RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

Background. Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way tomap and visualize the genome-wide information, such asGCcontent, gene and repeat density, DNAmethylation distribution, genomic synteny, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly, or have limited application scenarios. As more and more non-model species are sequenced with chromosome-level assembly being available, tools that can generate idiograms for a broad range of species and be capable of visualizing more data types are needed to help better understanding fundamental genome characteristics. Results. The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. Conclusion. The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics. Subjects Bioinformatics, Data Science, Graphics, Visual Analytics

[1]  Bernat Gel,et al.  karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data , 2017, bioRxiv.

[2]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[3]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[4]  Rui Fan,et al.  The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis , 2019, Nature Communications.

[5]  L. Rieseberg,et al.  The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution , 2017, Nature.

[6]  T Laver,et al.  Assessing the performance of the Oxford Nanopore Technologies MinION , 2015, Biomolecular detection and quantification.

[7]  J. Dekker,et al.  Capturing Chromosome Conformation , 2002, Science.

[8]  Korbinian Schneeberger,et al.  The impact of third generation genomic technologies on plant genome assembly. , 2017, Current opinion in plant biology.

[9]  Haibao Tang,et al.  Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. , 2008, Genome research.

[10]  David L. Steffen,et al.  The DNA sequence of the human X chromosome , 2005, Nature.

[11]  J. Janecka,et al.  chromDraw: an R package for visualization of linear and circular karyotypes , 2016, Chromosome Research.

[12]  Paul T. Spellman,et al.  GenomeGraphs: integrated genomic data visualization with R , 2009, BMC Bioinformatics.

[13]  Lila Vodkin,et al.  Genome-wide identification of binding sites for NAC and YABBY transcription factors and co-regulated genes during soybean seedling development by ChIP-Seq and RNA-Seq , 2013, BMC Genomics.

[14]  D. Cook,et al.  ggbio: an R package for extending the grammar of graphics for genomic data , 2012, Genome Biology.

[15]  Xun Xu,et al.  Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology , 2014, GigaScience.

[16]  Shaoling Zhang,et al.  Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and genome wide association studies in pear (Pyrus) , 2019, Plant biotechnology journal.

[17]  B. Gaut,et al.  Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. , 2009, Genome research.

[18]  Haibin Xu,et al.  Liriodendron genome sheds light on angiosperm phylogeny and species–pair differentiation , 2018, Nature Plants.

[19]  Karen Y. Oróstica,et al.  chromPlot: visualization of genomic data in chromosomal context , 2015, bioRxiv.

[20]  Bo Zhang,et al.  Global increase in DNA methylation during orange fruit development and ripening , 2019, Proceedings of the National Academy of Sciences.

[21]  Adam M Phillippy,et al.  New advances in sequence assembly , 2017, Genome research.

[22]  Taishin Kin,et al.  Idiographica: a general-purpose web application to build idiograms on-demand for human, mouse and rat , 2007, Bioinform..

[23]  Sukant Khurana,et al.  Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era , 2018, Current genomics.

[24]  Ling Min,et al.  Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense , 2018, Nature Genetics.

[25]  S. Turner,et al.  Real-time DNA sequencing from single polymerase molecules. , 2010, Methods in enzymology.

[26]  Lorena Pantano,et al.  Viewing RNA-seq data on the entire human genome , 2017, F1000Research.