Synteny from an ortholog table (grape, peach, cacao)

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.13. Desktop beta builds are coming soon.

MCScan, from the jcvi toolkit, lines up orthologous genes across more than two genomes at once, into one wide table with a column per species. We load that table directly in JBrowse and:

stack grape, peach and cacao as rows of one synteny view and zoom to a conserved block
read one grape locus against all seven genomes at once, one lane per genome
redraw each lane in the coordinates of the genome it shows

Prerequisites

a JBrowse to open the files in: Desktop takes a local file by path, Web through Add track
jcvi with the LAST aligner
Or any other ortholog table, converted as in building a table for MCScanBlocksAdapter
the NCBI datasets CLI
gffread
samtools

Where the data comes from

Show full URLs

Seven RefSeq assemblies, one per species, each fetched by accession with the datasets CLI.

The build script takes these files from their URLs, so there is nothing to download by hand.

What a `.blocks` file is

A .blocks file is a tab-delimited table. Each row is an orthologous group and each column a genome, with . where a genome has no member. The file names none of its columns, so blockAssemblies does, by position:

grape01	peach01	cacao01
grape02	peach02	cacao02
grape03	.	.

A real cell holds the gene id from the annotation (rna-XM_007225519.2 for NCBI); the table has no coordinates, so one .bed per genome places each id.

How a .blocks table holds a duplicated gene

Two conventions place a second copy of a gene

A cell holds one gene id; two conventions place a second copy.

mcscan writes a column per chain of synteny blocks, so a grape gene syntenic to two peach regions fills a second peach column (--iter caps the chains). At --iter=2:

grape01	peach01	peach01b
grape02	peach02	.
grape03	.	.

Name that column peach in blockAssemblies with peach.bed beside it, and the track draws both; assemblyNames on the track still names peach once.

The other convention repeats the grape id, one row per copy:

grape01	peach01	cacao01
grape02	peach02a	cacao02
grape02	peach02b	cacao02
grape03	.	.

OrthoFinder's converter, orthogroups_to_blocks.py, writes this shape by default; the MCScanX converter keeps the best-scoring copy.

Producing grape.blocks and the BEDs with jcvi

grape.blocks and the BEDs come from jcvi and the LAST aligner over the seven accessions, each providing one genome, annotation and CDS:

for sp in grape peach cacao; do
  gffread "$sp.gff3" -g "$sp.fa" -x "$sp.cds.fa"
  # --key=ID joins the two files; --primary_only keeps one transcript per gene
  python -m jcvi.formats.gff bed --type=mRNA --key=ID --primary_only \
    "$sp.gff3" -o "$sp.bed"
  python -m jcvi.formats.fasta format "$sp.cds.fa" "$sp.cds"
done

--key=ID writes the GFF3 id of each mRNA into BED column 4, matching the CDS name gffread wrote. An unresolved key becomes an id like mrna_494685 that joins nothing; --key=transcript_id and --key=Name give that same id on an NCBI annotation.

Then catalog orthologs against the reference, MCScan each pair, and join:

for sp in peach cacao; do
  # --no_strip_names keeps the ids matching the BEDs above
  python -m jcvi.compara.catalog ortholog --no_strip_names grape "$sp"
  # --iter=1 keeps one block per grape gene, so one mate per genome
  python -m jcvi.compara.synteny mcscan grape.bed "grape.$sp.lifted.anchors" \
    --iter=1 -o "grape.$sp.i1.blocks"
done
# each per-pair table lists grape then the mate, so the join emits the grape
# column twice; cut -f1,2,4 keeps it once, in the order blockAssemblies and
# bedLocations list
python -m jcvi.formats.base join grape.peach.i1.blocks grape.cacao.i1.blocks \
  --noheader | cut -f1,2,4 > grape.blocks

The commands above run the two mates the stack uses. The build script runs the same steps for arabidopsis, poplar, tomato and citrus too, joins all six tables and keeps column 1 and every even column after it, which writes the seven-column grape.blocks that the all-seven-genomes view reads.

Building a table for MCScanBlocksAdapter converts MCScanX, OrthoFinder, Ensembl Compara and reciprocal-best-hit output to the same shape, and the adapter reads the .blocks and BED files plain or gzipped.

