Synteny visualization (OrthoFinder orthogroups)

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.

Genomes too far apart to align base by base still keep their genes in order along the chromosomes. We stack related genomes on OrthoFinder orthogroups, sets of genes descended from one ancestral gene and inferred from protein similarity alone, and read where gene order holds and where a duplication doubles it. The page converts the orthogroups to a .blocks table that JBrowse reads and builds the wheat set through to a stacked view, then opens four more sets: vertebrates, drosophila, nightshades (solanaceae) and grasses.

Prerequisites

OrthoFinder with DIAMOND on PATH as orthofinder
MCScanX (MCScanX_h; bioconda mcscanx), for the collinear blocks
python3, htslib (bgzip, tabix), wget
node, for the JBrowse CLI
NCBI datasets CLI (datasets, dataformat), for wheat, drosophila and solanaceae
gffread, for your own genomes only
A running JBrowse instance (web or desktop)

Where the data comes from

Show full URLs

Each set takes its protein FASTA and GFF3 files from one Ensembl division.

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

vertebrates, Ensembl release 113: ftp.ensembl.org/…/release-113https://ftp.ensembl.org/pub/release-113/
wheat, solanaceae and grasses, Ensembl Plants release 63: ftp.ensemblgenomes.ebi.ac.uk/…/release-63https://ftp.ensemblgenomes.ebi.ac.uk/pub/plants/release-63/
drosophila, Ensembl Metazoa release 63: ftp.ensemblgenomes.ebi.ac.uk/…/release-63https://ftp.ensemblgenomes.ebi.ac.uk/pub/metazoa/release-63/
Sequence reports, fetched from NCBI by accession: T. timopheevii GCA_963921465.1, tomato GCA_000188115.5, and the non-melanogaster flies GCA_016746395.2, GCA_016746365.2, GCA_009870125.2 and GCA_030788295.1: ftp.ncbi.nlm.nih.gov/…/GCAhttps://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/

The wheat set: six genomes of one polyploid history

The wheat set is six genomes of wheat's polyploid history:

Aegilops tauschii, diploid D donor
bread wheat, hexaploid, A+B+D
durum, domesticated tetraploid, A+B
wild emmer, durum's wild tetraploid ancestor
Triticum urartu, diploid A donor
T. timopheevii, a second tetraploid also tracing to the A donor

Running OrthoFinder and building the blocks table

The build commands here produce the wheat set; the other four differ only in the proteomes used:

# -og stops after the orthogroups, skipping the gene trees and the species
# tree, which this table does not use and which are most of the runtime.
# -S diamond picks the aligner; -t is threads.
orthofinder -f proteomes -og -S diamond -t "$(getconf _NPROCESSORS_ONLN)"

The run writes proteomes/OrthoFinder/Results_<date>/Orthogroups/Orthogroups.tsv, which the next command reduces to one gene id per cell:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/orthogroups_to_blocks.py
python3 orthogroups_to_blocks.py Orthogroups.tsv -o tauschii.blocks \
  --bed tauschii=tauschii.bed --bed wheat=wheat.bed --bed durum=durum.bed \
  --bed emmer=emmer.bed --bed urartu=urartu.bed --bed timopheevii=timopheevii.bed \
  --max-copies 4

blockAssemblies must match the column order the script prints. --assembly COLUMN=NAME renames a column; a misspelled column there renames nothing and raises no error, while a typo in --bed is an error:

python3 orthogroups_to_blocks.py Orthogroups.tsv -o tauschii.blocks \
  --bed tauschii=tauschii.bed --bed wheat=wheat.bed \
  --assembly wheat=bread_wheat

Duplicated genes: one ribbon, two ribbons or none

In Orthogroups.tsv each cell lists one genome's genes in an orthogroup, so two genes in one cell have no single ribbon. --pick chooses among three treatments:

`--pick`	A rice gene with two maize orthologs	Use when
`first`	one ribbon, to whichever maize gene OrthoFinder listed first	you want maximum coverage and accept the arbitrary choice
`expand` (default)	two ribbons, one per maize copy	the duplication is part of what you are looking at
`single`	no ribbon	you want a strictly one-to-one table

A cell over --max-copies counts as a family and contributes no row:

python3 orthogroups_to_blocks.py Orthogroups.tsv -o tauschii.blocks \
  --bed tauschii=tauschii.bed --bed wheat=wheat.bed \
  --pick single --max-copies 2

Open the grasses set's hosted config (https://jbrowse.org/demos/orthofinder_grasses/config.json) as sorghum over rice over maize, with each genome's gene track on, and navigate the rows to 1:5,934,000-6,126,000[rev], 3:31,590,000-31,775,000 and 1:286,676,000-287,665,000 5:6,261,000-6,790,000[rev]. Sorghum is the control: it shares the ancestry and lacks the duplication.

