ArticleGenome biology and evolution2022
Gene Structure-Based Homology Search Identifies Highly Divergent Putative Effector Gene Family.
Article in Genome biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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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.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.bioRxiv : the preprint server for biology · 2026Article
- From genomes to interventions: computational strategies transforming parasitology.Frontiers in veterinary science · 2026Review
- Dasineura asteriae Reprograms the Flower Gene Expressions of Vegetative Organs to Create Flower-Like Gall in Aster scaber.Plant, cell & environment · 2025Article
- CAP peptides artificially induce insect-gall-like growth in different plant species.Plant & cell physiology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Sequence Variation and In Silico Protein Characterization ofInternational journal of molecular sciences · 2025Article
- Alternative splicing regulation in plants by SP7-like effectors from symbiotic arbuscular mycorrhizal fungi.Nature communications · 2024Article
- Two chromosome-level genome assemblies of galling aphids Slavum lentiscoides and Chaetogeoica ovagalla.Scientific data · 2024Article
- Tertiary structure assessment at CASP15.Proteins · 2023Article
- Advances in genome sequencing reveal changes in gene content that contribute to arthropod macroevolution.Development genes and evolution · 2023Review
- Molecular Aspects of Gall Formation Induced by Mites and Insects.Life (Basel, Switzerland) · 2023Review
- Discovery of the bicycle gene family provides new insights into insect manipulation of plant development during gall induction.Faculty reviews · 2023Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Homology of highly divergent genes often cannot be determined from sequence similarity alone. For example, we recently identified in the aphid Hormaphis cornu a family of rapidly evolving bicycle genes, which encode novel proteins implicated as plant gall effectors, and sequence similarity search methods yielded few putative bicycle homologs in other species. Coding sequence-independent features of genes, such as intron-exon boundaries, often evolve more slowly than coding sequences, however, and can provide complementary evidence for homology. We found that a linear logistic regression classifier using only structural features of bicycle genes identified many putative bicycle homologs in other species. Independent evidence from sequence features and intron locations supported homology assignments. To test the potential roles of bicycle genes in other aphids, we sequenced the genome of a second gall-forming aphid, Tetraneura nigriabdominalis and found that many bicycle genes are strongly expressed in the salivary glands of the gall forming foundress. In addition, bicycle genes are strongly overexpressed in the salivary glands of a non-gall forming aphid, Acyrthosiphon pisum, and in the non-gall forming generations of H. cornu. These observations suggest that Bicycle proteins may be used by multiple aphid species to manipulate plants in diverse ways. Incorporation of gene structural features into sequence search algorithms may aid identification of deeply divergent homologs, especially of rapidly evolving genes involved in host-parasite interactions.
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Registered trials
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