- Quick start
- Introduction
- Installation
- Subcommands
- Phylogenomics pipeline
- Input formats
- Output formats
- Citation
git clone https://github.com/zhangrengang/orthoindex.git
cd orthoindex
# install
conda env create -f OrthoIndex.yaml
conda activate OrthoIndex
python3 setup.py install
# test
cd example_data/
sh example.sh
# example.sh:
# dot plots
# A
soi dotplot -s Populus_trichocarpa-Salix_dunnii.collinearity.gz \
-g Populus_trichocarpa-Salix_dunnii.gff.gz -c Populus_trichocarpa-Salix_dunnii.ctl \
--kaks Populus_trichocarpa-Salix_dunnii.collinearity.ks.gz \
--xlabel '$Populus\ trichocarpa$' --ylabel '$Salix\ dunnii$' \
--ks-hist --max-ks 1.5 -o Populus_trichocarpa-Salix_dunnii \
--plot-ploidy --gene-axis --number-plots
# B
soi dotplot -s Populus_trichocarpa-Salix_dunnii.orthologs.gz \
-g Populus_trichocarpa-Salix_dunnii.gff.gz -c Populus_trichocarpa-Salix_dunnii.ctl \
--kaks Populus_trichocarpa-Salix_dunnii.collinearity.ks.gz \
--xlabel '$Populus\ trichocarpa$' --ylabel '$Salix\ dunnii$' \
--ks-hist --max-ks 1.5 -o Populus_trichocarpa-Salix_dunnii.o \
--plot-ploidy --gene-axis --number-plots \
--homology # homology input
# C
soi dotplot -s Populus_trichocarpa-Salix_dunnii.collinearity.gz \
-g Populus_trichocarpa-Salix_dunnii.gff.gz -c Populus_trichocarpa-Salix_dunnii.ctl \
--xlabel '$Populus\ trichocarpa$' --ylabel '$Salix\ dunnii$' \
--ks-hist -o Populus_trichocarpa-Salix_dunnii.io \
--plot-ploidy --gene-axis --number-plots \
--ofdir OrthoFinder/OrthoFinder/Results_*/ --of-color # coloring by Orthology Index
# D
soi dotplot -s Populus_trichocarpa-Salix_dunnii.collinearity.gz \
-g Populus_trichocarpa-Salix_dunnii.gff.gz -c Populus_trichocarpa-Salix_dunnii.ctl \
--kaks Populus_trichocarpa-Salix_dunnii.collinearity.ks.gz \
--xlabel '$Populus\ trichocarpa$' --ylabel '$Salix\ dunnii$' \
--ks-hist --max-ks 1.5 -o Populus_trichocarpa-Salix_dunnii.io \
--plot-ploidy --gene-axis --number-plots \
--ofdir OrthoFinder/OrthoFinder/Results_*/ --of-ratio 0.6 # filtering by Orthology Index
# filter orthologous synteny
soi filter -s Populus_trichocarpa-Salix_dunnii.collinearity.gz -o OrthoFinder/OrthoFinder/Results_*/ \
-c 0.6 > Populus_trichocarpa-Salix_dunnii.collinearity.ortho.test
# or (alter input format)
soi filter -s Populus_trichocarpa-Salix_dunnii.collinearity.gz -o Populus_trichocarpa-Salix_dunnii.orthologs.gz \
-c 0.6 > Populus_trichocarpa-Salix_dunnii.collinearity.ortho.test
# compare with the expected output: no output via `diff`
diff Populus_trichocarpa-Salix_dunnii.collinearity.ortho Populus_trichocarpa-Salix_dunnii.collinearity.ortho.test
Note: If you want to run the full phylogenomic pipeline of SOI,
GENE ID is needed to label with SPECIES ID (e.g. Angelica_sinensis|AS01G00001) for compatibility.
See details how to prepare the data.
Figure. The Orthology Index in identifying orthologous synteny: a typical case.
