Orthogroup intersections
Mutually exclusive core, pairwise-shared, and genome-specific orthogroup categories across Anise, Hass, and West Indian.
Avocado and Lauraceae evolution
Comparative genomics
Explore gene-family evolution, chromosome-scale synteny, structural variation, focused chromosome 12 evidence, and a model of ancestral Lauraceae chromosomes.
- 3
- avocado genomes
- 21,990
- core orthogroups
- 12
- ancestral clusters
- 44
- ancestral CARs
How to read this resource
Figures summarize the supplied comparative-genomics analyses. Structural rearrangements and ancestral chromosome arrangements are inference-based candidates, not validated molecular breakpoints. Open any figure for the full-resolution version or download its accompanying evidence.
01 · Evolutionary framework
Phylogeny and gene-family evolution
Orthogroup membership, gene partitions, divergence-time context, and CAFE5 gene-family turnover provide the evolutionary frame for the three avocado genomes.
Gene partition
Genes assigned to core, pairwise-shared, genome-specific orthogroups, or the unassigned category for each avocado genome.
Phylogeny and family turnover
Seven-species divergence-time framework and CAFE5 family expansion/contraction results, including the Anise branch.
02 · Chromosome-scale comparison
Synteny, structural variation, duplication, and WGD
Whole-genome alignments connect homologous chromosome segments; separate summaries report structural events, affected span, duplication classes, candidate families, and syntenic Ks distributions.
Three-genome chromosome synteny
Chromosome-scale relationships among West Indian T2T, Hass, and Anise. Colours distinguish syntenic, inverted, translocated, duplicated, and deleted segments.
Structural-event counts
Pairwise counts of inversion, translocation, and combined reference/query duplication events.
Structural-variant span
Cumulative reference-genome span associated with inversion, translocation, and reference-duplication calls.
Gene duplication classes
Annotated non-TE duplicated genes classified as tandem, proximal, dispersed, or high-confidence WGD/segmental duplication.
Syntenic Ks distributions
Pair-level and block-median Ks density profiles for strict non-TE interchromosomal syntenic anchors.
Candidate gene families
Selected immune, WRKY, terpene, cell-cycle, and lipid-metabolism family counts across the three genomes.
03 · Focused evidence
Anise candidates and chromosome 12
Focused analyses connect broad comparative patterns to candidate annotations, RNA support, and a large chromosome 12 orientation difference while retaining the documented limitations.
Anise candidate-gene reassessment
RNA evidence, TE/protein-quality filtering, prioritization, and homology back-search re-evaluate 9,176 annotation-defined candidates without treating them all as proven novel genes.
Chromosome 12 synteny
Three pairwise chr12 comparisons highlight large orientation differences involving Hass and a smaller local Anise–West Indian inversion candidate; boundaries are not validated breakpoints.
04 · Ancestral Genome Reconstruction (AGR)
Predicted Lauraceae ancestral chromosomes
A seven-species framework reconstructs 44 contiguous ancestral regions (CARs) assigned to 12 ancestral chromosome clusters and compares their dominant extant chromosome correspondence using 3,958 retained backbone anchors.
Lauraceae ancestral chromosome framework
Four-panel synthesis of phylogenetic context, ancestral CAR order and orientation, chromosome-level correspondence, and ancestral polarization of the Hass chromosome 12 rearrangement candidate.
Open the four AGR panels separately
A · Phylogenetic context
Six ingroup genomes and one outgroup define the topology; branch lengths and support values are intentionally not shown.
B · CAR order and orientation
Predicted order and orientation of 44 CARs across 12 ancestral clusters; unresolved orientations and provisional ANC07 ordering remain marked.
C · Extant chromosome correspondence
Dominant chromosome or sequence correspondence for each ancestral cluster across six Lauraceae ingroup species.
D · Hass12 rearrangement polarization
West Indian Pa12 follows the inferred ANC12 arrangement after axis normalization, while Hass12 shows reversed CAR0025/CAR0031 order and orientation; this is not breakpoint validation.
05 · Evidence downloads
Download the small tables behind the figures
These files support inspection and reuse of the displayed summaries. They do not replace complete alignment, SyRI, orthology, or ancestral-reconstruction working directories.Structural variationPairwise event counts and cumulative reference spans.Gene duplicationPer-genome duplication-class counts.Focused verificationAnise candidate verification results.Ancestral CAR orderCAR membership, rank, support, orientation, and status.Ancestor–extant mappingAncestral cluster to extant chromosome correspondence.AGR interpretation guideCaption, scope, limitations, and reproduction notes.
