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

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7 days ago
RT @TickingClock92: Visualizing genome-wide data https://t.co/NZMsjGqlxI
Visualizing genome-wide data https://t.co/NZMsjGqlxI
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Supplemental Information

Supplementary Figure 1: The distribution of 200,481 SNPs selected for the pear array design

The SNP markers are counted in a 100-Kb window. The light-yellow color represents a low content and the navy-blue color represents a high content of SNPs (range 0–215). The red circles represent the SNP markers which are significantly associated with nine traits. The plot shows that these 200,481 SNPs selected from original 18.3 million SNPs have a uniform distribution and are appropriate to be used to further develop the pear array.

DOI: 10.7287/peerj.preprints.27928v1/supp-1

Supplementary Figure 2: Fold changes of DNA methylation levels at hyper-DMRs along nine orange chromosomes during fruit ripening

The average fold changes are calculated in a 100-Kb window. The light-orange color represents a low fold enrichment change and the dark-orange color represents a high fold enrichment change of methylation (range 0.67–0.88). The green triangles represent genes that located in regions with a fold change of DNA methylation greater than one. The plot shows that the alteration of DNA methylation at hyper-DMRs during fruit ripening is unevenly distributed across the whole orange genome, with an obvious enrichment in some specific regions, probably the centromeric heterochromatin regions.

DOI: 10.7287/peerj.preprints.27928v1/supp-2

Supplementary Figure 3: The distribution of NAC binding sites and candidate genes potentially regulated by NAC during soybean seedling development

The light- and dark-purple colors represent an enriched peak detected from the ChIP-Seq data with a low and high fold enrichment (range 2.52–14.23), respectively. Boxes and circles represent genes that are up- and down-regulated during soybean seedling development, respectively. Genes which have no significantly changes during soybean seedling development are represented by triangles. This plot shows a DNA-binding-site landscape for the NAC transcription factor and potential target genes that are probably regulated by this transcription factor during soybean seedling development.

DOI: 10.7287/peerj.preprints.27928v1/supp-3

Supplementary Figure 4: The distribution of genetic diversity within two different geographical Liriodendrongroups along 19 chromosomes

Distributions of nucleotide diversity (p) along 19 Liriodendronchromosomes among accessions came from western China (range 8.34×10-5–4.87×10-3) and eastern China (range 7.26×10-5–4.09×10-3) are plotted. The nucleotide diversity in two groups are both calculated in a 2-Mb sliding window with a 1-Mb step. The plot shows that the nucleotide diversity dynamics across the whole Liriodendrongenome within eastern and western China groups share the same pattern.

DOI: 10.7287/peerj.preprints.27928v1/supp-4

Supplemental Data S1: Data and code for visualizing pear SNP density across the whole genome

DOI: 10.7287/peerj.preprints.27928v1/supp-5

Supplemental Data S2: Data and code for visualizing DNA methylation dynamics during orange fruit ripening across the whole genome

DOI: 10.7287/peerj.preprints.27928v1/supp-6

Supplemental Data S3: Data and code for visualizing NAC binging sites during soybean seeding development across the whole genome

DOI: 10.7287/peerj.preprints.27928v1/supp-7

Supplemental Data S4: Data and code for visualizing genetic diversity between two Liriodendron groups across the whole genome

DOI: 10.7287/peerj.preprints.27928v1/supp-8

Supplemental Article S1: Codes for examples

DOI: 10.7287/peerj.preprints.27928v1/supp-9

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Zhaodong Hao conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Dekang Lv performed the experiments, contributed reagents/materials/analysis tools, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Ying Ge performed the experiments, performed the computation work, authored or reviewed drafts of the paper, approved the final draft, typeset the code.

Jisen Shi performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Dolf Weijers authored or reviewed drafts of the paper, approved the final draft.

Guangchuang Yu conceived and designed the experiments, contributed reagents/materials/analysis tools, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Jinhui Chen conceived and designed the experiments, performed the computation work, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

Data and code are available at Github, URL : https://github.com/TickingClock1992/RIdeogram

Funding

This work was supported by Key Research and Development Plan of Jiangsu Province (BE2017376), Foundation of Jiangsu Forestry Bureau (LYKJ[2017]42), Qinglan Project of Jiangsu Province and Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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