RESEARCH DOSSIER · Evolutionary genomics
Comparative Genomics & Evolution
Comparative Genomics and Molecular Evolution of Tetrahymena
Investigating evolutionary relationships, gene-family dynamics, and molecular evolution across Tetrahymena species.
Ongoing research
Research question
What do orthologous and paralogous gene relationships reveal about evolutionary relationships, gene-family change, and sequence-level natural selection among six Tetrahymena species?
Scientific background
This six-species study connects phylogenomics with orthology, paralogy, and molecular evolution. Paramecium tetraurelia was considered in earlier analyses but is not part of the current six-species run.
Methods
The tools below reflect analysis experience and ongoing workflows; listing a method does not imply that every downstream analysis is complete.
- Orthogroup inference and single-copy ortholog identification with OrthoFinder
- Sequence alignment using MAFFT and MUSCLE, and phylogenetic reconstruction with IQ-TREE
- Codon-alignment and dN/dS workflows using ParaAT and PAML / codeml
- Ongoing gene-family expansion and contraction analysis with CAFE5
- Sequence searches, preprocessing, and reproducible Linux/HPC workflows
Prospective approaches
- OrthoMCL: implementation in this project is not confirmed; retained only as a prospective alternative.
Computational tools
Research progress & findings
A six-species OrthoFinder run identified approximately 9,916 single-copy orthogroups represented in all six species. This is an analytical output of that run, not a published biological conclusion. Gene-family analysis with CAFE5 is ongoing.
Figures & visualizations
No approved research figures are available for this dossier.
Interpretation
Shared single-copy orthogroups provide candidate loci for comparative analyses. Biological interpretation depends on alignment quality, orthology assessment, phylogenetic support, and downstream model checks. An omega (dN/dS) estimate greater than one alone does not establish statistically supported positive selection.
Limitations
Orthogroup counts depend on input assemblies, annotations, filtering, and software settings. Selection claims require appropriate model comparisons, statistical support, and checks for alignment errors and multiple testing. No final selection or gene-family conclusions are reported here.
Current status
The six-species OrthoFinder run is complete; downstream analyses and interpretation remain ongoing.
Future directions
Continue gene-family analyses and evaluate phylogenetic and sequence-level results with appropriate quality controls before drawing biological conclusions.
Posters & research outputs
Ongoing research