.. contents:: Table of Contents :depth: 3

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.

Main features

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

Data inputs

GeMo requires two types of datasets to generate the ideogram visualization

.. image:: ./docs/source/_images/menu.png :target: ./docs/source/_images/menu.png :width: 250 :alt: Menu

1. Input files

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

Genomic blocks

.. list-table:: :header-rows: 1

• • 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

.. list-table:: :header-rows: 1

• • 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

2. Chromosomes sizes and labels

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

.. list-table:: :widths: 25 25 25 :header-rows: 1

• • 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

.. list-table:: :header-rows: 1

• • 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.

.. list-table::

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

Data outputs

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.

.. image:: ./docs/source/_images/bloc.png :target: ./docs/source/_images/bloc.png :width: 500 :alt: blocks

2. 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.

.. image:: ./docs/source/_images/curve.png :target: ./docs/source/_images/curve.png :width: 700 :alt: 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.

Data curation and export

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.

Live demo

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.

Citation

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

Contact

For bug tracking purpose you can use the GitHub Issues or you can contact the developers at marilyne.summo@cirad.fr

Acknowledgements

GeMo has been developed in the framework of the Genome Harvest project <https://www.genomeharvest.fr>__ supported by the Agropolis fondation.

License

Licencied under CeCill-C <http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html>_ and GPLv3.

Troubleshooting and web browser compatibility

• 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:

.. list-table:: :header-rows: 1

• • 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