Setting up the grape, peach and cacao assemblies

Grape, peach and cacao are each a genome hub on genomes.jbrowse.org under the RefSeq accession the table was built from. Each row takes its assembly entry and gene track from there:

# a GenArk hub path is the accession cut into threes
curl -fO https://jbrowse.org/hubs/genark/GCF/000/346/465/GCF_000346465.2/config.json

The build keeps each hub entry, labels the row, and adds the short name as an alias, so a session can still say peach:

{
  "name": "GCF_000346465.2",
  "displayName": "peach",
  "aliases": ["peach"],
  "sequence": {
    "type": "ReferenceSequenceTrack",
    "trackId": "GCF_000346465.2-ReferenceSequenceTrack",
    "adapter": {
      "type": "TwoBitAdapter",
      "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/346/465/GCF_000346465.2/GCF_000346465.2.2bit",
      "chromSizes": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/346/465/GCF_000346465.2/GCF_000346465.2.chrom.sizes.txt"
    }
  },
  "refNameAliases": {
    "adapter": {
      "type": "RefNameAliasAdapter",
      "refNameColumnHeaderName": "ucsc",
      "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/000/346/465/GCF_000346465.2/GCF_000346465.2.chromAlias.txt"
    }
  }
}

refNameColumnHeaderName makes the UCSC names canonical, naming the first peach chromosome chrG1 where the BED says NC_034009.1.

Loading the blocks file with MCScanBlocksAdapter

One track backs each pair of adjacent rows. blockAssemblies names every column in order, and bedLocations gives the matching BED per column; the adapter needs no assemblyNames unless you mean to narrow it:

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_cacao_blocks",
  "name": "Grape / peach / cacao (MCScan blocks)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2", "GCF_000208745.1"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape.blocks.gz",
    "blockAssemblies": [
      "GCF_030704535.1",
      "GCF_000346465.2",
      "GCF_000208745.1"
    ],
    "bedLocations": ["grape.bed.gz", "peach.bed.gz", "cacao.bed.gz"]
  }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "grape_peach_cacao_blocks",
  "name": "Grape / peach / cacao (MCScan blocks)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2", "GCF_000208745.1"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape.blocks.gz",
    "blockAssemblies": [
      "GCF_030704535.1",
      "GCF_000346465.2",
      "GCF_000208745.1"
    ],
    "bedLocations": ["grape.bed.gz", "peach.bed.gz", "cacao.bed.gz"]
  }
}'

In the app

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_cacao_blocks",
  "name": "Grape / peach / cacao (MCScan blocks)",
  "assemblyNames": ["GCF_030704535.1", "GCF_000346465.2", "GCF_000208745.1"],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "grape.blocks.gz",
    "blockAssemblies": [
      "GCF_030704535.1",
      "GCF_000346465.2",
      "GCF_000208745.1"
    ],
    "bedLocations": ["grape.bed.gz", "peach.bed.gz", "cacao.bed.gz"]
  }
}

grape.blocks.gz, grape.bed.gz, peach.bed.gz, cacao.bed.gz are relative to a config.json. Replace each 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 hosted config.json holds the seven-column version of this track under the same trackId, named Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks). Every session and figure below runs on that one. Its assemblyNames stays the three declared genomes, since a lane takes just the table and that genome's BED.

Stacking grape, peach and cacao

Choose Add → Linear synteny view and pick grape_peach_cacao_blocks; the all-vs-all tutorial walks the dialog. As a defaultSession, the same stack ordered peach-cacao-grape:

Config file

Goes at the top level of config.json, replacing any defaultSession there. See Default session.

{
  "defaultSession": {
    "name": "Grape / Peach / Cacao multi-way synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "displayName": "Peach - Cacao - Grape (MCScan blocks)",
        "views": [
          { "assembly": "GCF_000346465.2" },
          { "assembly": "GCF_000208745.1" },
          { "assembly": "GCF_030704535.1" }
        ],
        "tracks": [["grape_peach_cacao_blocks"], ["grape_peach_cacao_blocks"]],
        "color": { "field": "reference" },
        "autoDiagonalize": true,
        "collapseEmptyRows": true
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "Grape / Peach / Cacao multi-way synteny",
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Peach - Cacao - Grape (MCScan blocks)",
      "views": [
        { "assembly": "GCF_000346465.2" },
        { "assembly": "GCF_000208745.1" },
        { "assembly": "GCF_030704535.1" }
      ],
      "tracks": [["grape_peach_cacao_blocks"], ["grape_peach_cacao_blocks"]],
      "color": { "field": "reference" },
      "autoDiagonalize": true,
      "collapseEmptyRows": true
    }
  ]
}
EOF

Open in JBrowse

Open this session in JBrowse Web ↗

tracks is one entry per band, and collapseEmptyRows gives each trackless row a bare scale bar.

