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Synteny from MCScan anchors (grape, peach)

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.17. Desktop beta builds are coming soon.

Grape and peach keep long runs of genes in the same order, though the genomes have diverged too far to align base by base. We:

  • produce the gene BEDs and anchor files with jcvi MCScan
  • load the assemblies, gene tracks, and the .anchors and .anchors.simple tracks
  • open a linear synteny view, with a ribbon for each gene pair and a bar for each block (a run of gene pairs in conserved order), and color by syntenic depth
  • open the same pairs in a dotplot, and convert an MCScanX run the same way

Prerequisites

# Debian/Ubuntu
sudo apt install samtools gffread last-align
# or conda, which has every tool above
conda install -c bioconda -c conda-forge samtools gffread ncbi-datasets-cli \
  last
# or Linux x86_64 binaries for the tools apt lacks
wget -P ~/.local/bin \
  https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/datasets \
  https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/v2/linux-amd64/dataformat
chmod +x ~/.local/bin/datasets ~/.local/bin/dataformat
# any platform
pip install jcvi

The data

Grape (Jaillon et al. 2007) and peach RefSeq assemblies and annotations, each fetched by accession with the datasets CLI: the same two genomes Synteny from an ortholog table (grape, peach, cacao) stacks with cacao.

The tracks below read hosted copies of the files the build script writes from these, so you don't need these files to follow the page; run Producing the BEDs and anchor files with jcvi on a GFF3 and a genome FASTA per genome of your own.

What it isFile
GrapeGCF_030704535.1_ASM3070453v1/
PeachGCF_000346465.2_Prunus_persica_NCBIv2/

What .anchors and .anchors.simple hold

The run writes two files that JBrowse loads as separate synteny tracks. .anchors, via MCScanAnchorsAdapter, is the gene-pair level: each line is one orthologous pair and its alignment score, with ### separating synteny blocks. Each id is an NCBI mRNA, grape first:

###
rna-XM_019221872.2	rna-XM_007222072.2	1120
rna-XM_010651756.3	rna-XM_020568908.1	526
rna-XM_010651744.3	rna-XM_007225432.2	2020

.anchors.simple, via MCScanSimpleAnchorsAdapter, is the same run reduced to one line per block: the first and last gene of the block on each side, a score, and the block's orientation:

rna-XM_019221872.2	rna-XM_010651102.3	rna-XM_007225348.2	rna-XM_007222072.2	86	-
rna-XM_002279913.5	rna-XM_002285264.5	rna-XM_007227461.2	rna-XM_007222578.2	370	+
rna-XM_002281938.5	rna-XM_010652331.3	rna-XM_007222787.2	rna-XM_020562574.1	39	+

.anchors.simple draws one ribbon per block where .anchors draws one per gene pair. The BED files supply the coordinates for both.

BED files mapping gene ids to coordinates

One BED per genome, prepared from its GFF3 before the ortholog run. The adapters read the first six columns, and column 4 must match the anchor gene ids byte for byte:

NC_081805.1	37288	41411	rna-XM_019221872.2	0	+
NC_081805.1	53914	63050	rna-XM_010651756.3	0	+

Column 1 must name a sequence the JBrowse assembly knows, directly or through its alias table: the hub assemblies below resolve NC_081805.1 to grape chr1.

A gene id in the anchors file that no BED names breaks the join, and some such mismatches load with no error; the synteny track guide lists which. The mismatch that matters here is jcvi stripping isoform suffixes from the ids unless run with --no_strip_names, which the command in the next section passes.