A) Ks-colored dot plots showing synteny detected by WGDI,
with an observable distinction of three categories of syntenic blocks derived from three evolutionary events
(three peaks: Ks ≈ 1.5, Ks ≈ 0.27, and Ks ≈ 0.13).
B) Ks-colored dot plots illustrating orthology inferred by OrthoFinder2, with an observable high proportion of hidden out-paralogs (Ks ≈ 0.27).
C) Orthology Index (OI)-colored dot plots: integrating synteny (A) and orthology (B),
with polarized and scalable distinction of three categories of syntenic blocks
(three peaks: OI ≈ 0, OI ≈ 0.1, and OI ≈ 0.9).
D) Ks-colored dot plots of synteny after applying an OI cutoff of 0.6,
with clean 1:1 orthology as expected from the evolutionary history.
A-D are plotted using the dotplot subcommand with four subplots:
a) dot plots with colored by Ks or OI (x-axis and y-axis, chromosomes of the two genomes;
a dot indicates a homologous gene pair between the two genomes),
b) histogram (with the same color map as the dot plots) of Ks or OI
(x-axis, Ks or OI; y-axis, number of homologous gene pairs),
c-d) synteny depth (relative ploidy) derived from 50-gene windows (x-axis, synteny depth; y-axis, number of windows).
Orthology Index (OrthoIndex or OI) incorporates algorithmic advances of two methods (orthology inference and synteny detection), to determine the orthology of a syntenic block. It is straightforward, representing the proportion of orthologous gene pairs within a syntenic block.
You can install the environment and the lasest verion using conda or mamba:
git clone https://github.com/zhangrengang/orthoindex.git
cd orthoindex
conda env create -f OrthoIndex.yaml
conda activate OrthoIndex
python3 setup.py install
soi -h
Alternatviely, the released version can by installed through conda or mamba:
mamba create -n OrthoIndex
mamba install -n OrthoIndex -c mouseking9 -c conda-forge -c bioconda orthoindex
mamba activate OrthoIndex
soi -h
To use the container, you need to have installed Apptainer or Singularity. Then you can download the container image and run:
apptainer remote add --no-login SylabsCloud cloud.sylabs.io
apptainer remote use SylabsCloud
apptainer pull orthoindex.sif library://shang-hongyun/collection/centos8dock-orthoindex.sif:1.0
./orthoindex.sif soi -h
The image can be found here.
$ soi -h
usage: soi [-h] {dotplot,filter,cluster,outgroup,phylo,stats} ...
Play with Orthology Index
positional arguments:
{dotplot,filter,cluster,outgroup,phylo,stats}
sub-command help
dotplot Generate colored dot plots
filter Filter synteny with Orthology Index (standard output)
cluster Cluster syntenic orthogroups (SOGs)
outgroup Add outgroups for SOGs from synteny
phylo Build gene trees from SOGs
stats Make statistics of SOGs for phylogeny
optional arguments:
-h, --help show this help message and exit
The subcommand filter filters orthologous blocks with a default minimum index of 0.6:
$ soi filter -h
usage: soi filter [-h] -s [FILE [FILE ...]] -o [FOLDER/FILE [FOLDER/FILE ...]] [-c FLOAT] [-upper FLOAT] [-n INT]
optional arguments:
-h, --help show this help message and exit
-s [FILE [FILE ...]], -synteny [FILE [FILE ...]]
Collinearity files output from MCscanX, WGDI, or MCscan/JCVI. [required]
-o [FOLDER/FILE [FOLDER/FILE ...]], -orthology [FOLDER/FILE [FOLDER/FILE ...]]