Peach, cacao and grape stacked, with one MCScan .blocks file backing both synteny bands. The view reorders and flips each row so the ribbons run along the diagonal, and Color by → Reference anchors both bands on the shared middle row.

Direct and transitive pairs

Every row starts from a grape gene, as in jcvi MCScan tables, which anchor on column 0. The adapter also loads an all-against-all table, where a row holds orthologs inferred across all genomes at once. Bands touching grape come straight from the table (direct pairs). Each ribbon in a peach-cacao band is transitive, since it passes through a grape gene both genomes share, and only rows where grape has a member draw. The stack above puts grape at the bottom, so its peach-cacao band is the transitive one; a peach, grape, cacao stack makes both bands direct. The script prints, per column pair, the rows where both cells resolve.

Zooming to one block conserved in all three genomes

Stack peach over grape over cacao, navigate the rows to chrG7:18,555,000-18,690,000, chr11:778,000-905,000 and chr9:3,890,000-3,995,000, and turn on each genome's NCBI RefSeq - RefSeq All track with Show only genes.

Gene-level view of one conserved block, peach chrG7 over grape chr11 over cacao chr9, with the gene track for each genome on. The orthologs step across all three in the same order until the ribbons fan, where three grape copies meet one peach and one cacao ortholog.

One grape locus against all seven genomes

grape.blocks has seven columns. A track naming all seven in blockAssemblies and bedLocations, as the earlier one names three, draws every mate (the ortholog in each other genome) at once in a linear genome view on grape:

Navigate to chr11:778,000-866,000 and turn on grape's NCBI RefSeq - RefSeq All track.
Turn on Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks), which draws every mate in one pileup.
Pick Group by... → Mate assembly for a lane per genome.

One grape locus against six other plants, the same MCScan blocks track grouped by mate assembly. Each lane is one genome, so the lanes read as presence and absence down a column: peach, cacao, poplar and citrus keep most of the block, while arabidopsis and tomato (the one asterid) keep a scattered few.

Lanes in per-genome coordinates

In the one-locus view above, every gene sits at its grape coordinate. Display types → Multi-way synteny display redraws the lanes, each in the coordinates of one genome:

the display fits each lane to the genome it shows, over the orthologs the window brings in
one grey ribbon per ortholog group joins adjacent lanes, bridging past an empty one
any track whose features have a mate per assembly feeds the same lanes, including an OrthoFinder table or an all-vs-all PAF

A lane draws gene models from a gene track under its own assembly name, and outlines the gene spans from the table where it has none. We'll add one for grape; the other genomes take the same track under their accessions. Swap the uri for your own GFF3, bgzipped and tabix-indexed (prep), with the same refNames as the assembly:

Config file

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

{
  "type": "FeatureTrack",
  "trackId": "grape_genes",
  "name": "grape genes",
  "assemblyNames": ["GCF_030704535.1"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "grape.sorted.gff3.gz"
  }
}

CLI (add-track)

jbrowse add-track grape.sorted.gff3.gz \
  --trackId grape_genes \
  --name "grape genes" \
  --assemblyNames GCF_030704535.1 \
  --load copy

In the app

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: grape.sorted.gff3.gz

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

Track name: grape genes
Assembly: GCF_030704535.1

Click Add.

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

The multi-way lanes as a defaultSession (the track ids come from the hosted config, so name your own trackId instead):

Config file

Goes at the top level of config.json, replacing any defaultSession there. See Default session.

