# Rearrangements between genomes by type (SyRI) :::caution JBrowse v5 beta The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the [download page](https://jbrowse.org/jb2/download/) 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.9`. Desktop beta builds are coming soon. ::: The Columbia and Landsberg accessions of _Arabidopsis thaliana_ differ by an inversion of more than a megabase on the short arm of chromosome 4, first seen under the microscope and later confirmed by assembling Landsberg. We find it again by aligning six assembled accessions and running [SyRI](https://github.com/schneebergerlab/syri), which sorts what an alignment contains into syntenic, inverted, translocated and duplicated regions. Each accession is compared with Columbia and with the accession above it, and every comparison goes into one file whose ribbons take their color from SyRI's type: the stack [plotsr](https://github.com/schneebergerlab/plotsr) draws, and the same accessions as lanes under Columbia's own coordinates, with every region open to zooming and clicking. ## Prerequisites - [`minimap2`](https://github.com/lh3/minimap2) and `samtools` - [SyRI](https://github.com/schneebergerlab/syri) (`syri`), from bioconda, or Docker, which runs its biocontainers image - The NCBI [`datasets`](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/command-line-tools/download-and-install/) CLI, to fetch the assemblies - `python3`, `bgzip` and `tabix` - A running JBrowse instance (the [web quickstart](https://jbrowse.org/jb2/docs/quickstart_web) or the [desktop quickstart](https://jbrowse.org/jb2/docs/quickstart_desktop)) ## Where the data comes from TAIR10 for Columbia, and the chromosome-level assemblies of five more accessions from [Jiao and Schneeberger 2020](https://doi.org/10.1038/s41467-020-14779-y), the first three the ones plotsr's own figure stacks. - Col-0, GCF_000001735.4: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/735/GCF_000001735.4_TAIR10.1/ - Ler, GCA_902460285.1: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/460/285/GCA_902460285.1_Arabidopsis_thaliana_Ler/ - Cvi-0, GCA_902460275.1: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/460/275/GCA_902460275.1_Arabidopsis_thaliana_Cvi-0/ - Eri-1, GCA_902460315.1: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/460/315/GCA_902460315.1_Arabidopsis_thaliana_Eri-1/ - Kyo, GCA_902460305.1: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/460/305/GCA_902460305.1_Arabidopsis_thaliana_Kyo/ - Sha, GCA_902460295.1: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/902/460/295/GCA_902460295.1_Arabidopsis_thaliana_Sha/ ## Aligning a pair and running SyRI SyRI reads a whole-genome alignment of two chromosome-level assemblies whose homologous chromosomes share a name. The [script](#reproduce-it-end-to-end) keeps each assembly's five nuclear chromosomes and names them `Chr1` to `Chr5`. Each accession is aligned to Col-0, and to the accession above it in the stack: ```bash # asm5 is the preset for genomes of one species # --eqx writes = and X in the CIGAR, which SyRI reads the mismatches from minimap2 -cx asm5 --eqx Col-0.fa Ler.fa >Col-0_Ler.aln.paf # -F P says the alignment is PAF # --nc runs that many chromosomes at once syri -c Col-0_Ler.aln.paf -r Col-0.fa -q Ler.fa -F P --prefix Col-0_Ler. --nc 5 ``` `Col-0_Ler.syri.out` holds one row per annotation. The structural regions are the rows with no parent: `SYN`, `INV`, `TRANS`, `INVTR`, `DUP` and `INVDP`, each with its interval on both genomes. ## SyRI's regions as one PAF A SyRI region is an interval on each of two genomes, the same shape as a PAF alignment record. [`syri_to_paf.py`](https://github.com/GMOD/jbrowse-components/blob/main/scripts/syri_to_paf.py) writes each region as one, naming sequences `#1#` so records from many pairs can share a file, with the inverted types on the minus strand and two tags: `syri`, the type, and `color`, that type's color in plotsr's palette. It reads each sequence's length from a `.chrom.sizes` file beside `syri.out`, the first two columns of the FASTA's index. Concatenating every pair's records gives one file for every view below: ```bash curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/syri_to_paf.py for name in Col-0 Ler; do samtools faidx $name.fa cut -f1,2 $name.fa.fai >$name.chrom.sizes done python3 syri_to_paf.py Col-0_Ler.syri.out --reference Col-0 --query Ler cat Col-0_*.paf Ler_Cvi.paf Cvi_Eri.paf Eri_Kyo.paf Kyo_Sha.paf >syri_pangenome.paf ``` The ribbons