Orthologues output from OrthoFinder (folder), or OrthoMCL (file). [required]
-c FLOAT, -cutoff FLOAT
Cutoff (lower limit) of Orthology Index [default=0.6]
-upper FLOAT Upper limit of Orthology Index [default=1]
-n INT, -min_n INT Minimum gene number in a block [default=0]
Usage examples:
# from outputs of WGDI and OrthoFinder
soi filter -s wgdi/*.collinearity -o OrthoFinder/OrthoFinder/Result*/ > collinearity.ortho
# from outputs of MCscanX and OrthoMCL
soi filter -s mcscanx/*.collinearity -o pairs/orthologs.txt > collinearity.ortho
# from a list file and increase the cutoff
ls wgdi/*.collinearity > collinearity.list
soi filter -s collinearity.list -o OrthoFinder/OrthoFinder/Result*/ -c 0.7 > collinearity.ortho
# filter a paralogous peak
soi filter -s wgdi/*.collinearity -o OrthoFinder/OrthoFinder/Result*/ -c 0.05 -upper 0.4 > collinearity.para
The subcommand ‘cluster’ groups orthologous syntenic genes into syntenic orthogroups (SOGs), through constructing an orthologous syntenic graph and applying the Markov Cluster (MCL) algorithm to perform graph clustering and break weak links.
$ soi cluster -h
usage: soi cluster [-h] -s [FILE [FILE ...]] [-o [FOLDER/FILE [FOLDER/FILE ...]]] [-I FLOAT] [-outgroup [TAXON/FILE [TAXON/FILE ...]]] [-ingroup [TAXON/FILE [TAXON/FILE ...]]]
[-prefix OUTPRE]
optional arguments:
-h, --help show this help message and exit
-s [FILE [FILE ...]], -synteny [FILE [FILE ...]]
Collinearity files from `filter` sub-command. [required]
-o [FOLDER/FILE [FOLDER/FILE ...]], -orthology [FOLDER/FILE [FOLDER/FILE ...]]
Orthologues output from OrthoFinder (folder), or OrthoMCL (file). This will use Orthology Index as weight for MCL [default=None]
-I FLOAT, -inflation FLOAT
Inflation for MCL (varying this parameter affects granularity) [default=1.5]
-outgroup [TAXON/FILE [TAXON/FILE ...]]
Outgroups to exclude from orthogroups (prior to `-ingroup`) [default=None]
-ingroup [TAXON/FILE [TAXON/FILE ...]]
Ingroups that are only included [default=None]
-prefix OUTPRE Output prefix [default=cluster]
Usage examples:
# all species to include
soi cluster -s collinearity.ortho -prefix cluster
# exclude outgroup species that do not share the INGROUP-specific WGD event
soi cluster -s collinearity.ortho -outgroup XXX YYY
The defualt output file is cluster.mcl, with the orthogroup format of legacy OrthoMCL.
The subcommand ‘outgroup’ retrieves syntenic orthologs from outgroups that lack WGDs shared with ingroups.
$ soi outgroup -h
usage: soi outgroup [-h] -s [FILE [FILE ...]] -og FILE -outgroup [TAXON [TAXON ...]] [-cutoff FLOAT]
optional arguments:
-h, --help show this help message and exit
-s [FILE [FILE ...]], -synteny [FILE [FILE ...]]
Collinearity files from `filter` sub-command. [required]
-og FILE, -orthogroup FILE
Orthogroups output from `cluster` sub-command. [required]
-outgroup [TAXON [TAXON ...]]
Outgroups to include to orthogroups [required]
-cutoff FLOAT Cutoff (lower limit) of links to outgroup genes [default=0.2]
Usage examples:
# If outgroups are excluded in the last `cluster` step:
soi outgroup -s collinearity.ortho -og cluster.mcl -outgroup XXX YYY > cluster.mcl.plus
The subcommand ‘phylo’ reconstructs multi-copy or single-copy gene trees, by aligning protein sequences with MAFFT v7.481 (Standley and Katoh 2013), converting protein alignment to codon alignment with PAL2NAL v14 (Suyama et al. 2006), trimming alignments with trimAl v1.2 (Capella-Gutierrez et al. 2009) (parameter: -automated1) and reconstructing maximum-likelihood trees with IQ-TREE v2.2.0.3 (Minh et al. 2020).