{
  "defaultSession": {
    "name": "Grape multi-way synteny track",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "GCF_030704535.1",
        "loc": "chr11:778,000-866,000",
        "tracks": [
          {
            "trackId": "GCF_030704535.1-ncbiRefSeq",
            "type": "LinearBasicDisplay",
            "showOnlyGenes": true,
            "displayMode": "compact"
          },
          {
            "trackId": "grape_peach_cacao_blocks",
            "type": "MultiWaySyntenyDisplay",
            "rows": {
              "domain": [
                "GCF_000346465.2",
                "GCF_000208745.1",
                "poplar",
                "citrus",
                "arabidopsis",
                "tomato"
              ]
            },
            "height": 340
          }
        ]
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "Grape multi-way synteny track",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GCF_030704535.1",
      "loc": "chr11:778,000-866,000",
      "tracks": [
        {
          "trackId": "GCF_030704535.1-ncbiRefSeq",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "grape_peach_cacao_blocks",
          "type": "MultiWaySyntenyDisplay",
          "rows": {
            "domain": [
              "GCF_000346465.2",
              "GCF_000208745.1",
              "poplar",
              "citrus",
              "arabidopsis",
              "tomato"
            ]
          },
          "height": 340
        }
      ]
    }
  ]
}
EOF

Open in JBrowse

Open this session in JBrowse Web ↗

The grape gene track above multi-way lanes, one per genome, all from a single MCScan blocks track. The peach and cacao lanes draw gene models from those genomes' gene tracks, the others draw gene spans from the table as boxes, and a chain of ribbons bridges past a lane that places nothing.

What a lane header shows

Each lane has a separate scale, shown in its header:

the left end shows where the lane starts, with [rev] where its gene order runs against grape's
the right end shows how much sequence the lane spans, and that span as a multiple of the grape span
the ticks fall at one interval shared by every mate lane

The view gridlines stop at the grape lane, the one lane they fit. A lane with no readable gene track (GFF3, GTF, BigBed or BED) outlines the gene spans from the table, labeled no annotation.

Ordering the lanes

rows.domain pins the lanes it names to the top; the rest follow densest-first, so the order holds across a pan
With Show... → Show ribbons across gaps off, a sparse lane mid-stack cuts every chain running through it

Zooming the lanes to a few genes

Zoom in until each ribbon connects one gene to its ortholog, fanning where copy number differs.

Hover a ribbon to highlight its ortholog group down every lane.
Click a ribbon to open the details for that pair, and click empty canvas to clear the outline.

Lanes zoomed to a few genes, with one ribbon clicked. Each ribbon links a gene to its ortholog in the lane below; the clicked ortholog group is outlined down every lane that chains it, and the details panel opens on the clicked pair.

Restacking the genomes around a locus

Two routes open a stacked synteny view from the lanes:

from the lane track, Launch → Linear synteny view (visible region) in its track menu offers a row to every aligning genome
from the scale bar, drag-select a locus and pick Launch → Linear synteny view. The dialog opens a row per genome, grape already seated between peach and cacao for the reference-in-the-middle layout, with arrows to reorder them

The ⋮ on a lane header, or a right-click on its name, opens the lane menu. Re-anchor on peach turns the track around on that genome, and Open peach at the matching region opens peach in a linear genome view, with its gene track.

The lane header menu: reorder or hide a lane, open peach at its span, or re-anchor the track on it.

Restacking around one grape locus: a scale-bar selection raises Launch, and the dialog lists a panel per genome with grape between its two mates.

Video

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

Select the locus on the scale bar and launch a synteny view
The dialog seats grape, the reference, between its two mates
Replace the lanes with the stack
Grape in the middle: each band compares it with a neighbour

Steps

Open this view in JBrowse Web ↗ · Open this view in JBrowse Desktop ↗

Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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%2Fgrape_peach_cacao%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22GCF_030704535.1%22%2C%22loc%22%3A%22chr11%3A778%2C000-866%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22GCF_030704535.1-ncbiRefSeq%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22displayMode%22%3A%22compact%22%2C%22showLabels%22%3A%22auto%22%7D%2C%7B%22trackId%22%3A%22grape_peach_cacao_blocks%22%2C%22type%22%3A%22LGVSyntenyDisplay%22%2C%22facet%22%3A%22mateAssembly%22%2C%22featureHeight%22%3A14%2C%22height%22%3A140%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Frestack_around_locus

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:

Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses GCF_030704535.1, loaded from a .2bit genome.
Add a track: check one your config has in the track selector, or File → Open 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 → Show only genes (checked)
2. Track menu → Feature height → Compact
3. Track menu → Show... → Labels → Auto
Add the next track the same way.This figure uses “Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)”.
1. Track menu → Group by... → Mate assemblySynteny tracks only: one section per assembly on the other side of the alignment.
2. Track menu → Feature height → Custom... → 14px
Type your region of interest into the location box and press Enter.This figure is at chr11:778,000-866,000.