Producing the BEDs and anchor files with jcvi

gffread extracts each genome's CDS from its GFF3 and FASTA, and jcvi writes the BED with the same ids:

gffread grape.gff3 -g grape.fa -x grape.cds.fa
# --key=ID writes each mRNA's GFF3 ID into BED column 4, the name gffread gave
# its CDS; --primary_only keeps one transcript per gene
python -m jcvi.formats.gff bed --type=mRNA --key=ID --primary_only \
  grape.gff3 -o grape.bed
python -m jcvi.formats.fasta format grape.cds.fa grape.cds

Peach goes through the same three commands. One ortholog run then writes the gene pairs, and screen --simple reduces them to blocks:

# --no_strip_names keeps the ids matching the BEDs; --no_dotplot skips jcvi's
# own PDF, which needs LaTeX
python -m jcvi.compara.catalog ortholog --no_strip_names --no_dotplot grape peach
# --simple writes grape.peach.anchors.simple; --minspan=30 keeps blocks of 30
# genes or more
python -m jcvi.compara.synteny screen --minspan=30 --simple \
  grape.peach.anchors grape.peach.anchors.new

The adapters read anchors and BED files plain or gzipped. The configs below name gzipped copies, which gzip -k makes of each of the four files; drop .gz from a uri to read the plain file.

Setting up the grape and peach assemblies

Grape and peach are each a genome hub on genomes.jbrowse.org under the RefSeq accession the BEDs were built from, and the build takes each assembly entry and NCBI RefSeq gene track from there, as the three-genome page shows. Each entry carries the short name as an alias, so a session can still say grape.

A genome of your own loads from its FASTA, with a .fai from samtools faidx beside it:

Goes in the assemblies array of config.json. See Assemblies.

{ "name": "myGenome", "uri": "myGenome.fa" }
jbrowse add-assembly myGenome.fa \
  --name myGenome \
  --load copy

In JBrowse Desktop, Open new genome on the start screen (or File → Open genome... in a session), then Open from a URL and paste, one per line:

myGenome.fa
myGenome.fa.fai

JBrowse reads the format off the file name. Then fill in:

  • Genome name: myGenome

myGenome.fa is relative to a config.json. Replace it with its URL or its path on this computer.

Each genome also gets a gene track, which the close-up below turns to Show only genes. Swap the uri for your own GFF3, bgzipped and tabix-indexed (prep):

Goes in the tracks array of config.json. See Tracks.

{
  "type": "FeatureTrack",
  "trackId": "myGenome_genes",
  "name": "myGenome genes",
  "assemblyNames": ["myGenome"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "myGenome.sorted.gff3.gz"
  }
}
jbrowse add-track myGenome.sorted.gff3.gz \
  --trackId myGenome_genes \
  --name "myGenome genes" \
  --assemblyNames myGenome \
  --load copy

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

  • Main file: myGenome.sorted.gff3.gz

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: myGenome genes
  • Assembly: myGenome

Click Add.

myGenome.sorted.gff3.gz is relative to a config.json. Replace it with its URL or its path on this computer.

Loading the .anchors and .anchors.simple tracks

Each adapter takes the anchor file plus the two BEDs, and assemblyNames lists the genomes in the order the anchor columns are in (column 1's genome first, grape here):

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_anchors",
  "name": "Grape peach synteny (MCScan, anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanAnchorsAdapter",
    "uri": "grape.peach.anchors.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  }
}
jbrowse add-track grape.peach.anchors.gz \
  --trackId grape_peach_anchors \
  --name "Grape peach synteny (MCScan, anchors)" \
  --assemblyNames GCF_030704535.1,GCF_000346465.2 \
  --bed1 grape.bed.gz \
  --bed2 peach.bed.gz \
  --load copy

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": "grape_peach_anchors",
  "name": "Grape peach synteny (MCScan, anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanAnchorsAdapter",
    "uri": "grape.peach.anchors.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  }
}

grape.peach.anchors.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

The .anchors.simple track takes the same shape with the adapter type and file swapped:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_anchors_simple",
  "name": "Grape peach synteny (MCScan, simple anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanSimpleAnchorsAdapter",
    "uri": "grape.peach.anchors.simple.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  }
}
jbrowse add-track grape.peach.anchors.simple.gz \
  --trackId grape_peach_anchors_simple \
  --name "Grape peach synteny (MCScan, simple anchors)" \
  --assemblyNames GCF_030704535.1,GCF_000346465.2 \
  --bed1 grape.bed.gz \
  --bed2 peach.bed.gz \
  --load copy

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": "grape_peach_anchors_simple",
  "name": "Grape peach synteny (MCScan, simple anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanSimpleAnchorsAdapter",
    "uri": "grape.peach.anchors.simple.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  }
}

grape.peach.anchors.simple.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

MCScanAnchorsAdapter and MCScanSimpleAnchorsAdapter read the whole file into memory, which MCScan output is small enough for.

