ArticleMolecular biology and evolution2020
Is Phylotranscriptomics as Reliable as Phylogenomics?
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 98 citations in OpenAlex.
- Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).Genome biology and evolution · 2026Article
- Convergent genomic trajectories shape adaptation to life on land across animal lineages.Nature communications · 2026Article
- 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
- Comparative phylotranscriptomics reveals glycolytic adaptation associated with prolonged larval development in the coastal slipper lobsterAnimal cells and systems · 2026Article
- Article
- Chromosome number variation and phylogenetic divergence of East Asian Cirsium sect. Onotrophe subsect. Nipponocirsium (Compositae), with a new species from Taiwan.Botanical studies · 2025Article
- High-level phylogenetic relationships withinIMA fungus · 2025Article
- Arthropod Phylotranscriptomics With a Special Focus on the Basal Phylogeny of the Myriapoda.Genome biology and evolution · 2024Article
- Selection and Gene Duplication Associated With High-Elevation Diversification in Pristimantis, the Largest Terrestrial Vertebrate Genus.Genome biology and evolution · 2024Article
- PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era.Molecular biology and evolution · 2024Article
- Using de novo transcriptomes to decipher the relationships in cutthroat trout subspecies (Evolutionary applications · 2024Article
- Comparative analysis shows high level of lineage sorting in genomic regions with low recombination in the extendedPlant diversity · 2024Article
- Progress in systematics and biogeography of Orchidaceae.Plant diversity · 2024Review
- Genetic mechanism of body size variation in groupers: Insights from phylotranscriptomics.Zoological research · 2024Article
- Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.Virus evolution · 2024Article
- Phylotranscriptomic discordance is best explained by incomplete lineage sorting withinPlant diversity · 2024Article
- Integrating high-volume molecular and morphological data into the evolutionary studies ofPlant diversity · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- Phylogenomic Analyses Reveal an Allopolyploid Origin of Core Didymocarpinae (Gesneriaceae) Followed by Rapid Radiation.Systematic biology · 2023Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Phylogenomics, the study of phylogenetic relationships among taxa based on their genome sequences, has emerged as the preferred phylogenetic method because of the wealth of phylogenetic information contained in genome sequences. Genome sequencing, however, can be prohibitively expensive, especially for taxa with huge genomes and when many taxa need sequencing. Consequently, the less costly phylotranscriptomics has seen an increased use in recent years. Phylotranscriptomics reconstructs phylogenies using DNA sequences derived from transcriptomes, which are often orders of magnitude smaller than genomes. However, in the absence of corresponding genome sequences, comparative analyses of transcriptomes can be challenging and it is unclear whether phylotranscriptomics is as reliable as phylogenomics. Here, we respectively compare the phylogenomic and phylotranscriptomic trees of 22 mammals and 15 plants that have both sequenced nuclear genomes and publicly available RNA sequencing data from multiple tissues. We found that phylotranscriptomic analysis can be sensitive to orthologous gene identification. When a rigorous method for identifying orthologs is employed, phylogenomic and phylotranscriptomic trees are virtually identical to each other, regardless of the tissue of origin of the transcriptomes and whether the same tissue is used across species. These findings validate phylotranscriptomics, brighten its prospect, and illustrate the criticality of reliable ortholog detection in such practices.
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Registered trials
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