Spec

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": "LinearGenomeView",
      "assembly": "GCF_030704535.1",
      "loc": "chr11:778,000-866,000",
      "tracks": [
        {
          "trackId": "GCF_030704535.1-ncbiRefSeq",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact",
          "showLabels": "auto"
        },
        {
          "trackId": "grape_peach_cacao_blocks",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "featureHeight": 14,
          "height": 140
        }
      ]
    }
  ]
}

Notebook

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": "LinearGenomeView",
            "assembly": "GCF_030704535.1",
            "loc": "chr11:778,000-866,000",
            "tracks": [
                {
                    "trackId": "GCF_030704535.1-ncbiRefSeq",
                    "type": "LinearBasicDisplay",
                    "showOnlyGenes": True,
                    "displayMode": "compact",
                    "showLabels": "auto"
                },
                {
                    "trackId": "grape_peach_cacao_blocks",
                    "type": "LGVSyntenyDisplay",
                    "facet": "mateAssembly",
                    "featureHeight": 14,
                    "height": 140
                }
            ]
        }
    ],
)
app  # display the widget

Image

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 with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/grape_peach_cacao/config.json \
  --assembly GCF_030704535.1 --loc chr11:778,000-866,000 \
  --track GCF_030704535.1-ncbiRefSeq display:LinearBasicDisplay '{"showOnlyGenes":true,"displayMode":"compact","showLabels":"auto"}' \
  --track grape_peach_cacao_blocks display:LGVSyntenyDisplay '{"facet":"mateAssembly","featureHeight":14,"height":140}' \
  --width 1920 --out figure.svg

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

Agent

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": "LinearGenomeView",
      "assembly": "GCF_030704535.1",
      "loc": "chr11:778,000-866,000",
      "tracks": [
        {
          "trackId": "GCF_030704535.1-ncbiRefSeq",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact",
          "showLabels": "auto"
        },
        {
          "trackId": "grape_peach_cacao_blocks",
          "type": "LGVSyntenyDisplay",
          "facet": "mateAssembly",
          "featureHeight": 14,
          "height": 140
        }
      ]
    }
  ]
}
JSON

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

Reproduce it end to end

build_grape_peach_cacao_synteny.sh runs everything above and writes a config.json with the hub assemblies, gene tracks, synteny track and default session:

Download the seven RefSeq genomes and annotations, and write a BED and a CDS file per genome keyed on the mRNA's GFF3 ID, so the two join.
Catalog orthologs against grape and MCScan each pair with --iter=1, one block per grape gene.
Join the six per-pair tables on the grape column into one seven-column grape.blocks.
Print, per column pair, the rows where both cells resolve, and write the config from the grape, peach and cacao hubs.

BLOCKS_ONLY_SPECIES lists the extra lanes; a genome added there needs only CDS and GFF3.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_grape_peach_cacao_synteny.sh
bash build_grape_peach_cacao_synteny.sh
npx --yes serve grape_peach_cacao_build  # then open config.json at the printed URL

The script needs the tools under Prerequisites.

Synteny from an ortholog table (grape, peach, cacao)

Prerequisites#

Where the data comes from#

What a .blocks file is#

How a .blocks table holds a duplicated gene#

Producing grape.blocks and the BEDs with jcvi#

Setting up the grape, peach and cacao assemblies#

Loading the blocks file with MCScanBlocksAdapter#

Stacking grape, peach and cacao#

Direct and transitive pairs#

Zooming to one block conserved in all three genomes#

One grape locus against all seven genomes#

Lanes in per-genome coordinates#

What a lane header shows#

Ordering the lanes#

Zooming the lanes to a few genes#

Restacking the genomes around a locus#

Reproduce it end to end#

See also#

Prerequisites

Where the data comes from

What a `.blocks` file is

How a .blocks table holds a duplicated gene

Producing grape.blocks and the BEDs with jcvi

Setting up the grape, peach and cacao assemblies

Loading the blocks file with MCScanBlocksAdapter

Stacking grape, peach and cacao

Direct and transitive pairs

Zooming to one block conserved in all three genomes

One grape locus against all seven genomes

Lanes in per-genome coordinates

What a lane header shows

Ordering the lanes

Zooming the lanes to a few genes

Restacking the genomes around a locus

Reproduce it end to end

See also