ArticlePLoS computational biology2022
AvP: A software package for automatic phylogenetic detection of candidate horizontal gene transfers.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
- Haplotype-resolved genome of a dry-preservable cell line reveals chromosome evolution and DNA damage.Life science alliance · 2026Article
- The genome and stage-specific transcriptomes of the carrot weevil, Listronotus oregonensis, reveal adaptive mechanisms for host specialisation and symbiotic interactions.Insect molecular biology · 2026Article
- What impact do new homologs have on detecting interdomain horizontal gene transfer in eukaryotes? A reassessment of Katz (2015).Biology open · 2026Article
- Genomic and Transcriptomic Insights into the Evolution and Parasitic Strategy of the Woody-Plant NematodeMolecular plant-microbe interactions : MPMI · 2026Article
- Genome-Wide Comparative and Phylogenetic Analysis of Putative Algal Carbohydrate Sulfotransferases.Journal of molecular evolution · 2026Article
- A machine learning framework for interpreting phylogenetic tree patterns in interkingdom horizontal gene transfer.Frontiers in bioinformatics · 2026Article
- Facultative mutualism betweenISME communications · 2026Article
- Developmental dynamic transcriptomics reveals multiple effectors and transcription factors critical for Ditylenchus destructor parasitism.BMC biology · 2025Article
- Reassessing Interkingdom Horizontal Gene Transfer Suggests Limited Influence on Plant Genomes.Ecology and evolution · 2025Article
- Jumbo phage-mediated transduction of genomic islands.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High-resolution genome assembly and linkage mapping in Meloidogyne hapla reveal non-canonical telomere repeats and recombination hotspots associated with effector proteins.PLoS pathogens · 2025Article
- Multiple Horizontal Transfers of Immune Genes Between Distantly Related Teleost Fishes.Molecular biology and evolution · 2025Article
- Functional Carbohydrate-Active Enzymes Acquired by Horizontal Gene Transfer from Plants in the Whitefly Bemisia tabaci.Genome biology and evolution · 2025Article
- Genomic and Transcriptomic Analysis of the Polyploidy Cyst Nematode,International journal of molecular sciences · 2025Article
- Article
- Horizontal Gene Transfer of a key Translation Factor and its Role in Polyproline Proteome Evolution.Molecular biology and evolution · 2024Article
- The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families ofJournal of fungi (Basel, Switzerland) · 2024Article
- Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization.Nature communications · 2023Article
- HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer.Briefings in bioinformatics · 2023Article
- Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops.Frontiers in bioengineering and biotechnology · 2023Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework.
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