Viewing gene pairs and blocks in one synteny view

We'll start with Add → Linear synteny view and pick peach and grape. Then:

  • Turn on both MCScan tracks in the band between them.
  • Turn on the simple-anchors track in each panel's track selector, where it draws as a row of bars.
Peach and grape with both MCScan tracks: .anchors.simple blocks as wide ribbons, the per-gene .anchors pairs over them. Marks along the top of the band are pairs whose grape gene is on a chromosome not shown.
Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: GCF_000346465.2, GCF_030704535.1.
  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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  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 one needs an MCScan .anchors.simple file.This figure uses “Grape peach synteny (MCScan, simple anchors)”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Drag the bar below a synteny level to resize it.This figure's level is 236px tall.
  8. Row 1 (GCF_000346465.2)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs an MCScan .anchors.simple file.This figure uses “Grape peach synteny (MCScan, simple anchors)”.
    2. Type your region of interest into the location box and press Enter.This figure is at chrG5:4,700,000-13,000,000.
  9. Row 2 (GCF_030704535.1)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs an MCScan .anchors.simple file.This figure uses “Grape peach synteny (MCScan, simple anchors)”.
    2. Type your region of interest into the location box and press Enter.This figure is at chr2:1-8,200,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "mark": {
        "interpolate": "bump"
      },
      "tracks": [
        [
          "grape_peach_anchors",
          "grape_peach_anchors_simple"
        ]
      ],
      "levelHeights": [
        236
      ],
      "views": [
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG5:4,700,000-13,000,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        },
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr2:1-8,200,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "mark": {
                "interpolate": "bump"
            },
            "tracks": [
                [
                    "grape_peach_anchors",
                    "grape_peach_anchors_simple"
                ]
            ],
            "levelHeights": [
                236
            ],
            "views": [
                {
                    "assembly": "GCF_000346465.2",
                    "loc": "chrG5:4,700,000-13,000,000",
                    "tracks": [
                        {
                            "trackId": "grape_peach_anchors_simple",
                            "height": 60
                        }
                    ]
                },
                {
                    "assembly": "GCF_030704535.1",
                    "loc": "chr2:1-8,200,000",
                    "tracks": [
                        {
                            "trackId": "grape_peach_anchors_simple",
                            "height": 60
                        }
                    ]
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "mark": {
        "interpolate": "bump"
      },
      "tracks": [
        [
          "grape_peach_anchors",
          "grape_peach_anchors_simple"
        ]
      ],
      "levelHeights": [
        236
      ],
      "views": [
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG5:4,700,000-13,000,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        },
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr2:1-8,200,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "mark": {
        "interpolate": "bump"
      },
      "tracks": [
        [
          "grape_peach_anchors",
          "grape_peach_anchors_simple"
        ]
      ],
      "levelHeights": [
        236
      ],
      "views": [
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG5:4,700,000-13,000,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        },
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr2:1-8,200,000",
          "tracks": [
            {
              "trackId": "grape_peach_anchors_simple",
              "height": 60
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 640 \
  --spec 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 bars in each panel come from the block track's LGVSyntenyDisplay, which draws synteny as features in an ordinary linear genome view row. Selecting it by name needs the full displays array:

Goes in the tracks array of config.json. See Tracks.

