ArticleMolecular biology and evolution2014
Orthology inference in nonmodel organisms using transcriptomes and low-coverage genomes: improving accuracy and matrix occupancy for phylogenomics.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers.
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164 citing papers in PubMed.
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- CAnDI: A New Tool to Investigate Conflict in Homologous Gene Trees and Explain Convergent Trait Evolution.Systematic biology · 2026Article
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- Evidence of introgression amid phylogenetic conflict in Brachyotum, a plant radiation from the Tropical Andes.American journal of botany · 2026Article
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- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
- Reliable Inference of Phylogenomic Relationship via Assembly-Based Strategy Accommodating Raw Reads and Proteins.Molecular ecology resources · 2026Article
- Origin of subgenomes in the circumboreal, allopolyploid, carnivorous plant Drosera anglica.American journal of botany · 2026Article
- Resolving the Taxonomic Enigma ofEcology and evolution · 2026Article
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- Evolutionary history of Australian samphires (Salicornieae, Amaranthaceae).Annals of botany · 2026Article
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- MYB regulator of "colorless" flavonols underlies the evolution of red flowers in Iochroma (Solanaceae).G3 (Bethesda, Md.) · 2025Article
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- Genome duplications, genomic conflict, and rapid phenotypic evolution characterize the Cretaceous radiation of Fagales.Journal of integrative plant biology · 2025Article
- Ortho2Web: a workflow for disentangling the roles of hybridization and allopolyploidization in reticulation within Campanulaceae.BMC biology · 2025Article
- Global phylogeny and taxonomy of Artemisia.Nature communications · 2025Article
- Fascination with RNA Editing: In the Lights of Evolution and Biology.Journal of molecular evolution · 2025Review
104 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Orthology inference is central to phylogenomic analyses. Phylogenomic data sets commonly include transcriptomes and low-coverage genomes that are incomplete and contain errors and isoforms. These properties can severely violate the underlying assumptions of orthology inference with existing heuristics. We present a procedure that uses phylogenies for both homology and orthology assignment. The procedure first uses similarity scores to infer putative homologs that are then aligned, constructed into phylogenies, and pruned of spurious branches caused by deep paralogs, misassembly, frameshifts, or recombination. These final homologs are then used to identify orthologs. We explore four alternative tree-based orthology inference approaches, of which two are new. These accommodate gene and genome duplications as well as gene tree discordance. We demonstrate these methods in three published data sets including the grape family, Hymenoptera, and millipedes with divergence times ranging from approximately 100 to over 400 Ma. The procedure significantly increased the completeness and accuracy of the inferred homologs and orthologs. We also found that data sets that are more recently diverged and/or include more high-coverage genomes had more complete sets of orthologs. To explicitly evaluate sources of conflicting phylogenetic signals, we applied serial jackknife analyses of gene regions keeping each locus intact. The methods described here can scale to over 100 taxa. They have been implemented in python with independent scripts for each step, making it easy to modify or incorporate them into existing pipelines. All scripts are available from https://bitbucket.org/yangya/phylogenomic_dataset_construction.
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