection signatures among wild strains as in previous studies using SNVs. We further identified STR variation in two mutation accumulation line panels that were derived from two wild strains and found background-dependent and fitness-dependent STR mutations. We also performed the first genome-wide association analyses between natural variation in STRs and organismal phenotypic variation among wild C. elegans strains. Overall, our results delineate the first large-scale characterization of STR variation in wild C. elegans strains and highlight the effects of selection on STR mutations. 

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