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_anchors_simple",
  "name": "Grape peach synteny (MCScan, simple anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanSimpleAnchorsAdapter",
    "uri": "grape.peach.anchors.simple.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  },
  "displays": [
    {
      "type": "LGVSyntenyDisplay",
      "height": 60
    }
  ]
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_anchors_simple",
  "name": "Grape peach synteny (MCScan, simple anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanSimpleAnchorsAdapter",
    "uri": "grape.peach.anchors.simple.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  },
  "displays": [
    {
      "type": "LGVSyntenyDisplay",
      "height": 60
    }
  ]
}'

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": "grape_peach_anchors_simple",
  "name": "Grape peach synteny (MCScan, simple anchors)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"],
  "adapter": {
    "type": "MCScanSimpleAnchorsAdapter",
    "uri": "grape.peach.anchors.simple.gz",
    "bed1": "grape.bed.gz",
    "bed2": "peach.bed.gz",
    "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2"]
  },
  "displays": [
    {
      "type": "LGVSyntenyDisplay",
      "height": 60
    }
  ]
}

grape.peach.anchors.simple.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

MCScan blocks on grape chr9 against peach chrG3. Top: .anchors alone. Bottom: both files on one band.
Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: GCF_030704535.1, GCF_000346465.2.
  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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  6. Drag the bar below a synteny level to resize it.This figure's level is 260px tall.
  7. Row 1 (GCF_030704535.1)
    1. Type your region of interest into the location box and press Enter.This figure is at chr9:1-11,300,000.
  8. Row 2 (GCF_000346465.2)
    1. Type your region of interest into the location box and press Enter.This figure is at chrG3:2,150,000-7,300,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "tracks": [
                [
                    "grape_peach_anchors"
                ]
            ],
            "mark": {
                "interpolate": "linear"
            },
            "levelHeights": [
                260
            ],
            "collapseEmptyRows": True,
            "views": [
                {
                    "assembly": "GCF_030704535.1",
                    "loc": "chr9:1-11,300,000",
                    "tracks": []
                },
                {
                    "assembly": "GCF_000346465.2",
                    "loc": "chrG3:2,150,000-7,300,000",
                    "tracks": []
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: Gene pairs

cat > session-1.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

cat > callouts-1.json <<'JSON'
[
  {
    "type": "text",
    "x": 24,
    "y": 56,
    "fontSize": 22,
    "maxWidth": 700,
    "text": ".anchors open; one ribbon per gene pair"
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 445 \
  --spec session-1.json --annotations callouts-1.json -o frame-1.png

Frame 2: Blocks

cat > session-2.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors_simple",
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

cat > callouts-2.json <<'JSON'
[
  {
    "type": "text",
    "x": 24,
    "y": 56,
    "fontSize": 22,
    "maxWidth": 700,
    "text": ".anchors and .anchors.simple open; one ribbon per gene\nrendered on top of chained synteny blocks"
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 445 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -append 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.

Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: GCF_030704535.1, GCF_000346465.2.
  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. This one needs an MCScan .anchors.simple file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Grape peach synteny (MCScan, simple anchors)”.
  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 one needs an MCScan .anchors file.This figure uses “Grape peach synteny (MCScan, anchors)”.
  5. Click Launch.
  6. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  7. Drag the bar below a synteny level to resize it.This figure's level is 260px tall.
  8. Row 1 (GCF_030704535.1)
    1. Type your region of interest into the location box and press Enter.This figure is at chr9:1-11,300,000.
  9. Row 2 (GCF_000346465.2)
    1. Type your region of interest into the location box and press Enter.This figure is at chrG3:2,150,000-7,300,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors_simple",
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "tracks": [
                [
                    "grape_peach_anchors_simple",
                    "grape_peach_anchors"
                ]
            ],
            "mark": {
                "interpolate": "linear"
            },
            "levelHeights": [
                260
            ],
            "collapseEmptyRows": True,
            "views": [
                {
                    "assembly": "GCF_030704535.1",
                    "loc": "chr9:1-11,300,000",
                    "tracks": []
                },
                {
                    "assembly": "GCF_000346465.2",
                    "loc": "chrG3:2,150,000-7,300,000",
                    "tracks": []
                }
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors_simple",
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: Gene pairs

cat > session-1.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

cat > callouts-1.json <<'JSON'
[
  {
    "type": "text",
    "x": 24,
    "y": 56,
    "fontSize": 22,
    "maxWidth": 700,
    "text": ".anchors open; one ribbon per gene pair"
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 445 \
  --spec session-1.json --annotations callouts-1.json -o frame-1.png

