31:T564,Across 258 species of plant, including mosses, liverworts, and flowering plants, we assembled the mitochondrial genomes. We then ran `mumemto` across all species for which the genome was assembled into a single contig/unitig. This meant we were able to ignore the graph-like structure and focus purely on synteny.

  
  mapfile -t fasta_paths < <(awk '$4 == "moss" {print "../../annotation/data/fastas/"$1}' single_unitigs_tax.tsv)
  
  echo "Running mumemto on the following fasta files:"
  for fasta in "\${fasta_paths[@]}"; do
    echo "$fasta"
  done
  
   /software/team301/mumemto/build/mumemto "\${fasta_paths[@]}" \
   -l 15 \
   -f 0 \
   -k -1 \
   -F 0 \
   -o ../data_mumemto/single_unitigs

Then with a python script:


  with open("../data_mumemto/single_unitigs.mems") as f:
    # mems_to_long_tsv.py
    for mem_id, line in enumerate(f):
        if not line.strip():
            continue
        fields = line.strip().split()
        length = int(fields[0])
        positions = list(map(int, fields[1].split(",")))
        genome_ids = list(map(int, fields[2].split(",")))
        strands = fields[3].split(",")

        for gid, pos, strand in zip(genome_ids, positions, strands):
            print(f"{mem_id}\t{gid}\t{pos}\t{strand}\t{length}")

