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Synteny by ancestral linkage group (sponge, comb jelly, jellyfish)

Certain sets of genes have ridden the same chromosome together since before animals existed, and those sets have names. odp writes, for every pair of genomes it compares, a table of their orthologs with the set each one belongs to and a color for it. JBrowse loads that table as a synteny track, paints every ortholog with its set's color, and sorts one genome's chromosomes by where their orthologs land on the other. In a sponge the colors fall in one block per chromosome along a diagonal; in a comb jelly each group is spread over several chromosomes; in a single-celled relative of animals the spread is everywhere. The color mode is a column of the table, so any label a pipeline puts beside an ortholog can drive it.

Prerequisites

Where the data comes from

The genomes and the ortholog tables are the Dryad deposit behind Schultz et al. 2023, released CC0. Dryad serves its files only to a browser, so the two tarballs are downloaded by hand and the build script extracts what it needs from them.

The tables are the ones odp plotted for the paper's own dot plots, and a run of odp over any two genomes writes the same files, so everything from the conversion on works unchanged on your own species.

A label that rides in the ortholog table

Simakov et al. 2022 named a set of gene families the BCnS linkage groups, after the bilaterians, cnidarians and sponges whose chromosomes carry them, and gave each a letter: A1a, A2, B1, and so on to R. A gene belongs to one of them or to none. odp ships the groups as a database of protein models, searches every proteome it is given against them, and writes the group each ortholog landed in beside the ortholog. That assignment is a column, and a column is something a synteny track can carry.

The dotplots use a jellyfish (RES, Rhopilema esculentum), a freshwater sponge (EMU, Ephydatia muelleri), a comb jelly (HCA, Hormiphora californensis) and Capsaspora owczarzaki (COW), a single-celled holozoan that sits outside animals altogether. The stack at the end adds a second comb jelly (BIN, Bolinopsis microptera), amphioxus (BFL, Branchiostoma floridae) and a second sponge (CLAa, a cladorhizid). odp compares genomes two at a time, so the deposit holds one table per pair. Each is every reciprocal best protein hit between the two, and a pair keeps several times the orthologs a table requiring a gene in all four genomes at once would, which is what keeps the plots dense enough to show a pattern.

A table's row is the gene pair, the group, where each gene sits, and the color:

rbh                    EMU_gene      RES_gene       gene_group  EMU_scaf  EMU_pos  RES_scaf  RES_pos   ...  color
rbh2way_EMU_RES_964    Em0019g38a    mRNA.RE04286   A1a         EMU19     180964   RES2      13815510  ...  #C23D51
rbh2way_EMU_RES_4123   Em0019g57a    mRNA.RE14076   None        EMU19     290216   RES8      13037026  ...  #000000

Gene intervals come from odp's .chrom files rather than from the table's own position column, which is one coordinate per gene and would make every feature one base long:

# --species sets the column order, anchor first, which the track then follows
# --chrom gives each species' genes their real start and stop
# gene_group and color pass through as the attribute columns
python3 rbh_to_blocks.py EMU_RES_xy_reciprocal_best_hits.coloredby_BCnS_LGs.plotted.rbh \
  -o RES_EMU.blocks --bed-dir RES_EMU \
  --species RES EMU --chrom RES=RES.chrom EMU=EMU.chrom

The helper prints what it resolved. Roughly half the orthologs carry a group: the BCnS table covers the gene families it covers, and an ortholog outside them gets ., which the browser draws in a recessive grey.

A .blocks row is the gene ids across the two genomes, then the attribute columns:

mRNA.RE04286  Em0019g38a  A1a  #C23D51
mRNA.RE14076  Em0019g57a  .    #000000

Loading it as a synteny track

attributeColumns is what makes the last two columns reachable. Each name in it becomes a color-by mode named after the column, so gene_group becomes a mode; color is the palette the file puts beside each label and is never offered as a mode of its own.