Frame 2: Blocks

cat > session-2.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "tracks": [
        [
          "grape_peach_anchors_simple",
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        260
      ],
      "collapseEmptyRows": true,
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr9:1-11,300,000",
          "tracks": []
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG3:2,150,000-7,300,000",
          "tracks": []
        }
      ]
    }
  ]
}
JSON

cat > callouts-2.json <<'JSON'
[
  {
    "type": "text",
    "x": 24,
    "y": 56,
    "fontSize": 22,
    "maxWidth": 700,
    "text": ".anchors and .anchors.simple open; one ribbon per gene\nrendered on top of chained synteny blocks"
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 445 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -append 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.

A single gene pair up close

Zoom to one block with both gene tracks on and set to Filter by... → Genes → Only genes.

One MCScan block with both gene tracks set to Only genes. Each ribbon is one .anchors line, spanning the two genes it pairs.
Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: GCF_030704535.1, GCF_000346465.2.
  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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  6. Drag the bar below a synteny level to resize it.This figure's level is 220px tall.
  7. Row 1 (GCF_030704535.1)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
      1. Track menu → Filter by... → Genes → Only genesGenes counts every gene, transcript and RNA type, the configured transcript and container types, and a top-level CDS; the rest of a GFF, such as NCBI region and match rows, is not a gene.
      2. Track menu → Feature height → Compact
      3. Track menu → Show... → Labels → Auto
    2. Type your region of interest into the location box and press Enter.This figure is at chr13:1,190,000-1,345,000.
  8. Row 2 (GCF_000346465.2)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
      1. Track menu → Filter by... → Genes → Only genesGenes counts every gene, transcript and RNA type, the configured transcript and container types, and a top-level CDS; the rest of a GFF, such as NCBI region and match rows, is not a gene.
      2. Track menu → Feature height → Compact
      3. Track menu → Show... → Labels → Auto
    2. Type your region of interest into the location box and press Enter.This figure is at chrG2:26,925,000-27,075,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr13:1,190,000-1,345,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG2:26,925,000-27,075,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {
                    "assembly": "GCF_030704535.1",
                    "loc": "chr13:1,190,000-1,345,000",
                    "tracks": [
                        {
                            "trackId": "GCF_030704535.1-ncbiRefSeq",
                            "filter": [
                                "geneLike"
                            ],
                            "displayMode": "compact",
                            "showLabels": "auto",
                            "height": 70
                        }
                    ]
                },
                {
                    "assembly": "GCF_000346465.2",
                    "loc": "chrG2:26,925,000-27,075,000",
                    "tracks": [
                        {
                            "trackId": "GCF_000346465.2-ncbiRefSeq",
                            "filter": [
                                "geneLike"
                            ],
                            "displayMode": "compact",
                            "showLabels": "auto",
                            "height": 70
                        }
                    ]
                }
            ],
            "tracks": [
                [
                    "grape_peach_anchors"
                ]
            ],
            "mark": {
                "interpolate": "linear"
            },
            "levelHeights": [
                220
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr13:1,190,000-1,345,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG2:26,925,000-27,075,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr13:1,190,000-1,345,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG2:26,925,000-27,075,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 616 \
  --spec 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.

MCScan anchors only the pairs it could call confidently, so most genes have no ribbon.

Copies sharing one ortholog

Pick Color by value → Syntenic depth on the palette button in the view header. A ribbon stays grey where its two genes pair only with each other, and turns orange where several genes share one ortholog. The count covers the whole .anchors file, so a gene whose other copies are off screen still takes color.