$ soi phylo -h
usage: soi phylo [-h] -og FILE -pep FILE [-cds FILE] [-both] [-fmt STR] [-root [TAXON [TAXON ...]]] [-pre STR] [-mm FLOAT] [-mc INT] [-sc] [-ss FILE] [-concat] [-p INT] [-tmp FOLDER]
[-clean]
optional arguments:
-h, --help show this help message and exit
-og FILE, -orthogroup FILE
Orthogroups output from `cluster` or `outgroup` sub-commands. [required]
-pep FILE Protein fasta file. [required]
-cds FILE CDS fasta file. [default=None]
-both To use both CDS and PEP to build gene trees. [default: only CDS when `-cds` is true]
-fmt STR Format of `-orthogroup` input. [default=orthomcl]
-root [TAXON [TAXON ...]], -outgroup [TAXON [TAXON ...]]
Outgroups to root gene trees [default=None]
-pre STR, -prefix STR
Output prefix. [default=sog]
-mm FLOAT, -max_missing FLOAT
To allow maximum ratio of missing species. [default=0.4]
-mc INT, -max_copies INT
To limit a common maximum copy number for every species. [default=6]
-sc, -singlecopy Only retrieve singlecopy genes (=`-max_copies 1`). [default=None]
-ss FILE, -spsd FILE To limit a specific copy number for each species (format: 'TAXON<tab>NUMBER'). [default=None]
-concat To concatenate alignments for tools such as IQTREE (valid when `-singlecopy` is true). [default=None]
-p INT, -ncpu INT Number of processors. [default=20]
-tmp FOLDER, -tmpdir FOLDER
Temporary folder. [default=./tmp/]
-clean Cleanup temporary folder. [default=None]
Usage examples:
# output multi-copy gene trees of both protein and CDS(-both); rooted with grape (-root)
soi phylo -og cluster.mcl.plus -pep pep.faa -cds cds.fa -both -root Vitis_vinifera -pre mc-sog -p 80
# output single-copy gene trees (-sc) and concatenated alignments (-concat) of both protein and CDS (-both); rooted with grape (-root)
soi phylo -og cluster.mcl.plus -pep pep.faa -cds cds.fa -both -root Vitis_vinifera -pre sc-sog -sc -concat -p 80
# output multi-copy gene trees of protein, allowing up to 50% taxa missing
soi phylo -og cluster.mcl.plus -pep pep.faa -mm 0.5
The subcommand dotplot enables visualization and evaluation of synteny,
with colored by the Orthology Index or Ks values.
$ soi dotplot -h
usage: soi dotplot [-h] -s FILE [FILE ...] -g FILE -c FILE [-o STR] [--format FORMAT] [--homology] [--cluster] [--diagonal] [--gene-axis] [--number-plots] [--min-block INT]
[--min-same-block INT] [--xlabel XLABEL] [--ylabel YLABEL] [--figsize NUM] [--fontsize NUM] [--dotsize NUM] [--ofdir FOLDER/FILE [FOLDER/FILE ...]] [--of-ratio FLOAT]
[--of-color] [--kaks FILE] [--ks-hist] [--max-ks Ks] [--ks-cmap Ks [Ks ...]] [--ks-step Ks] [--use-median] [--method STR] [--lower-ks Ks] [--upper-ks Ks]
[--plot-ploidy] [--window_size INT] [--window_step INT] [--min_block INT] [--max_distance INT] [--max_ploidy INT] [--min_overlap FLOAT] [--color COLOR]
[--edgecolor COLOR]
optional arguments:
-h, --help show this help message and exit
-s FILE [FILE ...] syntenic block file (*.collinearity, output of MCSCANX/WGDI)
-g FILE gene annotation gff file (*.gff, one of MCSCANX/WGDI input)
-c FILE chromosomes config file (*.ctl, same format as MCSCANX dotplotter)
-o STR output file prefix. [default: the same as `-c`]
--format FORMAT output figure format [default=['pdf', 'png']]
--homology `-s` is in homology format (gene1<tab>gene2). [default=False]
--cluster cluster chromosomes. [default=False]
--diagonal try to put blocks onto the diagonal. [default=False]
--gene-axis use gene as axis instead of base pair. [default=False]
--number-plots number subplots with (a-d). [default=False]
--min-block INT min gene number in a block. [default=None]
--min-same-block INT min gene number in a block on the same chromosome. [default=25]
Art settings:
art settings for plots
--xlabel XLABEL x label for dot plot. [default=None]
--ylabel YLABEL y label for dot plot. [default=None]
--figsize NUM figure size [default=18]
--fontsize NUM font size [default=10]
--dotsize NUM dot size [default=0.8]
Orthology Index filter/color:
filtering or coloring blocks by Orthology Index (prior to Ks color)
--ofdir FOLDER/FILE [FOLDER/FILE ...]
