ArticleGenome research2017
Increased taxon sampling reveals thousands of hidden orthologs in flatworms.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed, 1 synthesis or guideline pooled it, 52 citations in OpenAlex.
- Weighted gene co-expression network analysis identifies modules and functionally enriched pathways in the lactation process.Scientific reports · 2021Pooled it
- A novel activation-related gene P158 is essential for evagination and early development of Echinococcus multilocularis protoscoleces.Parasites & vectors · 2026Article
- Molecular mimicry: ecology, evolution, and applications of doppelgänger peptides.Trends in biochemical sciences · 2025Review
- Candidate orphan genes: Reassessing uniqueness.PloS one · 2025Article
- A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence.Nature communications · 2024Article
- The promise and pitfalls of synteny in phylogenomics.PLoS biology · 2024Article
- Incongruence in the phylogenomics era.Nature reviews. Genetics · 2023Review
- The NIH Comparative Genomics Resource: addressing the promises and challenges of comparative genomics on human health.BMC genomics · 2023Review
- Distinct genomic routes underlie transitions to specialised symbiotic lifestyles in deep-sea annelid worms.Nature communications · 2023Article
- Genome-Scale Analysis Reveals Extensive Diversification of Voltage-Gated K+ Channels in Stem Cnidarians.Genome biology and evolution · 2023Article
- Marine animal evolutionary developmental biology-Advances through technology development.Evolutionary applications · 2023Article
- Building Phylogenies from Transcriptomic Data.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The state of Medusozoa genomics: current evidence and future challenges.GigaScience · 2022Review
- Article
- Nemertean, Brachiopod, and Phoronid Neuropeptidomics Reveals Ancestral Spiralian Signaling Systems.Molecular biology and evolution · 2021Article
- Article
- Regeneration of Planarian Auricles and Reestablishment of Chemotactic Ability.Frontiers in cell and developmental biology · 2021Article
- Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity.Frontiers in microbiology · 2021Article
- The Evolutionary Traceability of a Protein.Genome biology and evolution · 2019Article
- PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.Nucleic acids research · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Gains and losses shape the gene complement of animal lineages and are a fundamental aspect of genomic evolution. Acquiring a comprehensive view of the evolution of gene repertoires is limited by the intrinsic limitations of common sequence similarity searches and available databases. Thus, a subset of the gene complement of an organism consists of hidden orthologs, i.e., those with no apparent homology to sequenced animal lineages-mistakenly considered new genes-but actually representing rapidly evolving orthologs or undetected paralogs. Here, we describe Leapfrog, a simple automated BLAST pipeline that leverages increased taxon sampling to overcome long evolutionary distances and identify putative hidden orthologs in large transcriptomic databases by transitive homology. As a case study, we used 35 transcriptomes of 29 flatworm lineages to recover 3427 putative hidden orthologs, some unidentified by OrthoFinder and HaMStR, two common orthogroup inference algorithms. Unexpectedly, we do not observe a correlation between the number of putative hidden orthologs in a lineage and its "average" evolutionary rate. Hidden orthologs do not show unusual sequence composition biases that might account for systematic errors in sequence similarity searches. Instead, gene duplication with divergence of one paralog and weak positive selection appear to underlie hidden orthology in Platyhelminthes. By using Leapfrog, we identify key centrosome-related genes and homeodomain classes previously reported as absent in free-living flatworms, e.g., planarians. Altogether, our findings demonstrate that hidden orthologs comprise a significant proportion of the gene repertoire in flatworms, qualifying the impact of gene losses and gains in gene complement evolution.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.