Grape chr3 against peach chrG8, the .anchors track colored by syntenic depth.
Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure's rows, top to bottom: GCF_030704535.1, GCF_000346465.2.
  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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (unchecked)
  6. Drag the bar below a synteny level to resize it.This figure's level is 220px tall.
  7. Synteny view header → palette button → Color by value → Syntenic depthThe palette button's tooltip reads "Color by: ...".
  8. Row 1 (GCF_030704535.1)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
      1. Track menu → Filter by... → Genes → Only genesGenes counts every gene, transcript and RNA type, the configured transcript and container types, and a top-level CDS; the rest of a GFF, such as NCBI region and match rows, is not a gene.
      2. Track menu → Feature height → Compact
      3. Track menu → Show... → Labels → Auto
    2. Type your region of interest into the location box and press Enter.This figure is at chr3:2,825,000-2,970,000.
  9. Row 2 (GCF_000346465.2)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a BigBed file (.bb).This figure uses “NCBI RefSeq - RefSeq All”.
      1. Track menu → Filter by... → Genes → Only genesGenes counts every gene, transcript and RNA type, the configured transcript and container types, and a top-level CDS; the rest of a GFF, such as NCBI region and match rows, is not a gene.
      2. Track menu → Feature height → Compact
      3. Track menu → Show... → Labels → Auto
    2. Type your region of interest into the location box and press Enter.This figure is at chrG8:18,055,000-18,225,000.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr3:2,825,000-2,970,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG8:18,055,000-18,225,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ],
      "encoding": {
        "color": "syntenicDepth"
      }
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "views": [
                {
                    "assembly": "GCF_030704535.1",
                    "loc": "chr3:2,825,000-2,970,000",
                    "tracks": [
                        {
                            "trackId": "GCF_030704535.1-ncbiRefSeq",
                            "filter": [
                                "geneLike"
                            ],
                            "displayMode": "compact",
                            "showLabels": "auto",
                            "height": 70
                        }
                    ]
                },
                {
                    "assembly": "GCF_000346465.2",
                    "loc": "chrG8:18,055,000-18,225,000",
                    "tracks": [
                        {
                            "trackId": "GCF_000346465.2-ncbiRefSeq",
                            "filter": [
                                "geneLike"
                            ],
                            "displayMode": "compact",
                            "showLabels": "auto",
                            "height": 70
                        }
                    ]
                }
            ],
            "tracks": [
                [
                    "grape_peach_anchors"
                ]
            ],
            "mark": {
                "interpolate": "linear"
            },
            "levelHeights": [
                220
            ],
            "encoding": {
                "color": "syntenicDepth"
            }
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr3:2,825,000-2,970,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG8:18,055,000-18,225,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ],
      "encoding": {
        "color": "syntenicDepth"
      }
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        {
          "assembly": "GCF_030704535.1",
          "loc": "chr3:2,825,000-2,970,000",
          "tracks": [
            {
              "trackId": "GCF_030704535.1-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        },
        {
          "assembly": "GCF_000346465.2",
          "loc": "chrG8:18,055,000-18,225,000",
          "tracks": [
            {
              "trackId": "GCF_000346465.2-ncbiRefSeq",
              "filter": [
                "geneLike"
              ],
              "displayMode": "compact",
              "showLabels": "auto",
              "height": 70
            }
          ]
        }
      ],
      "tracks": [
        [
          "grape_peach_anchors"
        ]
      ],
      "mark": {
        "interpolate": "linear"
      },
      "levelHeights": [
        220
      ],
      "encoding": {
        "color": "syntenicDepth"
      }
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 616 \
  --spec 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.

Viewing the gene pairs as a dotplot

The anchors track and the simple anchors track also load in a dotplot, where a gene pair is one point and a block a run of them; Add → Dotplot view opens one. The axes start in index order; Re-order chromosomes, in the overflow menu of the dotplot header, sorts the vertical axis to follow the horizontal one.

The dotplot axes in index order, then re-sorted from the header's overflow menu.