{
  "type": "SyntenyTrack",
  "trackId": "RES_EMU",
  "name": "RES vs EMU orthologs, colored by BCnS linkage group",
  "assemblyNames": ["RES", "EMU"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "RES_EMU.blocks.gz",
    "blockAssemblies": ["RES", "EMU"],
    "bedLocations": [
      { "uri": "RES_EMU.RES.bed.gz" },
      { "uri": "RES_EMU.EMU.bed.gz" }
    ],
    "attributeColumns": ["gene_group", "color"]
  }
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "RES_EMU",
  "name": "RES vs EMU orthologs, colored by BCnS linkage group",
  "assemblyNames": ["RES", "EMU"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "RES_EMU.blocks.gz",
    "blockAssemblies": ["RES", "EMU"],
    "bedLocations": [
      { "uri": "RES_EMU.RES.bed.gz" },
      { "uri": "RES_EMU.EMU.bed.gz" }
    ],
    "attributeColumns": ["gene_group", "color"]
  }
}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "type": "SyntenyTrack",
  "trackId": "RES_EMU",
  "name": "RES vs EMU orthologs, colored by BCnS linkage group",
  "assemblyNames": ["RES", "EMU"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "RES_EMU.blocks.gz",
    "blockAssemblies": ["RES", "EMU"],
    "bedLocations": [
      { "uri": "RES_EMU.RES.bed.gz" },
      { "uri": "RES_EMU.EMU.bed.gz" }
    ],
    "attributeColumns": ["gene_group", "color"]
  }
}

The build script adds one such track per pair: the jellyfish against each of the three genomes the dotplots compare it with, then the neighbouring pairs of the six-genome stack at the end.

One block per linkage group

Open the jellyfish-against-sponge table as a dotplot and pick gene_group under Color by value on the palette button in the view header; the legend comes up with it. Then Re-order chromosomes on the view menu: it sorts the vertical genome's chromosomes by where their orthologs land along the horizontal one, which is what turns one block per group into a diagonal. The same view as a session, with the sponge's unplaced scaffolds left off its axis:

{
  "defaultSession": {
    "name": "Ancestral linkage groups",
    "views": [
      {
        "type": "DotplotView",
        "displayName": "Rhopilema (jellyfish) vs Ephydatia (sponge)",
        "views": [
          { "assembly": "RES" },
          { "assembly": "EMU", "displayedRegionNames": ["EMU*"] }
        ],
        "tracks": ["RES_EMU"],
        "colorBy": "attribute:gene_group",
        "autoDiagonalize": true,
        "lineWidth": 4,
        "height": 860
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "Ancestral linkage groups",
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Ephydatia (sponge)",
      "views": [
        { "assembly": "RES" },
        { "assembly": "EMU", "displayedRegionNames": ["EMU*"] }
      ],
      "tracks": ["RES_EMU"],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}
EOF

Open this session in JBrowse

Rhopilema against Ephydatia, every ortholog colored by the BCnS linkage group odp assigned it and the sponge chromosomes sorted against the jellyfish. Each group is one block where a jellyfish chromosome meets a sponge chromosome, and the blocks run down the diagonal. The grey points are the orthologs in no group. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure has RES on X and EMU on Y.
  2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
  3. Point the import form at your own file: use the track panel under the two axis selectors, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in both axes itself.This figure uses the “RES_EMU” track.
  4. Click Launch.
  5. Click the view's title in its header and enter "Rhopilema (jellyfish) vs Ephydatia (sponge)"
  6. Dotplot header → palette button → Color by value → gene_groupThe palette button's tooltip reads "Color by: ...".
  7. Dotplot header → the ⋮ menu → Re-order chromosomesReorders and flips the vertical axis so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fodp_linkage_groups%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22displayName%22%3A%22Rhopilema+%28jellyfish%29+vs+Ephydatia+%28sponge%29%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22RES%22%7D%2C%7B%22assembly%22%3A%22EMU%22%2C%22displayedRegionNames%22%3A%5B%22EMU*%22%5D%7D%5D%2C%22tracks%22%3A%5B%22RES_EMU%22%5D%2C%22colorBy%22%3A%22attribute%3Agene_group%22%2C%22autoDiagonalize%22%3Atrue%2C%22lineWidth%22%3A4%2C%22height%22%3A860%7D%5D%7D&sessionName=JBrowse+docs%3A+linkage_groups%2Falg_dotplot_res_emu

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Ephydatia (sponge)",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "EMU",
          "displayedRegionNames": [
            "EMU*"
          ]
        }
      ],
      "tracks": [
        "RES_EMU"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/odp_linkage_groups/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Ephydatia (sponge)",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "EMU",
          "displayedRegionNames": [
            "EMU*"
          ]
        }
      ],
      "tracks": [
        "RES_EMU"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/odp_linkage_groups/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The blocks are the whole claim. Inside a block the points fill the square: gene order has been shuffled thoroughly, while the membership of the chromosome has not, and that membership is what a linkage group is.