One rice locus between sorghum and maize, off the grasses set's orthogroups track, with a gene track under each row. Sorghum has one ortholog per rice gene and maize has two, one into each of the two maize regions, and the genes that kept only one maize copy sit among them.

Matching gene ids between the table and the BEDs

Column 4 of each BED must match the ids in the table exactly. The build script keeps each gene's longest protein and names it by the gene id, so OrthoFinder sees one protein per gene under the id the BED has. --bed name=file reports the share of ids placed, and the conversion stops if it places none.

Loading the wheat orthogroups as a synteny track

One track backs each pair of adjacent rows in the stack:

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "wheat_orthogroups",
  "name": "Wheat orthogroups (OrthoFinder)",
  "assemblyNames": [
    "tauschii",
    "wheat",
    "durum",
    "emmer",
    "urartu",
    "timopheevii"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "tauschii.blocks.gz",
    "blockAssemblies": [
      "durum",
      "emmer",
      "tauschii",
      "timopheevii",
      "urartu",
      "wheat"
    ],
    "bedLocations": [
      "durum.bed.gz",
      "emmer.bed.gz",
      "tauschii.bed.gz",
      "timopheevii.bed.gz",
      "urartu.bed.gz",
      "wheat.bed.gz"
    ]
  }
}

CLI (add-track-json)

jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "wheat_orthogroups",
  "name": "Wheat orthogroups (OrthoFinder)",
  "assemblyNames": [
    "tauschii",
    "wheat",
    "durum",
    "emmer",
    "urartu",
    "timopheevii"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "tauschii.blocks.gz",
    "blockAssemblies": [
      "durum",
      "emmer",
      "tauschii",
      "timopheevii",
      "urartu",
      "wheat"
    ],
    "bedLocations": [
      "durum.bed.gz",
      "emmer.bed.gz",
      "tauschii.bed.gz",
      "timopheevii.bed.gz",
      "urartu.bed.gz",
      "wheat.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": "wheat_orthogroups",
  "name": "Wheat orthogroups (OrthoFinder)",
  "assemblyNames": [
    "tauschii",
    "wheat",
    "durum",
    "emmer",
    "urartu",
    "timopheevii"
  ],
  "adapter": {
    "type": "MCScanBlocksAdapter",
    "uri": "tauschii.blocks.gz",
    "blockAssemblies": [
      "durum",
      "emmer",
      "tauschii",
      "timopheevii",
      "urartu",
      "wheat"
    ],
    "bedLocations": [
      "durum.bed.gz",
      "emmer.bed.gz",
      "tauschii.bed.gz",
      "timopheevii.bed.gz",
      "urartu.bed.gz",
      "wheat.bed.gz"
    ]
  }
}

tauschii.blocks.gz, durum.bed.gz, emmer.bed.gz, tauschii.bed.gz, timopheevii.bed.gz, urartu.bed.gz, wheat.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.

A mismatch between blockAssemblies and the column order the conversion printed raises a track error naming both lists.

Assemblies from a chrom.sizes

A gene-level synteny view reads no sequence, so each assembly is a ChromSizesAdapter over a .chrom.sizes file (a name and a length per line) built from the ##sequence-region header in its GFF3. We'll load wheat; the other genomes repeat the block under their own names:

Config file

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

{ "name": "wheat", "uri": "wheat.chrom.sizes" }

CLI (add-assembly)

jbrowse add-assembly wheat.chrom.sizes \
  --name wheat \
  --load copy

JBrowse Desktop

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

wheat.chrom.sizes

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

Genome name: wheat

wheat.chrom.sizes is relative to a config.json. Replace it with its URL or its path on this computer.