And saved the output of that to what you see in this notebook.32:T545,idToSpecies = ({ 0: "Antitrichia curtipendula", 1: "Bryoerythrophyllum caledonicum", 2: "Calliergon cordifolium", 3: "Cratoneuron filicinum", 4: "Draba incana", 5: "Gnaphalium uliginosum", 6: "Herbertus hutchinsiae", 7: "Heterocladium heteropterum", 8: "Humulus lupulus", 9: "Hyocomium armoricum", 10: "Hypnum cupressiforme", 11: "Ilex aquifolium", 12: "Isopterygiella pulchella", 13: "Isothecium myosuroides", 14: "Lemna minuta", 15: "Lepidium didymum", 16: "Logfia minima", 17: "Lunularia cruciata", 18: "Matricaria chamomilla", 19: "Misopates orontium", 20: "Myrica gale", 21: "Neckera pumila", 22: "Plagiothecium denticulatum", 23: "Polygonum aviculare", 24: "Polytrichastrum sexangulare", 25: "Polytrichum commune", 26: "Polytrichum formosum", 27: "Populus tremula", 28: "Pseudoscleropodium purum", 29: "Rhynchostegiella tenella", 30: "Rhynchostegium megapolitanum", 31: "Rhytidiadelphus loreus", 32: "Rosa agrestis", 33: "Rosa rugosa", 34: "Scutellaria galericulata", 35: "Sphagnum contortum", 36: "Sphagnum girgensohnii", 37: "Sphagnum tenellum", 38: "Straminergon stramineum", 39: "Tanacetum vulgare", 40: "Thuidium tamariscinum", 41: "Ulmus glabra", 42: "Ulota crispa", 43: "Umbilicus rupestris", 44: "Vaccinium vitis idaea", 45: "Viola odorata" })33:[{"id":"17cd694ec10ed87c732126aeb05850798000e0fe48df6facd80b52a8ce8567286044af4a770ff104cd0558b1faa37fca20f089deb6ffc4ea59fad32e1962766f","href":"https://static.observableusercontent.com/files/17cd694ec10ed87c732126aeb05850798000e0fe48df6facd80b52a8ce8567286044af4a770ff104cd0558b1faa37fca20f089deb6ffc4ea59fad32e1962766f","name":"single_unitig_mems.tsv","type":"text/tab-separated-values","lastModified":1753262623086.374,"size":546519},{"id":"880f4136e6c4bd113a9173cb9a38170dd48d5123d8cc9bc20a55d74212bcdabd616e1ba93f4a0483d5852c776b73d6296100f46da8f5785cd105ccfc64a930c8","href":"https://static.observableusercontent.com/files/880f4136e6c4bd113a9173cb9a38170dd48d5123d8cc9bc20a55d74212bcdabd616e1ba93f4a0483d5852c776b73d6296100f46da8f5785cd105ccfc64a930c8","name":"single_unitig_mems@1.tsv","type":"text/tab-separated-values","lastModified":1753283702139.56,"size":549859},{"id":"c9028e4de4feec3366d53245df8dc39dc5f8c35db89313c0f0741bb36bb297905eae74ac2e7984f9dadb35139db69f4ec2522fb72a8dd718a9e174fb15024016","href":"https://static.observableusercontent.com/files/c9028e4de4feec3366d53245df8dc39dc5f8c35db89313c0f0741bb36bb297905eae74ac2e7984f9dadb35139db69f4ec2522fb72a8dd718a9e174fb15024016","name":"single_unitig_mems_20.tsv","type":"text/tab-separated-values","lastModified":1753285957335.157,"size":136104}] 2f:{"title":"Synteny across MEMs","cells":[{"id":0,"value":"# Synteny across MEMs","pinned":false,"hidden":false,"mode":"md"},{"id":325,"value":"$31","pinned":false,"hidden":false,"mode":"md"},{"id":453,"value":"It seems that flowering plants are pretty non-syntenic. Mosses seem more so, limited to large inversions mainly.","pinned":false,"hidden":false,"mode":"md"},{"id":323,"value":"## Flowering plants","pinned":false,"hidden":false,"mode":"md"},{"id":124,"value":"Plot.plot({\n width: 900,\n height: 1000,\n marginLeft: 200,\n x: { label: \"Proportion along mitogenome\" },\n y: {\n label: \"Genome ID\",\n domain: flspp\n },\n marks: [\n Plot.lineY(\n // make sure vertical order is consistent\n standardizedData\n .map((d) => ({\n ...d,\n y: flsppIndex.get(d.genome_id) // vertical order\n }))\n .sort((a, b) => a.y - b.y), // ensure vertical connection order,\n {\n x: \"relative_position\",\n y: \"genome_id\",\n stroke: \"mem_id\",\n curve: \"linear\",\n strokeOpacity: 0.3\n }\n )\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":377,"value":"## Moss species","pinned":false,"hidden":false,"mode":"md"},{"id":379,"value":"Plot.plot({\n width: 900,\n height: 1000,\n marginLeft: 200,\n x: { label: \"Proportion along mitogenome\", domain: [0, 1] },\n y: {\n label: \"Genome ID\",\n domain: mossspp\n },\n marks: [\n Plot.lineY(\n // make sure vertical order is consistent\n standardizedData\n .map((d) => ({\n ...d,\n y: mosssppIndex.get(d.genome_id) // vertical order\n }))\n .sort((a, b) => a.y - b.y), // ensure vertical connection order,\n {\n x: \"relative_position\",\n y: \"genome_id\",\n stroke: \"mem_id\",\n curve: \"linear\",\n strokeOpacity: 0.3\n }\n )\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":496,"value":"## Liverworts","pinned":false,"hidden":false,"mode":"md"},{"id":421,"value":"Plot.plot({\n width: 900,\n height: 400,\n marginLeft: 200,\n x: { label: \"Position\", domain: [0, 200000] },\n y: {\n label: \"Genome ID\",\n domain: livspp\n },\n marks: [\n Plot.lineY(\n // make sure vertical order is consistent\n sum3\n .map((d) => ({\n ...d,\n y: livsppIndex.get(d.genome_id) // vertical order\n }))\n .sort((a, b) => a.y - b.y), // ensure vertical connection order,\n {\n x: \"position\",\n y: \"genome_id\",\n stroke: \"mem_id\",\n curve: \"linear\",\n strokeOpacity: 0.3\n }\n )\n ]\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":329,"value":"## Data","pinned":false,"hidden":false,"mode":"md"},{"id":478,"value":"standardizedData = sum3.map((d) => {\n const genomeLength = genomeLengths.get(d.genome_id);\n const relPos = genomeLength ? d.position / genomeLength : null;\n\n return {\n ...d,\n relative_position: relPos\n };\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":474,"value":"genomeLengths = d3.rollup(\n sum3,\n (v) => d3.max(v, (d) => d.position + (d.length ?? 0)),\n (d) => d.genome_id\n)","pinned":false,"hidden":false,"mode":"ojs"},{"id":334,"value":"To get vertical ordering of MEMs, we need a species map.","pinned":false,"hidden":false,"mode":"md"},{"id":246,"value":"flsppIndex = new Map(flspp.map((name, i) => [name, i]))","pinned":false,"hidden":false,"mode":"ojs"},{"id":385,"value":"mosssppIndex = new Map(mossspp.map((name, i) => [name, i]))","pinned":false,"hidden":false,"mode":"ojs"},{"id":412,"value":"livsppIndex = new Map(livspp.map((name, i) => [name, i]))","pinned":false,"hidden":false,"mode":"ojs"},{"id":336,"value":"After running `mumemto`, the names of the species are the same as the indexes of the assemblies given to the program. We can convert to species names here.","pinned":false,"hidden":false,"mode":"md"},{"id":99,"value":"$32","pinned":false,"hidden":false,"mode":"ojs"},{"id":339,"value":"Format the data properly, and convert types.","pinned":false,"hidden":false,"mode":"md"},{"id":73,"value":"// Convert values to correct types\nsum3 = {\n return sum2.map((d) => {\n return {\n mem_id: +d[0],\n genome_id: idToSpecies[d[1]],\n position: +d[2],\n strand: d[3],\n length: +d[4]\n };\n });\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":60,"value":"sum2 = d3.tsvParseRows(sum)","pinned":false,"hidden":false,"mode":"ojs"},{"id":91,"value":"// sum = FileAttachment(\"single_unitig_mems@1.tsv\").text()\nsum = FileAttachment(\"single_unitig_mems@1.tsv\").text()","pinned":false,"hidden":false,"mode":"ojs"},{"id":225,"value":"flspp = [\n // // asterids, aquifoliales\n \"Ilex aquifolium\",\n // asterales\n \"Logfia minima\",\n \"Matricaria chamomilla\",\n \"Tanacetum vulgare\",\n \"Gnaphalium uliginosum\",\n // asterids, lamiales\n \"Misopates orontium\",\n \"Scutellaria galericulata\",\n // rosids, fagales\n \"Myrica gale\",\n \"Polygonum aviculare\",\n // rosids, malphigiales\n \"Viola odorata\",\n \"Populus tremula\",\n // rosids, rosales\n \"Humulus lupulus\",\n \"Rosa agrestis\",\n \"Rosa rugosa\",\n \"Ulmus glabra\",\n // saxifragales\n \"Umbilicus rupestris\",\n // ericales\n \"Vaccinium vitis idaea\",\n // brassicales\n \"Lepidium didymum\",\n \"Draba incana\",\n // monocot\n \"Lemna minuta\"\n]","pinned":false,"hidden":false,"mode":"ojs"},{"id":371,"value":"mossspp = [\n \"Antitrichia curtipendula\",\n \"Bryoerythrophyllum caledonicum\",\n \"Calliergon cordifolium\",\n \"Cratoneuron filicinum\",\n \"Heterocladium heteropterum\",\n \"Hyocomium armoricum\",\n \"Hypnum cupressiforme\",\n \"Isopterygiella pulchella\",\n \"Isothecium myosuroides\",\n \"Neckera pumila\",\n \"Plagiothecium denticulatum\",\n \"Polytrichastrum sexangulare\",\n \"Polytrichum commune\",\n \"Polytrichum formosum\",\n \"Pseudoscleropodium purum\",\n \"Rhynchostegiella tenella\",\n \"Rhynchostegium megapolitanum\",\n \"Rhytidiadelphus loreus\",\n \"Sphagnum contortum\",\n \"Sphagnum girgensohnii\",\n \"Sphagnum tenellum\",\n \"Straminergon stramineum\",\n \"Thuidium tamariscinum\",\n \"Ulota crispa\"\n]","pinned":false,"hidden":false,"mode":"ojs"},{"id":374,"value":"livspp = [\"Herbertus hutchinsiae\", \"Lunularia cruciata\"]","pinned":false,"hidden":false,"mode":"ojs"},{"id":501,"value":"","pinned":false,"hidden":false,"mode":"html"}],"files":"$W33","stdlib":"1","titling":"auto"}