# Synteny from MCScan anchors (grape, peach) **TL;DR:** a pairwise [jcvi](https://github.com/tanghaibao/jcvi) MCScan run writes two files that JBrowse loads as separate synteny tracks: `.anchors` (one orthologous gene pair per line, via `MCScanAnchorsAdapter`) and `.anchors.simple` (one synteny block per line, via `MCScanSimpleAnchorsAdapter`). Both pair genes by name, so each also needs a BED per genome mapping gene ids to coordinates. ## Prerequisites - [jcvi](https://github.com/tanghaibao/jcvi) with the [LAST](https://gitlab.com/mcfrith/last) aligner - Or, in place of jcvi, an existing [MCScanX](https://github.com/wyp1125/MCScanX) run: [converting one](#coming-from-mcscanx) needs only python3 - `samtools` - htslib (`bgzip`, `tabix`) - `wget` - `node`, for the [JBrowse CLI](https://jbrowse.org/jb2-staging/docs/cli) - A running JBrowse instance (the [web quickstart](https://jbrowse.org/jb2-staging/docs/quickstart_web) or the [desktop quickstart](https://jbrowse.org/jb2-staging/docs/quickstart_desktop)) On Debian/Ubuntu, `apt install samtools tabix wget last-align` covers the aligner and the file tools; jcvi installs with `pip install jcvi` and `node` comes from [nodejs.org](https://nodejs.org/). ## Where the data comes from Grape ([Jaillon et al. 2007](https://doi.org/10.1038/nature06148)) and peach genomes and gene annotations, Ensembl Plants release 58. - grape (Vitis_vinifera, PN40024.v4) genome and CDS FASTA: http://ftp.ensemblgenomes.org/pub/plants/release-58/fasta/vitis_vinifera/ - grape gene annotation: http://ftp.ensemblgenomes.org/pub/plants/release-58/gff3/vitis_vinifera/ - peach (Prunus_persica, Prunus_persica_NCBIv2) genome and CDS FASTA: http://ftp.ensemblgenomes.org/pub/plants/release-58/fasta/prunus_persica/ - peach gene annotation: http://ftp.ensemblgenomes.org/pub/plants/release-58/gff3/prunus_persica/ ## What MCScan compares MCScan works through the two genomes' gene annotations, which finds synteny between species too divergent to line up base by base with [minimap2](https://jbrowse.org/jb2-staging/docs/tutorials/synteny_visualization). An anchor is a gene pair, so there is no CIGAR and nothing to draw below the level of a gene. For three or more genomes from one MCScan run, see [ortholog tables](https://jbrowse.org/jb2-staging/docs/tutorials/multiway_synteny_grape_peach_cacao), which loads a `.blocks` table with one track backing every band. ## What `.anchors` and `.anchors.simple` hold `.anchors` is the gene-pair level. Each line is one orthologous pair and its alignment score, with `###` separating synteny blocks: ``` ### VIT_201s0011g00070.1 Prupe.1G290900.1 1430 VIT_201s0011g00080.1 Prupe.1G290800.1 446 VIT_201s0011g00090.1 Prupe.1G290700.1 147 ``` `.anchors.simple` 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: ``` VIT_201s0011g00070.1 VIT_201s0011g00910.1 Prupe.1G281700.1 Prupe.1G290900.1 149 - VIT_201s0011g02000.1 VIT_201s0011g02280.2 Prupe.1G345900.1 Prupe.1G348100.1 53 - VIT_201s0011g02300.1 VIT_201s0011g02530.1 Prupe.1G299800.1 Prupe.1G303200.1 39 + ``` The adapter turns those four gene ids into one feature spanning the block on each genome, so `.anchors.simple` draws one ribbon per block where `.anchors` draws one per gene pair. Neither file carries coordinates; the BED files supply them.