OrthoFinder output folder/ OrthoMCL output pair file. [default=None]
--of-ratio FLOAT Orthology Index cutoff [default=0]
--of-color coloring dots by Orthology Index [default=None]
Ks plot:
options to plot with Ks
--kaks FILE kaks output from KaKs_Calculator/WGDI. [default=None]
--ks-hist plot histogram or not [default=None]
--max-ks Ks max Ks (x limit) [default=1]
--ks-cmap Ks [Ks ...]
color map for Ks. [default=None]
--ks-step Ks Ks step of histogram [default=0.02]
--use-median use median Ks for a block. [default=False]
--method STR Ks calculation method [default=NG86]
--lower-ks Ks lower limit of median Ks. [default=None]
--upper-ks Ks upper limit of median Ks. [default=None]
ploidy plot:
options to plot relative ploidy (synteny depth)
--plot-ploidy plot relative ploidy. [default=False]
--window_size INT window_size. [default=50]
--window_step INT window_step. [default=10]
--min_block INT min genes for a block. [default=10]
--max_distance INT max distance. [default=20]
--max_ploidy INT x limit. [default=10]
--min_overlap FLOAT min overlap. [default=0.4]
--color COLOR bar fill color. [default=None]
--edgecolor COLOR bar edge color. [default=None]
Usage examples: see Quick Start.
See evolution_example for a pipeline of phylogenomics analyses based on Orthology Index.
All the output format of state-of-the-art synteny detectors, including JCVI, MCscanX and WGDI, are supported:
# WGDI -icl (*.collinearity):
# Alignment 1: score=3194 pvalue=0.0265 N=80 Dc1&Lj1 plus
Daucus_carota|DCAR_003996 3506 Lonicera_japonica|Lj1C1189G6 4566 -1
Daucus_carota|DCAR_004004 3514 Lonicera_japonica|Lj1P1192T21 4580 1
Daucus_carota|DCAR_004005 3515 Lonicera_japonica|Lj1P1192T26 4581 1
.....
# MCscanX (*.collinearity):
############### Parameters ###############
# MATCH_SCORE: 50
# ....
## Alignment 28: score=500.0 e_value=1.3e-24 N=11 Ac1&Ah1 plus
28- 0: Ananas_comosus|Aco009515.1 Arabidopsis_thaliana|AT1G72340 0
28- 1: Ananas_comosus|Aco009511.1 Arabidopsis_thaliana|AT1G72360 0
28- 2: Ananas_comosus|Aco009507.1 Arabidopsis_thaliana|AT1G72370 0
28- 3: Ananas_comosus|Aco009502.1 Arabidopsis_thaliana|AT1G72410 0
28- 4: Ananas_comosus|Aco009492.1 Arabidopsis_thaliana|AT1G72480 0
.....
