About HGTstart
HGTstart is a systematic platform to browse, search and predict the horizontal gene transfers (HGTs). HGTstart comprised a built-in extensive background database (>50M protein sequences covering nearly all clades in tree of life) which intergrate >1200 complete gneomes, REFSEQ and MMETSP and the powerful yet user-friendly ‘routinetree’ pipline for predictions of the HGT to a given fasta protein sequence. This tool is implemented in Perl and JAVA, with a ready to start installation, and runs in command line on linux and Mac OS platforms. One can also download the pipeline and the database then run locally. HGTstart compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) identify the Horizontal Gene Transfer events based on phylogenetic trees ii)and homology similarity.
This pipeline predicts HGTs based on phylogeny and verifies them by AI, hU and hBL. (Please see “Learn more” for details about AI, hU and hBL)
If HGTs exist, you will receive files with all information about HGT (DonorNode, DNtime, ReceptorNode, RNtime, MSMH_OUT, MSMH_IN, AI, hU, hBL) and annotation (OG1157Term, EGGNOGTerm, PANTHERTerm, SuperFamilyTerm, InterproscanTerm, GOTerm, KEGGTerm, PfamTerm, KO).
What is HGT?
Horizontal gene transfer (HGT, or Lateral Gene transefer, LGT ) is often defined as the exchange of genetic material between two ‘non-genealogical’ species, and is commonly seen in prokaryotes as conjugation, transduction and transformation. It is proposed as opposed to vertical gene transfer (parent to offspring), which breaks the boundaries of kinship and complicates the possibilities of gene flow.
The phenomenon of HGT was observed as early as 1959. A series of articles reported that high frequency transduction (Hfr) strains of Escherichia coli could laterally transfer genetic information to specific Salmonella typhimurium mutant strains; in the same year, Tomochiro Akiba and Kunitaro Ochiai discovered resistance plasmids in pathogenic bacteria, which further led to the discovery that plasmids carrying resistance could be transferred between strains.
However, the concept of HGT did not exist at that time. It was not until the 1990s that the concept of horizontal gene transfer was gradually used to explain the discovery of horizontal gene transfer due to the application of gene engineered organisms (GEOs), especially gene engineered microorganisms (GEMs), and the emergence of a large number of drug-resistant pathogens that could no longer be explained by genetic mutations alone, and horizontal gene transfer gradually became a research hotspot.
Similar phenotypes between organisms that spans genetic distance are often explained by the shared genes in their genomes. The absence of the genes in the closely branched lineages can be explained by multiple independent gene losses. Alternatively, the gene sharing could be due to horizontal gene transfer (HGT) across distantly related lineages. HGT can, in principle, occur between any two organisms that contain DNA genomes. Contrast to vertically gene transmission that underlies the conservation of biological heritage and the stability of life tree in eukaryotes, HGT drives the diversification of eukaryotic species acting as a significant force leading to adaptation to various environments. Whereas HGT as a major force driving prokaryote evolution is well accepted, its role in eukaryote evolution is highly disputed, due to the complicated history, complex genomes and frequent sequence contaminations.