Two things in the frame are worth knowing before reading too much into it. The column structure is true by construction, since the BCnS groups were defined so that each one is a jellyfish chromosome. The row structure is not: the sponge was one of the genomes the groups were built on, but its chromosomes were free to disagree, and they largely do not.

Outside the genomes the groups were built on

The comb jelly and Capsaspora are in neither table's definition, so the vertical axis is free; the columns are still the jellyfish's. Swapping the vertical genome is the whole change.

The jellyfish against Hormiphora, sorted and colored the same way. The groups still favor particular comb jelly chromosomes, and each one is spread over several of them. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure has RES on X and HCA on Y.
  2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
  3. Point the import form at your own file: use the track panel under the two axis selectors, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in both axes itself.This figure uses the “RES_HCA” track.
  4. Click Launch.
  5. Click the view's title in its header and enter "Rhopilema (jellyfish) vs Hormiphora (comb jelly)"
  6. Dotplot header → palette button → Color by value → gene_groupThe palette button's tooltip reads "Color by: ...".
  7. Dotplot header → the ⋮ menu → Re-order chromosomesReorders and flips the vertical axis so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fodp_linkage_groups%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22displayName%22%3A%22Rhopilema+%28jellyfish%29+vs+Hormiphora+%28comb+jelly%29%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22RES%22%7D%2C%7B%22assembly%22%3A%22HCA%22%2C%22displayedRegionNames%22%3A%5B%22HCA*%22%5D%7D%5D%2C%22tracks%22%3A%5B%22RES_HCA%22%5D%2C%22colorBy%22%3A%22attribute%3Agene_group%22%2C%22autoDiagonalize%22%3Atrue%2C%22lineWidth%22%3A4%2C%22height%22%3A860%7D%5D%7D&sessionName=JBrowse+docs%3A+linkage_groups%2Falg_dotplot_res_hca

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Hormiphora (comb jelly)",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "HCA",
          "displayedRegionNames": [
            "HCA*"
          ]
        }
      ],
      "tracks": [
        "RES_HCA"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/odp_linkage_groups/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Hormiphora (comb jelly)",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "HCA",
          "displayedRegionNames": [
            "HCA*"
          ]
        }
      ],
      "tracks": [
        "RES_HCA"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/odp_linkage_groups/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The jellyfish against Capsaspora, sorted and colored the same way. Each group spreads over several Capsaspora chromosomes, and fewer of the points gather into clusters than in the comb jelly. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure has RES on X and COW on Y.
  2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
  3. Point the import form at your own file: use the track panel under the two axis selectors, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in both axes itself.This figure uses the “RES_COW” track.
  4. Click Launch.
  5. Click the view's title in its header and enter "Rhopilema (jellyfish) vs Capsaspora"
  6. Dotplot header → palette button → Color by value → gene_groupThe palette button's tooltip reads "Color by: ...".
  7. Dotplot header → the ⋮ menu → Re-order chromosomesReorders and flips the vertical axis so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fodp_linkage_groups%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22DotplotView%22%2C%22displayName%22%3A%22Rhopilema+%28jellyfish%29+vs+Capsaspora%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22RES%22%7D%2C%7B%22assembly%22%3A%22COW%22%2C%22displayedRegionNames%22%3A%5B%22COW*%22%5D%7D%5D%2C%22tracks%22%3A%5B%22RES_COW%22%5D%2C%22colorBy%22%3A%22attribute%3Agene_group%22%2C%22autoDiagonalize%22%3Atrue%2C%22lineWidth%22%3A4%2C%22height%22%3A860%7D%5D%7D&sessionName=JBrowse+docs%3A+linkage_groups%2Falg_dotplot_res_cow

