Karyotype

• Blast

  Sequence alignment between arbitrary species

• ColinearScan

  Syntenic matching tool

• Blastp dotplot

  Plotting blastp dotplot diagrams

• Block dotplot

  Drawing block dotplot function

• Correspondence_mc

  Inter- and intra-genomic comparisons

• Fabaceae karyotype

  Ancestral genome of Fabaceae

• Blast visualization

  Matching visualization

• Syntenic visualization

  Syntenic matching tool

Inferring ancestral karyotypes and evolution

The inference of ancestral genome structure and paleogenome remodelling trajectories is divided into 7 main steps.

1. Genome-wide comparison of the species involved, based on BLAST software, to confirm conserved homologous genes between and within genomes.
2. The homology information obtained from BLASTP was entered into CollinearScan or MCScanX for collinearity analysis to identify the synteny blocks.
3. Identification of orthologs and paralogs associated with speciation and polyploidy by inter- and intra-genomic comparisons.
4. Identification of conserved ancestral regions (CARs) by the combination of dotplots and gene collinearity between genomes.
5. Identification of ancient chromosomal rearrangements in conjunction with species trees.
6. Then, by identifying and collating all the CAR rearrangements, we can bottom-up infer the ancestral karyotype and its composition of the study species.
7. After determining the ancestral genome, we can identify the fusion patterns and rearrangement trajectories of paleochromosome by comparing the CRAs in the dotplot between the modern and ancestral genome.

See the list on the left for the relevant process