# JCVI (*.anchors):
###
Tetracendron_sinense|Tesin01G0059600 Trochodendron_aralioides|evm.TU.group9.733 1780
Tetracendron_sinense|Tesin01G0060100 Trochodendron_aralioides|evm.TU.group9.725 334
Tetracendron_sinense|Tesin01G0060800 Trochodendron_aralioides|evm.TU.group9.710 868
Tetracendron_sinense|Tesin01G0061600 Trochodendron_aralioides|evm.TU.group9.757 294
Tetracendron_sinense|Tesin01G0062600 Trochodendron_aralioides|evm.TU.group9.777 1400
....
The outputs from OrthoFinder2, OrthoMCL, Proteinortho6, Broccoli, InParanoid, SonicParanoid2 are supported:
# OrthoFinder2 output directory like:
OrthoFinder/OrthoFinder/Results_Jun25/
# OrthoMCL:
Tetracendron_sinense|Tesin01G0059600 Trochodendron_aralioides|evm.TU.group9.733 ...
Tetracendron_sinense|Tesin01G0060100 Trochodendron_aralioides|evm.TU.group9.725
Tetracendron_sinense|Tesin01G0060800 Trochodendron_aralioides|evm.TU.group9.710
...
# SonicParanoid2 output directory via `-o sonicparanoid_output --project-id my_run`:
sonicparanoid_output/runs/my_run/
# InParanoid output directory via `-out-dir ip-output -out-table`:
ip-output/
# or InParanoid output ortholog file via `-out-dir ip-output -out-allPairs`:
ip-output/allPairs
# Proteinortho6 output ortholog file:
*.proteinortho-graph
# Broccoli output ortholog file:
dir_step4/orthologous_pairs.txt
The gff/bed format for JCVI, MCscanX and WGDI are supported:
# gff for WGDI:
Dc1 Daucus_carota|DCAR_000504 20809 26333 + 1 Daucus_carota|DCAR_000504
Dc1 Daucus_carota|DCAR_000505 30205 39120 + 2 Daucus_carota|DCAR_000505
Dc1 Daucus_carota|DCAR_000506 53069 54763 + 3 Daucus_carota|DCAR_000506
Dc1 Daucus_carota|DCAR_000507 56557 60502 - 4 Daucus_carota|DCAR_000507
....
# gff for MCscanX:
Dc1 Daucus_carota|DCAR_000504 20809 26333
Dc1 Daucus_carota|DCAR_000505 30205 39120
Dc1 Daucus_carota|DCAR_000506 53069 54763
Dc1 Daucus_carota|DCAR_000507 56557 60502
....
# bed for JCVI:
Dc1 20809 26333 Daucus_carota|DCAR_000504 0 +
Dc1 30205 39120 Daucus_carota|DCAR_000505 0 +
Dc1 53069 54763 Daucus_carota|DCAR_000506 0 +
....
The outputs from KaKsCalculator and WGDI are supported:
# KaKsCalculator:
Sequence Method Ka Ks Ka/Ks P-Value(Fisher) Length S-Sites N-Sites Fold-Sites(0:2:4) Substitutions S-Substitutions N-Substitutions Fold-S-Substitutions(0:2:4) Fold-N-Substitutions(0:2:4) Divergence-Time Substitution-Rate-Ratio(rTC:rAG:rTA:rCG:rTG:rCA/rCA) GC(1:2:3) ML-Score AICc Akaike-Weight Model
Arabidopsis_thaliana|AT1G29430-Oryza_sativa|LOC_Os09g37470 YN 0.650185 3.49784 0.185882 3.0186e-10 420 106.037 313.963 NA 218 82.1279 135.872 NA NA 1.36913 2.07932:2.07932:1:1:1:1 0.477381(0.467857:0.428571:0.535714) NA NA NA NA
Arabidopsis_thaliana|AT1G29440-Oryza_sativa|LOC_Os09g37420 YN 0.541299 3.27405 0.16533 3.75171e-12 330 78.6813 251.319 NA 161 64.364 96.636 NA NA 1.19287 1.62285:1.62285:1:1:1:1 0.468182(0.431818:0.459091:0.513636) NA NA NA NA
Arabidopsis_thaliana|AT1G29460-Oryza_sativa|LOC_Os09g37410 YN 0.60446 3.48369 0.173511 1.7716e-11 408 104.055 303.945 NA 207 81.5585 125.441 NA NA 1.33877 2.28955:2.28955:1:1:1:1 0.470588(0.452206:0.419118:0.540441) NA NA NA NA
....