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Capsaspora",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "COW",
          "displayedRegionNames": [
            "COW*"
          ]
        }
      ],
      "tracks": [
        "RES_COW"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/odp_linkage_groups/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "Rhopilema (jellyfish) vs Capsaspora",
      "views": [
        {
          "assembly": "RES"
        },
        {
          "assembly": "COW",
          "displayedRegionNames": [
            "COW*"
          ]
        }
      ],
      "tracks": [
        "RES_COW"
      ],
      "colorBy": "attribute:gene_group",
      "autoDiagonalize": true,
      "lineWidth": 4,
      "height": 860
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/odp_linkage_groups/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The sponge holding the groups whole while the comb jelly holds them loosely is the shape of the argument Schultz et al. make for the comb jellies branching off before the sponges did, and the outgroup frame is what the other two are read against.

Six genomes stacked

The paper's first figure is the same tables stacked: one row per genome, the ribbons between neighbours colored by group, each row's chromosomes sorted against the row above. The linear synteny view does that with one pair's track per band. The build script loads the pairs for the paper's own order, two comb jellies over the jellyfish, amphioxus and two sponges, and the session below sets what the figure needs: autoDiagonalize sorts every row against the one above it, Hide unlabelled rows on the palette menu (hideUnlabelled) draws only the orthologs in a group, drawCurves bundles the ribbons, and the fade a whole-genome view applies to sub-pixel ribbons is off, since the ribbons' color is the figure.

{
  "defaultSession": {
    "name": "Ancestral linkage groups, six genomes",
    "views": [
      {
        "type": "LinearSyntenyView",
        "displayName": "Comb jellies, jellyfish, amphioxus, sponges",
        "views": [
          { "assembly": "BIN", "displayedRegionNames": ["BIN*"] },
          { "assembly": "HCA", "displayedRegionNames": ["HCA*"] },
          { "assembly": "RES", "displayedRegionNames": ["RES*"] },
          { "assembly": "BFL", "displayedRegionNames": ["BFL*"] },
          { "assembly": "EMU", "displayedRegionNames": ["EMU*"] },
          { "assembly": "CLAa", "displayedRegionNames": ["CLA*_hapA"] }
        ],
        "tracks": [
          ["BIN_HCA"],
          ["RES_HCA"],
          ["RES_BFL"],
          ["BFL_EMU"],
          ["EMU_CLAa"]
        ],
        "colorBy": "attribute:gene_group",
        "hideUnlabelled": true,
        "autoDiagonalize": true,
        "drawCurves": true,
        "fadeThinAlignmentsMode": "off",
        "alpha": 0.45,
        "levelHeights": [130, 130, 130, 130, 130],
        "collapseEmptyRows": true
      }
    ]
  }
}
jbrowse set-default-session --session - << 'EOF'
{
  "name": "Ancestral linkage groups, six genomes",
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Comb jellies, jellyfish, amphioxus, sponges",
      "views": [
        { "assembly": "BIN", "displayedRegionNames": ["BIN*"] },
        { "assembly": "HCA", "displayedRegionNames": ["HCA*"] },
        { "assembly": "RES", "displayedRegionNames": ["RES*"] },
        { "assembly": "BFL", "displayedRegionNames": ["BFL*"] },
        { "assembly": "EMU", "displayedRegionNames": ["EMU*"] },
        { "assembly": "CLAa", "displayedRegionNames": ["CLA*_hapA"] }
      ],
      "tracks": [
        ["BIN_HCA"],
        ["RES_HCA"],
        ["RES_BFL"],
        ["BFL_EMU"],
        ["EMU_CLAa"]
      ],
      "colorBy": "attribute:gene_group",
      "hideUnlabelled": true,
      "autoDiagonalize": true,
      "drawCurves": true,
      "fadeThinAlignmentsMode": "off",
      "alpha": 0.45,
      "levelHeights": [130, 130, 130, 130, 130],
      "collapseEmptyRows": true
    }
  ]
}
EOF

