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GeMo is a WebApp to represent Genome Mosaics with current focus on plants. However, GeMo is developed in a generic way it can be also applied to other organisms.

  1. Dynamic chromosome painting visualisation
  2. Online Data curation of mosaic prediction
  3. Markers or Genes Plots on mosaic karyotypes
  4. Data and high quality image export

GeMo requires two types of datasets to generate the ideogram visualization

Menu
  1. Input files

The position of the mosaic blocks along the chromosomes. It accepts two types of files:

Genomic blocks

chr haplotype start end ancestral_group
chr01 0 1 29070452 g4
chr01 1 1 29070452 g4
chr02 0 1 29511734 g4
chr02 1 1 29511734 g4

Normalized curves

chr start end V T S
chr01 1145 189582 0.001671988 0.014082301 0.001638686
chr01 189593 356965 0.001244196 0.012867256 0.001810139
chr01 356968 488069 0.001117959 0.010035172 0.000759437
chr01 488097 633373 0.002678213 0.010470727 0.003896031
  1. Chromosomes sizes and labels

Chromosome data format, each column tab separated chr, len, centromereInf (optional), centromereSup (optional), label (optional)

chr len label
chr01 37945898 AB
chr02 34728925 AB
chr03 40528553 AB
chr04 34728925 AB
chr05 44598304 AB
chr06 46248384 AB
chr07 42818424 AB
chr08 38870123 AB

Optional files

Users can provide their own color codes or use the online features (custom or color blind friendly palettes)

Color

group name hex
g1 group1 #000000
g2 group2 #ffc000
g3 group3 #1440cd
g4 group4 #00b009

Annotations

A list of genomic coordinates (e.g. genes of interest, QTLs) can be provided in a BED-like to visually spot the corresponding regions on the chromosomes. This can be particularly useful to check correlations between parental/ancestral blocks and genes/regions of interest.

chr01 5287838 5289224 gene 0
chr01 15485703 15486813 gene 0
chr02 2276353 2277821 gene 0

Once data is provided the chromosome diagram is generated on the fly. Chromosomes display colored blocks usually corresponding to their ancestral/parental origin. An interactive legend is present to label each group with a corresponding color. The user can modify the color of a group directly in the legend.

  1. Blocks

In the example below, the 11 chromosomes of an doploid organism is visualized. Three main colors (green, blue and red) are visible and corresponds to 3 distinct genepools that contributed to the genetic make up of this genotype. The segements in grey corresponds to unknown.

blocks
  1. Curves

In this mode, the graph represents the proportion of haplotypes of each ancestral origin along chromosomes. They are the results of a normalisation of the number of reads supporting each origin on a given window.

curves

In this example, allelic ratio for a range of founding genepools are respresented by different colors for chromosome 1. Two genepools in green is the main contributor with smaller contribtuons from the blue and red gene pools.

Uploaded datasets are automatically loaded in the text box of the GeMo menu, allowing users to update the content and reflect it on the image by clicking on the "update image" button.

In curve mode, The user can visually set the threshold on the graph to recalculate the mosaic block contribution. This can be particularly useful when multiple putative parental gene pools with unclear signals can create noisy mosaics or to switch segments from one haplotype to another for better consistency. Once a threshold is changed, the karyotype diagram is automatically updated.

GeMo offers the possibility to download the latest version of the data sets and export the output graphics as SVG for publication purposes. In addition, data can be also stored temporarily online with a unique URL allowing to share it with multiple users.

GeMo is available for free to use at https://gemo.southgreen.fr/ where anyone can upload its own data or test with pre-loaded mosaics/datasets.

Summo M, Comte A, Martin G, Weitz E, Perelle P, Droc G and Rouard M. GeMo: A mosaic genome painting tool for plant genomes. Database, Volume 2022, 2022, baac057, https://doi.org/10.1093/database/baac057

For bug tracking purpose you can use the GitHub Issues or you can contact the developers at [email protected]

GeMo has been developed in the framework of the Genome Harvest project supported by the Agropolis fondation.

Licencied under CeCill-C and GPLv3.

  • Some issues were reported for color management when using the exported SVG with Inkscape.
  • It is optimized for Chrome and works in Firefox and Edge but some design issues may occur with Safari.

The web interfaces were tested with the following platforms and web browsers:

OS Version Chrome Firefox Edge Safari
Windows 10 10 88.0.4324.150 94.0.1 96.0.1054.29 n/a
Mac OS 11.2 97.0.4692.36 94.0.2 n/a 14.0.3