# WGDI -ks:
id1 id2 ka_NG86 ks_NG86 ka_YN00 ks_YN00
Angelica_sinensis|AS08G00315 Daucus_carota|DCAR_007041 0.0685 0.3645 0.0717 0.328
Angelica_sinensis|AS01G00334 Daucus_carota|DCAR_027727 0.0871 0.4938 0.0815 0.8313
Angelica_sinensis|ASUnG00186 Daucus_carota|DCAR_004673 0.1858 0.5447 0.1871 0.5516
....
The ctl format for MCscanX (dot_plotter) is supported:
1500
1500
As1,As2,As3,As4,As5,As6,As7,As8,As9,As10,As11 // y
Dc1,Dc2,Dc3,Dc4,Dc5,Dc6,Dc7,Dc8,Dc9 // x
In summary, users may be not needed to preprare additional files for this tool. And other popular format can be supported upon request.
But it is important to label GENE ID with SPECIES ID (e.g. Angelica_sinensis|AS01G00001) (see details in evolution_example).
The output fommat is just the same as the input format.
The output format of cluster and outgroup subcommands is the same as the OrthoMCL output format (legacy format):
SOG3000: Angelica_sinensis|AS08G01493 Angelica_sinensis|AS09G02085 Apium_graveolens|Ag7G00949 Aralia_elata|AE10G00968 Centella_asiatica|evm.TU.Scaffold_1.3269 Coriandrum_sativum|Cs09G02292 Coriandrum_sativum|Cs09G02294 Daucus_carota|DCAR_003880 Daucus_carota|DCAR_007867 Eleutherococcus_senticosus|Ese12G000172 Panax_ginseng|GWHGBEIL036624.1 Panax_ginseng|GWHGBEIL065014.1 Panax_notoginseng|PN028370
SOG3001: Angelica_sinensis|AS08G03434 Angelica_sinensis|AS08G03435 Apium_graveolens|Ag6G02640 Aralia_elata|AE12G02374 Centella_asiatica|evm.TU.Scaffold_7.2677 Coriandrum_sativum|Cs09G00377 Daucus_carota|DCAR_001654 Eleutherococcus_senticosus|Ese19G002246 Panax_ginseng|GWHGBEIL023685.1 Panax_ginseng|GWHGBEIL043114.1 Panax_ginseng|GWHGBEIL043118.1 Panax_ginseng|GWHGBEIL043125.1 Panax_notoginseng|PN013450
SOG3002: Angelica_sinensis|AS10G01791 Apium_graveolens|Ag1G00857 Apium_graveolens|Ag6G02641 Aralia_elata|AE12G02379 Centella_asiatica|evm.TU.Scaffold_7.2680 Coriandrum_sativum|Cs06G01941 Coriandrum_sativum|Cs06G01943 Coriandrum_sativum|Cs09G00381 Daucus_carota|DCAR_001660 Daucus_carota|DCAR_029095 Panax_ginseng|GWHGBEIL023683.1 Panax_ginseng|GWHGBEIL043112.1 Panax_notoginseng|PN013453
...
Zhang RG, Shang HY, Zhou MJ et. al. Robust identification of orthologous synteny with the Orthology Index and its applications in reconstructing the evolutionary history of plant genomes. bioRxiv, 2024 [http://doi.org/10.1101/2024.08.22.609065]