need no sequence, so each accession is an assembly of those chromosome lengths alone, a `ChromSizesAdapter` over its `.chrom.sizes`. On the track: - **`attributeColumns`** names the tags the palette button offers: `syri` becomes a color-by mode, and `color` is the color the file puts beside each type - **The `MultiWaySyntenyDisplay` entry** sets up the [lanes view](#every-accession-in-columbias-coordinates): `domain` names the lanes and `ribbonColor` colors the bands by `syri` ```json addtrack { "type": "SyntenyTrack", "trackId": "syri_pangenome", "name": "SyRI regions", "assemblyNames": ["Col-0", "Ler", "Cvi", "Eri", "Kyo", "Sha"], "adapter": { "type": "MultiGenomePAFAdapter", "uri": "syri_pangenome.paf", "attributeColumns": ["syri", "color"] }, "displays": [ { "type": "MultiWaySyntenyDisplay", "displayId": "syri_pangenome-MultiWaySyntenyDisplay", "domain": ["Ler", "Cvi", "Eri", "Kyo", "Sha"], "ribbonColor": { "field": "syri", "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"] } } ] } ``` ## Columbia against Landsberg on chromosome 4 Open the first 6 Mb of chromosome 4 in both accessions and pick **syri** under **Color by value** on the palette button in the view header: ```json session config=test_data/syri/config.json { "defaultSession": { "name": "Col-0 vs Ler, chromosome 4", "views": [ { "type": "LinearSyntenyView", "views": [ { "assembly": "Col-0", "loc": "Chr4:1-6,000,000" }, { "assembly": "Ler", "loc": "Chr4:1-6,000,000" } ], "tracks": [["syri_pangenome"]], "color": { "field": "syri", "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"] }, "drawCurves": true, "alpha": 0.9, "fadeThinAlignmentsMode": "off", "collapseEmptyRows": true, "levelHeights": [260] } ] } } ``` The syntenic regions run straight down in grey, and one inverted region crosses over between them. The thin ribbons leaving the frame are duplications and translocations whose other end sits on another chromosome, which the label at the frame's edge names. The `domain` lists the types in plotsr's order, and the key has one row per color: plotsr paints an inverted translocation as a translocation and an inverted duplication as a duplication, so `INVTR` shares a row with `TRANS` and `INVDP` with `DUP`.
## Six accessions The same track stacks all six, each band drawing the SyRI run between the two genomes it joins: ```json session config=test_data/syri/config.json { "defaultSession": { "name": "Six Arabidopsis accessions, SyRI regions", "views": [ { "type": "LinearSyntenyView", "views": [ { "assembly": "Col-0" }, { "assembly": "Ler" }, { "assembly": "Cvi" }, { "assembly": "Eri" }, { "assembly": "Kyo" }, { "assembly": "Sha" } ], "tracks": [ ["syri_pangenome"], ["syri_pangenome"], ["syri_pangenome"], ["syri_pangenome"], ["syri_pangenome"] ], "color": { "field": "syri", "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"] }, "drawCurves": true, "alpha": 0.9, "fadeThinAlignmentsMode": "off", "collapseEmptyRows": true, "levelHeights": [150, 150, 150, 150, 150] } ] } } ```
## Every accession in Columbia's coordinates The stack answers how each accession differs from its neighbour. A reader annotating Col-0 wants each accession's difference from Col-0, in Col-0's coordinates. `syri_to_paf.py` also writes each pair's regions on the reference alone, one BED row per region, named by its type, colored by `itemRgb` and carrying the accession's name in a `query` column. The rows against Col-0 concatenate into one track: ```bash { head -n1 Col-0_Ler.regions.bed for name in Ler Cvi Eri Kyo Sha; do tail -n +2 Col-0_$name.regions.bed done | sort -k1,1 -k2,2n } | bgzip >syri_regions.bed.gz tabix -p bed syri_regions.bed.gz ``` `rows.field` gives the track one row per accession: ```json addtrack { "type": "FeatureTrack", "trackId": "syri_regions_on_Col-0", "name": "SyRI regions on Col-0, by accession", "assemblyNames": ["Col-0"], "adapter": { "type": "BedTabixAdapter", "uri": "syri_regions.bed.gz", "disableGeneHeuristic": true }, "displays": [ { "type": "LinearMultiRowFeatureDisplay", "displayId": "syri_regions_on_Col-0-LinearMultiRowFeatureDisplay", "rows": { "field": "query", "domain": ["Ler", "Cvi", "Eri", "Kyo", "Sha"] }, "color": { "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"] } } ] } ``` Open a linear genome view on Col-0 at `Chr4:1-6,000,000` and turn the track on. Turn on **SyRI regions** under it and switch it to **Display types → Multi-way synteny display**, which takes its lanes and colors from the track's display entry above: - **Each accession is a lane** drawn in its own coordinates, placed by its SyRI run against Col-0 - **The band between two lanes** comes from the run between those two accessions, so it carries the type SyRI gave that pair ```json session config=test_data/syri/config.json { "defaultSession": { "name": "Six accessions in Col-0's coordinates", "views": [ { "type": "LinearGenomeView", "assembly": "Col-0", "loc": "Chr4:1-6,000,000", "tracks": [ { "trackId": "syri_regions_on_Col-0", "type": "LinearMultiRowFeatureDisplay", "height": 110 }, { "trackId": "syri_pangenome", "type": "MultiWaySyntenyDisplay", "height": 640 } ] } ] } } ```
## Twenty-six accessions against TAIR10 Every one of the five accessions is inverted against Col-0 over the same stretch, which raises the question of which arrangement is the common one. The 1001 Genomes Plus project assembled accessions from across the species' range ([Igolkina et al. 2025](https://doi.org/10.1038/s41588-025-02293-0)), and the same pipeline runs on 26 of them against TAIR10. The result is hosted with each accession's genes, transposons and methylation from the [1001 Genomes](https://1001genomes.org/) data centre. Open it over the chromosome 4 inversion with the SyRI rows, ordered by admixture group: ```json session config=https://jbrowse.org/demos/arabidopsis_pangenome/config.json { "defaultSession": { "name": "26 accessions against TAIR10, chromosome 4", "views": [ { "type": "LinearGenomeView", "assembly": "TAIR10", "loc": "Chr4:1-4,000,000", "tracks": [ { "trackId": "syri_regions_on_TAIR10", "type": "LinearMultiRowFeatureDisplay", "height": 644 } ] } ] } } ```
The hosted demo also carries the 1135-accession Fst scan, the 1001 Genomes SNPs and a minigraph pangenome of the same genomes, all built by [`build_arabidopsis_pangenome.sh`](https://github.com/GMOD/jbrowse-components/blob/main/scripts/build_arabidopsis_pangenome.sh). [](https://jbrowse.org/jb2/docs/tutorials/pangenome_prepare_graph) turns a graph of your own into the files the pangenome's tracks read. ## Check it against syri.out The largest inverted region of the Col-0 and Ler run, straight from SyRI's table: ```bash awk -F'\t' '$11=="INV" {print $3-$2+1, $1, $2, $3}' Col-0_Ler.syri.out | sort -nr | head -1 ``` It is 1,170,016 bp on `Chr4`, from 1,612,606 to 2,782,621, the interval the crossed ribbon spans and the orange block on the Ler row. ## Reproduce it end to end The script fetches the six assemblies, runs SyRI on each accession against Col-0 and against the one above it, converts each table and writes the config; see [Prerequisites](#prerequisites). ```bash curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_syri_synteny.sh bash build_syri_synteny.sh ``` For genomes of your own, pass a rows file after the output directory: - **One ` [accession]` line per genome**, in stack order, the reference first - **A chromosome-level `.fa` in the output directory** is used as it is, so a row that has one needs no accession - **Homologous chromosomes are spelled alike** in every FASTA, since SyRI pairs them by name ```bash bash build_syri_synteny.sh my_syri rows.txt ``` ## See also - [](https://jbrowse.org/jb2/docs/tutorials/synteny_visualization) - [](https://jbrowse.org/jb2/docs/tutorials/allvsall_synteny) - [](https://jbrowse.org/jb2/docs/tutorials/multiway_synteny_grape_peach_cacao) - [](https://jbrowse.org/jb2/docs/tutorials/odp_linkage_groups_synteny) - [](https://jbrowse.org/jb2/docs/tutorials/hg002_haplotypes) - [](https://jbrowse.org/jb2/docs/tutorials/alu_age) ## References - Goel M, Sun H, Jiao WB, Schneeberger K. SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies. Genome Biol (2019). https://doi.org/10.1186/s13059-019-1911-0 - Goel M, Schneeberger K. plotsr: visualizing structural similarities and rearrangements between multiple genomes. Bioinformatics (2022). https://doi.org/10.1093/bioinformatics/btac196 - Jiao WB, Schneeberger K. Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. Nat Commun (2020). https://doi.org/10.1038/s41467-020-14779-y - Igolkina AA, et al. A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism. Nat Genet (2025). https://doi.org/10.1038/s41588-025-02293-0 - Zapata L, et al. Chromosome-level assembly of Arabidopsis thaliana Ler reveals the extent of translocation and inversion polymorphisms. PNAS (2016). https://doi.org/10.1073/pnas.1607532113 - Fransz PF, et al. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell (2000). https://doi.org/10.1016/S0092-8674(00)80670-5