Open this session in JBrowse

Six genomes stacked in the order of the paper's figure 1d, ribbons colored by linkage group and only the grouped orthologs drawn. Between the two comb jellies each chromosome pairs with one chromosome. Between the comb jelly and the jellyfish every comb jelly chromosome fans out over several jellyfish chromosomes. From the jellyfish down through amphioxus and the two sponges the groups travel as bundles, one chromosome to one chromosome. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure's rows, top to bottom: BIN, HCA, RES, BFL, EMU, CLAa.
  2. Open the view: Add → Linear synteny view, and set the rows to those assemblies in the import form.
  3. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in the rows itself.This figure uses the “BIN_HCA” track.
  4. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.This figure uses the “RES_HCA” track.
  5. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.This figure uses the “RES_BFL” track.
  6. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.This figure uses the “BFL_EMU” track.
  7. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.This figure uses the “EMU_CLAa” track.
  8. Click Launch.
  9. Click the view's title in its header and enter "Comb jellies, jellyfish, amphioxus, sponges"
  10. Synteny view header → palette button → Color by value → gene_groupThe palette button's tooltip reads "Color by: ...".
  11. Synteny view header → View options → Rows → Re-order chromosomesReorders and flips each row so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.
  12. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  13. Synteny display settings (the sliders button in the view header) → Opacity → drag to 0.45Lower values let dense overlapping ribbons show through each other.
  14. Drag the bar below a synteny level to resize it.This figure's 5 levels are 130, 130, 130, 130, 130px tall.
  15. Launch synteny view dialog → Collapse panels to rulers (checked)Checked by default. A row the launch gave no tracks opens as its ruler alone instead of a "No tracks active" block; any row expands again from its own controls afterwards.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fodp_linkage_groups%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22displayName%22%3A%22Comb+jellies%2C+jellyfish%2C+amphioxus%2C+sponges%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22BIN%22%2C%22displayedRegionNames%22%3A%5B%22BIN*%22%5D%7D%2C%7B%22assembly%22%3A%22HCA%22%2C%22displayedRegionNames%22%3A%5B%22HCA*%22%5D%7D%2C%7B%22assembly%22%3A%22RES%22%2C%22displayedRegionNames%22%3A%5B%22RES*%22%5D%7D%2C%7B%22assembly%22%3A%22BFL%22%2C%22displayedRegionNames%22%3A%5B%22BFL*%22%5D%7D%2C%7B%22assembly%22%3A%22EMU%22%2C%22displayedRegionNames%22%3A%5B%22EMU*%22%5D%7D%2C%7B%22assembly%22%3A%22CLAa%22%2C%22displayedRegionNames%22%3A%5B%22CLA*_hapA%22%5D%7D%5D%2C%22tracks%22%3A%5B%5B%22BIN_HCA%22%5D%2C%5B%22RES_HCA%22%5D%2C%5B%22RES_BFL%22%5D%2C%5B%22BFL_EMU%22%5D%2C%5B%22EMU_CLAa%22%5D%5D%2C%22colorBy%22%3A%22attribute%3Agene_group%22%2C%22hideUnlabelled%22%3Atrue%2C%22autoDiagonalize%22%3Atrue%2C%22drawCurves%22%3Atrue%2C%22fadeThinAlignmentsMode%22%3A%22off%22%2C%22alpha%22%3A0.45%2C%22levelHeights%22%3A%5B130%2C130%2C130%2C130%2C130%5D%2C%22collapseEmptyRows%22%3Atrue%7D%5D%7D&sessionName=JBrowse+docs%3A+linkage_groups%2Falg_stack

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Comb jellies, jellyfish, amphioxus, sponges",
      "views": [
        {
          "assembly": "BIN",
          "displayedRegionNames": [
            "BIN*"
          ]
        },
        {
          "assembly": "HCA",
          "displayedRegionNames": [
            "HCA*"
          ]
        },
        {
          "assembly": "RES",
          "displayedRegionNames": [
            "RES*"
          ]
        },
        {
          "assembly": "BFL",
          "displayedRegionNames": [
            "BFL*"
          ]
        },
        {
          "assembly": "EMU",
          "displayedRegionNames": [
            "EMU*"
          ]
        },
        {
          "assembly": "CLAa",
          "displayedRegionNames": [
            "CLA*_hapA"
          ]
        }
      ],
      "tracks": [
        [
          "BIN_HCA"
        ],
        [
          "RES_HCA"
        ],
        [
          "RES_BFL"
        ],
        [
          "BFL_EMU"
        ],
        [
          "EMU_CLAa"
        ]
      ],
      "colorBy": "attribute:gene_group",
      "hideUnlabelled": true,
      "autoDiagonalize": true,
      "drawCurves": true,
      "fadeThinAlignmentsMode": "off",
      "alpha": 0.45,
      "levelHeights": [
        130,
        130,
        130,
        130,
        130
      ],
      "collapseEmptyRows": true
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/odp_linkage_groups/config.json