### BED files One BED per genome, prepared from its GFF3 before the ortholog run. Only the first six columns are read, and column 4 must match the anchor gene ids byte for byte: ``` chr1 12836 26777 VIT_201s0011g00010.1 0 + chr1 33170 35791 VIT_201s0011g00030.1 0 + ``` Column 1 must use the same reference sequence names as the JBrowse assembly. Which mismatches are loud and which are silent is the [adapters' own gotcha](https://jbrowse.org/jb2-staging/docs/config_guides/synteny_track#gene-ids-are-the-join-in-the-mcscan-adapters). The one that bites this pipeline is jcvi stripping isoform suffixes unless run with `--no_strip_names`, which the [script](#reproduce-it-end-to-end) passes: strip them on one side only and no row resolves. ## Producing the data One jcvi command writes both anchor files and the BEDs are prepared from each GFF3 beforehand: ```bash python -m jcvi.formats.gff bed --type=mRNA --key=transcript_id \ --primary_only grape.gff3.gz -o grape.bed python -m jcvi.formats.gff bed --type=mRNA --key=transcript_id \ --primary_only peach.gff3.gz -o peach.bed python -m jcvi.formats.fasta format grape.cds.fa.gz grape.cds python -m jcvi.formats.fasta format peach.cds.fa.gz peach.cds python -m jcvi.compara.catalog ortholog --no_strip_names grape peach ``` That leaves `grape.peach.anchors` and `grape.peach.anchors.simple` in the working directory. The adapters read anchors and BED files plain or gzipped. ## Loading both 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): ```json addtrack { "type": "SyntenyTrack", "trackId": "grape_peach_anchors", "name": "Grape peach synteny (MCScan, anchors)", "assemblyNames": ["grape", "peach"], "adapter": { "type": "MCScanAnchorsAdapter", "uri": "grape.peach.anchors.gz", "bed1": "grape.bed.gz", "bed2": "peach.bed.gz", "assemblyNames": ["grape", "peach"] } } ``` The simple-anchors track is the same shape with the adapter type and file swapped: ```json addtrack { "type": "SyntenyTrack", "trackId": "grape_peach_anchors_simple", "name": "Grape peach synteny (MCScan, simple anchors)", "assemblyNames": ["grape", "peach"], "adapter": { "type": "MCScanSimpleAnchorsAdapter", "uri": "grape.peach.anchors.simple.gz", "bed1": "grape.bed.gz", "bed2": "peach.bed.gz", "assemblyNames": ["grape", "peach"] } } ``` Both BEDs are `jbrowse add-track` flags, which is the CLI tab on each block above: `--bed1` and `--bed2` beside the anchors file, and `--load copy` copies all three into the config's directory. Both adapters read the whole file into memory, which suits MCScan's scale. PAF's indexed [PIF](https://jbrowse.org/jb2-staging/docs/config_guides/synteny_track) has no MCScan equivalent. ## Both tracks in one synteny view The two tracks describe the same run at different granularity. Add a linear synteny view (**Add → Linear synteny view**), pick peach and grape, and turn on both.
The block track is drawn here as an `LGVSyntenyDisplay`: a synteny track in an ordinary linear genome view row, drawn as features. No `add-track` flag covers the `displays` array, so this goes in with `jbrowse add-track-json`, which copies no data files. ```json { "type": "SyntenyTrack", "trackId": "grape_peach_anchors_simple", "name": "Grape peach synteny (MCScan, simple anchors)", "assemblyNames": ["grape", "peach"], "adapter": { "type": "MCScanSimpleAnchorsAdapter", "uri": "grape.peach.anchors.simple.gz", "bed1": "grape.bed.gz", "bed2": "peach.bed.gz", "assemblyNames": ["grape", "peach"] }, "displays": [ { "type": "LGVSyntenyDisplay", "displayId": "grape_peach_anchors_simple-LGVSyntenyDisplay", "height": 60 } ] } ``` Read the two together: a bar says a block is there and which way round it runs, and the ribbons above it say whether the genes inside hold their order. ## What an anchor looks like up close Zoom to one block with both gene tracks on and set to **Show only genes**, and the unit the file is made of is on screen.
MCScan anchors the genes it could pair confidently, so most genes in these windows carry no ribbon. Zooming further widens the ribbons, since the file says only which gene pairs with which. ## The same anchors as a dotplot Either track also loads in a dotplot (**Add → Dotplot view**), where a gene pair is one point and a block is a run of them. The axes start in each assembly's index order, which scatters the runs; **Re-order chromosomes** sorts the vertical axis to follow the horizontal one, using the alignments themselves.