Open the session the video starts in ↗, then take the steps it shows:

  1. Grape's chromosomes in file order scatter the alignments
  2. Re-order chromosomes, from the view menu
  3. Start re-sorts grape's axis to follow peach's, which stays put
  4. Re-sorted, the grape-peach synteny runs down the diagonal
Open this view in JBrowse Web ↗ ·

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure has GCF_000346465.2 on X and GCF_030704535.1 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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  4. Click Launch.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ]
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "views": [
                {
                    "assembly": "GCF_000346465.2"
                },
                {
                    "assembly": "GCF_030704535.1"
                }
            ],
            "tracks": [
                "grape_peach_anchors"
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ]
    }
  ]
}
JSON

npx @jbrowse/img dotplot --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1920 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1920 --height 768 \
  --spec 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.

Peach against grape after Re-order chromosomes, every point one .anchors gene pair.
Open in JBrowse Web ↗

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.This figure has GCF_000346465.2 on X and GCF_030704535.1 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. This one needs an MCScan .anchors file.A synteny track the session already has is quicker: pick it under Quick start, which fills in both axes itself.This figure uses “Grape peach synteny (MCScan, anchors)”.
  4. Click Launch.
  5. Dotplot header → the ⋮ menu → Re-order chromosomes...Reorders 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.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/grape_peach_cacao/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ],
      "autoDiagonalize": true
    }
  ]
}

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/grape_peach_cacao/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "views": [
                {
                    "assembly": "GCF_000346465.2"
                },
                {
                    "assembly": "GCF_030704535.1"
                }
            ],
            "tracks": [
                "grape_peach_anchors"
            ],
            "autoDiagonalize": True
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file: a data file opens as the track its name says.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ],
      "autoDiagonalize": true
    }
  ]
}
JSON

npx @jbrowse/img dotplot --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --spec session.json \
  --width 1500 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "views": [
        {
          "assembly": "GCF_000346465.2"
        },
        {
          "assembly": "GCF_030704535.1"
        }
      ],
      "tracks": [
        "grape_peach_anchors"
      ],
      "autoDiagonalize": true
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --width 1500 --height 800 \
  --spec 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.

Re-order chromosomes puts each peach chromosome's strongest grape partner on the diagonal, and its other partners stay off it.

Converting an MCScanX run

MCScanX is a different program from jcvi's MCScan. It writes one .collinearity holding every block, self-synteny and cross-species together, and tells genomes apart by a two-letter tag on each chromosome name. mcscanx_to_anchors.py splits a run into the four files jcvi writes, in place of the jcvi step:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/mcscanx_to_anchors.py
python3 mcscanx_to_anchors.py --gff xyz.gff --collinearity xyz.collinearity \
  --species vv=grape --species pp=peach --strand-gff3 peach=peach.gff3.gz

The track configs above load the converted files unchanged. --species order is the anchors column order, so it has to match the track's assemblyNames. Two options decide whether the result draws:

  • --chr-prefix peach=chrG prepends to the refNames, and --keep-chr-tag keeps MCScanX's tag, stripped by default (vv1 becomes 1)
  • --strand-gff3 peach=peach.gff3.gz recovers strand from the annotation, so an inverted .anchors pair draws as inverted

--fai peach=peach.fa.fai checks the refNames against the assembly; an unknown name draws empty. An anchors score becomes -log10 of MCScanX's e-value.

The number of --species names sets what the run writes:

Reproduce it end to end

build_grape_peach_anchors.sh runs everything above and writes a config.json with both assemblies, gene tracks, both MCScan tracks and a default session opening them together:

  1. Download the grape and peach RefSeq genomes and annotations by accession, dropping organelle genes, which gffread rejects.
  2. Write a BED and a CDS file per genome keyed on the mRNA ID, and run jcvi with --no_strip_names so the anchor ids match the BEDs.
  3. Screen the gene pairs into blocks for .anchors.simple.
  4. Write the config with both hub assemblies and gene tracks, both MCScan tracks and a session.
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_grape_peach_anchors.sh
bash build_grape_peach_anchors.sh
npx --yes serve grape_peach_anchors_build  # then open config.json there

See also

Citations