Gene tracks, one per genome

The multi-way display draws a lane per genome, with gene models from a gene track on that genome's assembly. The grasses session below names a hosted one (rice_genes). For your own annotation, add one per genome from a bgzipped, tabix-indexed GFF3 (prep) that uses the assembly's refNames:

Config file

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

{
  "type": "FeatureTrack",
  "trackId": "wheat_genes",
  "name": "wheat genes",
  "assemblyNames": ["wheat"],
  "adapter": {
    "type": "Gff3TabixAdapter",
    "uri": "wheat.gff.gz"
  }
}

CLI (add-track)

jbrowse add-track wheat.gff.gz \
  --trackId wheat_genes \
  --name "wheat genes" \
  --assemblyNames wheat \
  --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: wheat.gff.gz

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

Track name: wheat genes
Assembly: wheat

Click Add.

wheat.gff.gz is relative to a config.json. Replace it with its URL or its path on this computer.

Stacking the wheat genomes

Add → Linear synteny view, pick wheat_orthogroups and add the six genomes in the order tauschii, wheat, durum, emmer, urartu, timopheevii; the all-vs-all tutorial walks the dialog. Two view-menu items shape the stack, and the session below sets both:

Show all regions - same bp per pixel (sameScale in a session spec) puts the rows on one bp/px, so row length on screen matches genome size.
Rows → Re-order chromosomes (autoDiagonalize in a session spec) sorts each row's chromosomes against its neighbour so the links run along a diagonal.

The wheat stack as a session over the hosted wheat config, the page's heaviest, so the bands take a while to draw:

Config file

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

{
  "defaultSession": {
    "name": "Wheat lineage stack",
    "views": [
      {
        "type": "LinearSyntenyView",
        "views": [
          { "assembly": "tauschii" },
          { "assembly": "wheat" },
          { "assembly": "durum" },
          { "assembly": "emmer" },
          { "assembly": "urartu" },
          { "assembly": "timopheevii" }
        ],
        "tracks": [
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"],
          ["wheat_orthogroups"]
        ],
        "sameScale": true,
        "autoDiagonalize": true,
        "collapseEmptyRows": true,
        "opacity": 0.15
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "Wheat lineage stack",
  "views": [
    {
      "type": "LinearSyntenyView",
      "views": [
        { "assembly": "tauschii" },
        { "assembly": "wheat" },
        { "assembly": "durum" },
        { "assembly": "emmer" },
        { "assembly": "urartu" },
        { "assembly": "timopheevii" }
      ],
      "tracks": [
        ["wheat_orthogroups"],
        ["wheat_orthogroups"],
        ["wheat_orthogroups"],
        ["wheat_orthogroups"],
        ["wheat_orthogroups"]
      ],
      "sameScale": true,
      "autoDiagonalize": true,
      "collapseEmptyRows": true,
      "opacity": 0.15
    }
  ]
}
EOF

Open in JBrowse

Open this session in JBrowse Web ↗

Six wheat-lineage genomes stacked on OrthoFinder orthogroups, in evolutionary order. All six rows are on one genomic scale, so row length matches genome size: the two diploid donors against the hexaploid they built, with the tetraploids between.

Coloring wheat 4A by its tauschii chromosomes

We'll open tauschii over wheat from Add → Linear synteny view, with wheat_orthogroups between them. Then:

Navigate the wheat row to 4A.
Pick Query in the palette button menu. The palette sets the links' color, a color scale from a field to colors, and Query paints each link by its tauschii chromosome.

Aegilops tauschii's seven D-genome chromosomes over bread wheat chromosome 4A, from the same wheat_orthogroups track. Color by → Query gives each chromosome a distinct color, and 4A resolves into three runs of genes in order along it: 4D, then 5D, then 7D.

Other chromosomes appear on 4A only as single genes. The 5D and 7D runs are the 4AL/5AL and 4AL/7BS translocations (Devos et al. 1995; Dvorak et al. 2018).

Vertebrates: runs of conserved genes out to zebrafish

The other four sets build with bash build_orthofinder_synteny.sh <set> (Reproduce it end to end), and each has a hosted config at https://jbrowse.org/demos/orthofinder_<set>/config.json. Open the vertebrates config and stack human over chicken, frog, gar and zebrafish as for wheat, with vertebrates_orthogroups in each band, and pick Reference in the palette button menu.

