This repository contains the data and code associated with our study on ancestral karyotype reconstruction in angiosperms. It includes genome data for 30+ species, reconstructed ancestral karyotypes, a fusion points database, and step-by-step construction workflows using the WGDI toolkit.
| Directory | Description |
|---|---|
genome/ |
Genome data (gff, lens, cds, pep) for all sampled species |
Karyotype/ |
Reconstructed ancestral karyotypes: AAK, AEK, AMAK, AMK-A |
fusion_points_database/ |
Chromosomal fusion points database — 49 gene sets, each capturing one fusion event observed in an extant species, used to validate ancestral karyotype reconstructions |
AAK_construction/ |
Step-by-step workflow and intermediate files for AAK construction (includes pairwise dotplots) |
figures/ |
Related figures referenced in this repository |
Four ancestral karyotypes are reconstructed and provided in Karyotype/:
| Abbreviation | Full name |
|---|---|
| AAK | Ancestral angiosperm karyotype |
| AMAK | Ancestral Mesangiospermae karyotype |
| AMK-A | Ancestral monocot karyotype (excluding Acoraceae) |
| AEK | Ancestral eudicot karyotype |
Each karyotype folder contains four files:
.ancestor.txt— chromosome-to-color mapping for visualization.gff— gene annotation (location and length).lens— chromosome length and gene count per chromosome.pep.fa— protein sequences
Note: the ancestral gene sets are intended to represent collinearity between ancestral chromosomes, not as comprehensive gene catalogs.
A subset of the species used in this study is listed below (abbreviations match the filenames in genome/). This is a partial list; the full set is documented in genome/readme.md.
| Species | Abbreviation |
|---|---|
| Amborella trichopoda | atr42s |
| Nymphaea colorata | nc476s |
| Brasenia schreberi | bsc1s |
| Illicium verum | ive |
| Liriodendron chinense | lc2s |
| Cinnamomum kanehirae | cm170s |
| Chloranthus sessilifolius | cs471s |
| Aristolochia fimbriata | afi49s |
| Ceratophyllum demersum | cd4s |
| Vitis vinifera | vvi161s |
| Aquilegia coerulea | ac472s |
| Acorus gramineus | agr8s |
| Acorus americanus | aam1s |
| Asparagus setaceus | ase9s |
| Acanthochlamys bracteata | abr7s |
| Ananas comosus | aco40s |
| Dioscorea alata | da480s |
| Elaeis guineensis | elg3s |
| Musa acuminata | mac41s |
| Oryza sativa | os53s |
| Zostera marina | zma82s |
| Spirodela polyrhiza | spo4s |
| Dendrobium chrysotoxum | dch50s |
| Euryale ferox | ef3s |
| Ginkgo biloba | gbi44s |
| Sequoiadendron giganteum | sgi44s |
| Azolla filiculoides | afi61s |
| Selaginella moellendorffii | smo62s |
| Physcomitrium patens | ppt60s |
| Trithuria bibracteata | tau2s |
| Theobroma cacao | tc180s |
| Arabidopsis thaliana | at600s |
All analyses depend on the WGDI toolkit.
The AAK_construction/commond.md file documents the full step-by-step process used to build the AAK, including WGDI commands and intermediate dotplot checkpoints.
- karyotype-phylogenomics-simulator — automated simulator for karyotype evolution
- Karyotype_Evolution.md — minimal worked example of karyotype reconstruction
- Shared_fusion_positions.md — worked example of using shared fusion points
- wgdi-example — additional WGDI walkthroughs
(Paper citation to be added upon publication)
Karyotype comprises both chromosome numbers and character of each chromosome for one species. Karyotype evolution represents chromosomal changes from the ancestral genome to the modern genome. This information is critical for reconstructing ancestral karyotypes and tracing how modern species evolved step by step.
In the long evolutionary history of a species, ancestral chromosomes fuse or fission gradually and randomly in offspring lineages, meaning each intact ancestral chromosome (protochromosome) could be retained across highly diverged lineages. Lineages closer to the common ancestor with fewer genome changes (e.g., fewer whole-genome duplications, WGD) tend to retain more protochromosomes. Syntenic blocks serve as the key evidence for identifying fusion and fission events.
Previous approaches define contiguous ancestral regions (CARs) based on collinearity, but suffer from gap regions caused by structural abnormalities and short syntenic blocks. Our approach instead identifies protochromosomes by searching for shared intact chromosomes or chromosome-like syntenic blocks (CLSBs) across highly diverged lineages.
The spiral workflow consists of three iterative steps:
- Identify CLSBs by pairwise genome comparisons
- Extract the most intact CLSBs as protochromosomes, adding telomeres at their ends
- Remove identified protochromosomes and connect flanking regions, then repeat until no genomic block remains
Three basic inter-chromosomal rearrangement types are recognized:
- RCT — Reciprocal chromosome translocation
- EEJ — End-to-end joining (Robertsonian translocation)
- NCF — Nested chromosome fusion
Compound and mixed events are denoted with parentheses or mix, e.g. (1_9/RCT)_6/EEJ (chromosomes 1 and 9 first joined by RCT, then end-joined with chromosome 6) and 1_4_13/mix for complex multi-chromosome rearrangements.
Fusion points are highly specific: the probability that a later structural variation breakpoint coincides with a protochromosome fusion point is extremely low, making fusion points reliable phylogenetic markers. Inversions similarly have little effect on karyotype reconstruction.
- Paleogenomics — reconstructing evolutionary trajectories of species
- Phylogenetics and species taxonomy
- Verification of genome assembly quality
- Detection of autopolyploidy or allopolyploidy