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Comb jellies, jellyfish, amphioxus, sponges",
      "views": [
        {
          "assembly": "BIN",
          "displayedRegionNames": [
            "BIN*"
          ]
        },
        {
          "assembly": "HCA",
          "displayedRegionNames": [
            "HCA*"
          ]
        },
        {
          "assembly": "RES",
          "displayedRegionNames": [
            "RES*"
          ]
        },
        {
          "assembly": "BFL",
          "displayedRegionNames": [
            "BFL*"
          ]
        },
        {
          "assembly": "EMU",
          "displayedRegionNames": [
            "EMU*"
          ]
        },
        {
          "assembly": "CLAa",
          "displayedRegionNames": [
            "CLA*_hapA"
          ]
        }
      ],
      "tracks": [
        [
          "BIN_HCA"
        ],
        [
          "RES_HCA"
        ],
        [
          "RES_BFL"
        ],
        [
          "BFL_EMU"
        ],
        [
          "EMU_CLAa"
        ]
      ],
      "colorBy": "attribute:gene_group",
      "hideUnlabelled": true,
      "autoDiagonalize": true,
      "drawCurves": true,
      "fadeThinAlignmentsMode": "off",
      "alpha": 0.45,
      "levelHeights": [
        130,
        130,
        130,
        130,
        130
      ],
      "collapseEmptyRows": true
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/odp_linkage_groups/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The band to read is the second one. The comb jelly chromosomes are each a mixture of groups, and the mixture is different from the one any jellyfish chromosome carries, so the ribbons cross. Every band below it is bundles, and the two comb jellies agree with each other in the band above.

Checking it against the table

The pictures are the tables, so the counts behind them come out of the tables with no browser involved. For one group, tally the chromosomes its orthologs sit on in the other genome:

# gene_group is column 4 and EMU_scaf column 5 of the EMU-RES table
awk -F'\t' 'NR>1 && $4=="A1a" {print $5}' \
  EMU_RES_xy_reciprocal_best_hits.coloredby_BCnS_LGs.plotted.rbh \
  | sort | uniq -c | sort -rn

Running that over the six largest groups, in each of the three jellyfish tables, gives how many of a group's orthologs there are and how many sit on the one chromosome that holds most of them:

groupspongecomb jellyCapsaspora
A1a229 / 22948 / 17643 / 160
D205 / 20544 / 16222 / 150
G201 / 20158 / 16020 / 124
H189 / 18956 / 14836 / 119
F162 / 16225 / 11620 / 97
M152 / 15226 / 12222 / 101

The sponge column settles the first figure, and says why: the group database was built with the sponge in it, so an ortholog it assigns to a group is on that group's sponge chromosome by definition. The other two columns are the ones the figures are about. In both, the chromosome holding most of a group holds a minority of it, and the comb jelly leads Capsaspora by a margin that varies from group to group. A group at a time, the comb jelly and the outgroup are hard to tell apart; the difference the second and third figures show is a property of the table as a whole.

Reproduce it end to end

Download genomes.tar.gz and supplementary_information.tar.gz from the Dryad page into ~/Downloads first, since Dryad has no direct download URL. The script fetches everything else, converts the seven tables, and writes a config with the seven assemblies and a default session; see Prerequisites.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_odp_linkage_groups_synteny.sh
DRYAD_DIR=~/Downloads bash build_odp_linkage_groups_synteny.sh

For your own genomes, run odp with plot_LGs: True and point the conversion at the tables it writes under synteny_analysis/step2-figures/synteny_coloredby_BCnS_LGs/.

See also

References