Five vertebrate genomes stacked on OrthoFinder orthogroups: human, chicken, frog, spotted gar, zebrafish, all four bands off one vertebrates_orthogroups track. Gar against zebrafish, past the teleost duplication, is the dense band.

The human HOXD cluster against four vertebrates

Open human at 2:176,090,000-176,290,000, the HOXD cluster of body-axis patterning genes, with the human gene track and the orthogroups track on the multi-way synteny display. A lane (one horizontal strip per genome) for each of chicken, frog, gar and zebrafish draws under it.

The human HOXD cluster over chicken, frog, gar and zebrafish lanes from one OrthoFinder orthogroups track. Every lane draws its genome's genes across the cluster, but the ribbons there are scattered slivers; the solid chains sit to the right of it, on single-copy genes the orthogroup table could resolve.

Drosophila: chromosome arms keep their genes while gene order changes

The drosophila set stacks D. melanogaster with close relatives D. simulans and D. yakuba and the distant D. pseudoobscura and D. virilis. Across these flies the chromosome arms (Muller elements) keep their gene content, while inversions reorder the genes inside each arm.

In the drosophila config, stack the flies as simulans, melanogaster, yakuba, melanogaster, pseudoobscura, melanogaster, virilis, so every band sets one fly against melanogaster. Pick Reference in the palette button menu to paint each ribbon by the melanogaster arm it leaves.

simulans, yakuba, pseudoobscura and virilis stacked on OrthoFinder orthogroups with melanogaster between each pair, on one bp/px. Ribbons take the color of their melanogaster arm, so one color follows one arm down the stack; each arm's bundle stays together in every fly, and ribbons cross inside a bundle where inversions reordered the genes.

Gene order in one 3L window across the flies

Open melanogaster at 3L:5,789,000-5,931,000 with the multi-way synteny display, which draws a lane per fly. Every fly keeps this window's melanogaster genes.

A window on melanogaster 3L over four Drosophila lanes from one orthogroups track. simulans and yakuba draw the same genes in the same order on their 3L; pseudoobscura and virilis draw them reversed, and the pseudoobscura lane's chromosome is X.

Collinear blocks from the same orthogroups

An orthogroup says which genes are related, and nothing about which of them still sit in order. MCScanX's MCScanX_h chains ortholog pairs that keep their order into collinear blocks. Start by writing every gene pair an orthogroup holds between two flies:

# every melanogaster-simulans pair in an orthogroup, each copy of a duplicated
# gene included, so MCScanX_h picks the collinear copy by gene order
python3 orthogroups_to_blocks.py Orthogroups.tsv -o melanogaster.blocks \
  --homology melanogaster:simulans=x.homology

MCScanX_h reads those pairs and x.gff, four columns per gene (chromosome, gene id, start, end) with each chromosome name prefixed by a two-letter code for its genome:

# -s 10: a block holds at least 10 gene pairs
# -m 24: at most 24 genes skipped between two pairs of a block
# -g 0: a skipped gene costs nothing, so -s alone sets the size cutoff
# -b 2: blocks between the two genomes only, none within one
# -a: write the .collinearity file and skip the HTML
MCScanX_h x -a -b 2 -s 10 -m 24 -g 0

Convert the blocks to PAF, one line per block, with each sequence named for its assembly (melanogaster#1#2L):

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/mcscanx_to_anchors.py
python3 mcscanx_to_anchors.py --gff x.gff --collinearity x.collinearity \
  --species aa=melanogaster --species bb=simulans \
  --paf melanogaster.simulans.paf \
  --chrom-sizes melanogaster=melanogaster.chrom.sizes \
  --chrom-sizes simulans=simulans.chrom.sizes

The PAF files of every pair, concatenated, back every band of a stack from one track:

Config file

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

{
  "type": "SyntenyTrack",
  "trackId": "drosophila_blocks",
  "name": "Drosophila collinear blocks (MCScanX)",
  "assemblyNames": [
    "melanogaster",
    "simulans",
    "yakuba",
    "pseudoobscura",
    "virilis"
  ],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "https://jbrowse.org/demos/orthofinder_drosophila/drosophila.blocks.paf.gz",
    "assemblyNames": [
      "melanogaster",
      "simulans",
      "yakuba",
      "pseudoobscura",
      "virilis"
    ]
  }
}

CLI (add-track)

jbrowse add-track https://jbrowse.org/demos/orthofinder_drosophila/drosophila.blocks.paf.gz \
  --trackId drosophila_blocks \
  --name "Drosophila collinear blocks (MCScanX)" \
  --assemblyNames melanogaster,simulans,yakuba,pseudoobscura,virilis \
  --adapterType MultiGenomePAFAdapter

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": "drosophila_blocks",
  "name": "Drosophila collinear blocks (MCScanX)",
  "assemblyNames": [
    "melanogaster",
    "simulans",
    "yakuba",
    "pseudoobscura",
    "virilis"
  ],
  "adapter": {
    "type": "MultiGenomePAFAdapter",
    "uri": "https://jbrowse.org/demos/orthofinder_drosophila/drosophila.blocks.paf.gz",
    "assemblyNames": [
      "melanogaster",
      "simulans",
      "yakuba",
      "pseudoobscura",
      "virilis"
    ]
  }
}

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.

Stack the flies in the same order as above and pick drosophila_blocks for every band:

The stack above drawn from the drosophila_blocks track, one ribbon per collinear block. simulans keeps each melanogaster arm in a few long blocks and yakuba in more, while pseudoobscura and virilis break every arm into many short ones. Nearly every block stays inside one arm.

Nightshades: the same genes over genomes of very different sizes

The solanaceae set is tomato, potato, pepper and Nicotiana attenuata (the row labelled tobacco), with coffee as the outgroup. Open the solanaceae config and stack them as for wheat with Show all regions - same bp per pixel, so row length matches genome size.

Tomato, potato, pepper and Nicotiana attenuata (nightshades) over coffee, the outgroup, stacked on OrthoFinder orthogroups at one bp per pixel. Pepper's row is by far the longest yet matches potato's genes band for band, and coffee's is the shortest.

Grasses: the maize whole-genome duplication

Open the grasses config and stack the five grasses as for wheat, with grasses_orthogroups in each band.

Five grass genomes stacked on OrthoFinder orthogroups: rice, sorghum, maize, brachypodium, foxtail millet. The maize whole-genome duplication shows as more ribbons per gene in the two maize bands than in the other pairs.

A rice window against four grasses

Open the same five grasses as a multi-way synteny track, under the rice gene track:

Config file

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

{
  "defaultSession": {
    "name": "Grasses multi-way synteny track",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "rice",
        "loc": "3:31,590,000-31,775,000",
        "tracks": [
          {
            "trackId": "rice_genes",
            "type": "LinearBasicDisplay",
            "showOnlyGenes": true,
            "displayMode": "compact"
          },
          {
            "trackId": "grasses_orthogroups",
            "type": "MultiWaySyntenyDisplay",
            "rows": {
              "domain": ["sorghum", "brachypodium", "setaria", "maize"]
            },
            "height": 320
          }
        ]
      }
    ]
  }
}

CLI (set-default-session)

jbrowse set-default-session --session - << 'EOF'
{
  "name": "Grasses multi-way synteny track",
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "rice",
      "loc": "3:31,590,000-31,775,000",
      "tracks": [
        {
          "trackId": "rice_genes",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "grasses_orthogroups",
          "type": "MultiWaySyntenyDisplay",
          "rows": {
            "domain": ["sorghum", "brachypodium", "setaria", "maize"]
          },
          "height": 320
        }
      ]
    }
  ]
}
EOF

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A rice window over sorghum, brachypodium, setaria and maize lanes from one OrthoFinder orthogroups track, each lane drawing that grass's gene models. The window is syntenic in all four, and the maize lane shows whichever of the two maize copies places more of the window.

A stacked view shows both maize copies at once. Launch → Linear synteny view (visible region) in the lane track menu offers a full row per grass.

Launching a stack from the grasses lane track: the track menu entry, the dialog offering a checkbox per grass row, and Replace current view swapping the lane view for the stack.

Video

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

Rice's genes, with one ortholog lane per grass under them
From the track menu, launch a synteny view of this region
The dialog lists a panel per grass, with the span each opens at
The stack replaces the lanes: rice on top, each grass below it

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%2Forthofinder_grasses%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22rice%22%2C%22loc%22%3A%223%3A31%2C590%2C000-31%2C775%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22rice_genes%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22showOnlyGenes%22%3Atrue%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22grasses_orthogroups%22%2C%22type%22%3A%22MultiWaySyntenyDisplay%22%2C%22rows%22%3A%7B%22domain%22%3A%5B%22sorghum%22%2C%22brachypodium%22%2C%22setaria%22%2C%22maize%22%5D%7D%2C%22height%22%3A320%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+synteny%2Fmultiway_launch_stack

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 rice.
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 bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “rice genes”.
1. Track menu → Show only genes (checked)
2. Track menu → Feature height → Compact
Add the next track the same way.This figure uses “Grasses orthogroups (OrthoFinder)”.
1. Track menu → Lanes → Lane menusOpen a lane's submenu and choose Move up or Move down, or drag the lane's name in the left gutter. This figure's order, top to bottom: sorghum, brachypodium, setaria, maize.
Type your region of interest into the location box and press Enter.This figure is at 3:31,590,000-31,775,000.

Spec

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "rice",
      "loc": "3:31,590,000-31,775,000",
      "tracks": [
        {
          "trackId": "rice_genes",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "grasses_orthogroups",
          "type": "MultiWaySyntenyDisplay",
          "rows": {
            "domain": [
              "sorghum",
              "brachypodium",
              "setaria",
              "maize"
            ]
          },
          "height": 320
        }
      ]
    }
  ]
}

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/orthofinder_grasses/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "rice",
            "loc": "3:31,590,000-31,775,000",
            "tracks": [
                {
                    "trackId": "rice_genes",
                    "type": "LinearBasicDisplay",
                    "showOnlyGenes": True,
                    "displayMode": "compact"
                },
                {
                    "trackId": "grasses_orthogroups",
                    "type": "MultiWaySyntenyDisplay",
                    "rows": {
                        "domain": [
                            "sorghum",
                            "brachypodium",
                            "setaria",
                            "maize"
                        ]
                    },
                    "height": 320
                }
            ]
        }
    ],
)
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/orthofinder_grasses/config.json \
  --assembly rice --loc 3:31,590,000-31,775,000 \
  --track rice_genes display:LinearBasicDisplay '{"showOnlyGenes":true,"displayMode":"compact"}' \
  --track grasses_orthogroups display:MultiWaySyntenyDisplay '{"rows":{"domain":["sorghum","brachypodium","setaria","maize"]},"height":320}' \
  --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": "rice",
      "loc": "3:31,590,000-31,775,000",
      "tracks": [
        {
          "trackId": "rice_genes",
          "type": "LinearBasicDisplay",
          "showOnlyGenes": true,
          "displayMode": "compact"
        },
        {
          "trackId": "grasses_orthogroups",
          "type": "MultiWaySyntenyDisplay",
          "rows": {
            "domain": [
              "sorghum",
              "brachypodium",
              "setaria",
              "maize"
            ]
          },
          "height": 320
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/orthofinder_grasses/config.json \
  --width 1920 --height 830 \
  --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_orthofinder_synteny.sh runs everything above and writes a config.json with the assemblies, gene tracks, the synteny track and a stacked default session:

Download each genome's proteome and GFF3, keeping each gene's longest protein under its gene id so the table and the BEDs agree, and write a gene BED and chrom.sizes per genome.
Run OrthoFinder to the orthogroups only.
Convert the orthogroups to a .blocks table, dropping cells over MAXCOPIES as gene families, and print how one-to-one each adjacent pair of genomes is.
Chain every pair of genomes into collinear blocks with MCScanX_h, and collect the blocks into one PAF.
Write the assemblies, gene tracks, the orthogroups and blocks tracks and a stacked session.

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_orthofinder_synteny.sh
bash build_orthofinder_synteny.sh wheat   # or: vertebrates, grasses, drosophila, solanaceae
npx --yes serve orthofinder_wheat_build/jbrowse2  # then open the printed URL

The sets the script accepts, and what each costs to build:

Set	Genomes	DIAMOND runs	Annotation source
`vertebrates`	human, chicken, frog, gar, zebrafish	25	Ensembl 113
`grasses`	rice, sorghum, maize, brachypodium, setaria	25	Ensembl Plants 63
`wheat`	tauschii, wheat, durum, emmer, urartu, timopheevii	36	Ensembl Plants 63
`drosophila`	melanogaster, simulans, yakuba, pseudoobscura, virilis	25	Ensembl Metazoa 63
`solanaceae`	tomato, potato, pepper, tobacco, coffee	25	Ensembl Plants 63

Two cuts are environment variables:

Variable	Default	What it cuts
`MAXSEQ`	30	sequence regions kept per genome, the ones carrying the most genes
`MAXCOPIES`	4	genes in one orthogroup cell past which it is a gene family rather than a set of copies

MAXSEQ=60 MAXCOPIES=6 bash build_orthofinder_synteny.sh wheat

The NCBI datasets CLI names chromosomes that a GFF3 gives as INSDC accessions, each from its sequence report.

Your own genomes

A set name tells the script which Ensembl files to download. Your own genomes need a FASTA and a GFF3 per genome. gffread translates each CDS into the proteome and prints the transcript-to-gene map and FASTA index alongside.

Name the files in a manifest, one line per genome:

cat > my_genomes.tsv <<'EOF'
# name    genome                    annotation              aliases
speciesA  data/speciesA.fa.gz       data/speciesA.gff3.gz
speciesB  https://host/B.fa.gz      https://host/B.gff3.gz  GCF_000001405.40
EOF

bash build_orthofinder_synteny.sh my_genomes.tsv
npx --yes serve orthofinder_my_genomes_build/jbrowse2  # then open the printed URL

Column 1 names the assembly, and columns 2 and 3 take a local path or URL.
Column 4 is optional. An INSDC accession fetches NCBI's sequence report for chromosome names, and a file name supplies a two-column alias table.
Column 2 also takes a proteome directly, which skips translation; its headers then need a gene:<id> tag matching ID=gene:<id> in the GFF3.
Two genomes make a valid manifest.

Citations

Emms and Kelly (2019). OrthoFinder: phylogenetic orthology inference for comparative genomics
Wang et al. (2012). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Devos et al. (1995). Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination
Dvorak et al. (2018). Reassessment of the evolution of wheat chromosomes 4A, 5A, and 7B

Feedback on this tutorial is welcome: contact us.

Synteny visualization (OrthoFinder orthogroups)

Prerequisites#

Where the data comes from#

The wheat set: six genomes of one polyploid history#

Running OrthoFinder and building the blocks table#

Duplicated genes: one ribbon, two ribbons or none#

Matching gene ids between the table and the BEDs#

Loading the wheat orthogroups as a synteny track#

Assemblies from a chrom.sizes#

Gene tracks, one per genome#

Stacking the wheat genomes#

Coloring wheat 4A by its tauschii chromosomes#

Vertebrates: runs of conserved genes out to zebrafish#

The human HOXD cluster against four vertebrates#

Drosophila: chromosome arms keep their genes while gene order changes#

Gene order in one 3L window across the flies#

Collinear blocks from the same orthogroups#

Nightshades: the same genes over genomes of very different sizes#

Grasses: the maize whole-genome duplication#

A rice window against four grasses#

Reproduce it end to end#

Your own genomes#

See also#

Citations#

Prerequisites

Where the data comes from

The wheat set: six genomes of one polyploid history

Running OrthoFinder and building the blocks table

Duplicated genes: one ribbon, two ribbons or none

Matching gene ids between the table and the BEDs

Loading the wheat orthogroups as a synteny track

Assemblies from a chrom.sizes

Gene tracks, one per genome

Stacking the wheat genomes

Coloring wheat 4A by its tauschii chromosomes

Vertebrates: runs of conserved genes out to zebrafish

The human HOXD cluster against four vertebrates

Drosophila: chromosome arms keep their genes while gene order changes

Gene order in one 3L window across the flies

Collinear blocks from the same orthogroups

Nightshades: the same genes over genomes of very different sizes

Grasses: the maize whole-genome duplication

A rice window against four grasses

Reproduce it end to end

Your own genomes

See also

Citations