1.1 Horizontal gene transfer
Horizontal gene transfer means genetic materials transfer from one species to another, and this is a non- sexual process. Different from Darwin inheritance, genetic materials transmitted generation by generation in the same phylogenetic clade, HGT events transfer from one clade to a different clade. HGT events could be occurred by transformation, transduction and conjugation in prokaryotes, while occurred by phagocytosis and endosymbiont process in eukaryotes[1] . Evidences showed that HGTs are more frequently found in prokaryotes than in eukaryotes[2]. HGT is a considerable driving force of prokaryotic evolution. Based on Charles Darwin’s theory, biologists construct a tree-like phylogenetic relationship. If a wide sequence region or whole genome is transferred to unrelated lineage, the phylogenetic tree will become a network-like diagram. It has been obscured that the ancestor of eukaryotes is the Bacteria or the Archea. It is hard to distinguish the origin of the Eukaryote depending on one gene. Rivera and Lake suggest that genome fusion or horizontal gene transfers occur within diverse prokaryotic genomes becoming the origin of the Eukaryote and convert the phylogenetic trees into rings[3]. As more and more genetic activities are explored among genomes, the HGT process is an important cofactor
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infecting the phylogenetic relationship especially in prokaryotes[4].
Accumulating HGT events suggest that genes transferred particularly. Genes of genome are divided into operational genes and informational genes. Operational genes are responsible for metabolic process; in contrast, informational genes are responsible for transcriptional and translational process. Informational genes are far less transferred than operational genes in horizontal transfer events. It is summarized that functional genes are transferred preferentially in HGT process[5]. Because not every gene transfer event is kept expand in recipient species, it must be profitable under nature selection. For instance, Dehalococcoides ethenogenes acquir dehalogenase genes that are important for dehalorespiration process to resist the polluted environment. Moreover, many studies showed that HGTs occur commonly for antibiotic-resistance and the frequencies of transfer events must higher than observed [6]. Through HGT process, host could gain a new function for pathogenicity or virulent resistance increasing the host fitness and colonizing new environments [7-8].
There are some genes acquired from HGT events occurred in fungi that can cause diseases. For instance, A gene encoding ToxA, encoding host-selective toxin, is transferred from Stagonospora nodorum to Pyrenophora tritici-repentis can cause tan spot disease on wheat [9-10]. The ToxA protein of pathogens can bind with Tsn1
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protein in host plant. The recognition of ToxA by Tsn1 in wheat subverts the plant pathogens resistance mechanism [11]. The ToxA genes are found both in host Stagonospora nodorum and pathogen Pyrenophora tritici-repentis but not in other
related species of Pyrenophora tritici-repentis. The comparison of ToxA gene in pathogen fungi shows that the pathogen fungi both contain highly similar region surrounding ToxA gene, and 57 ToxA gene sequences of Pyrenophora tritici-repentis are almost identical to ToxA gene sequences of 600 Stagonospora nodorum strain [11-12]. That suggests the ToxA gene is transferred to Pyrenophora tritici-repentis and make that fungi cause tan spot on wheat.
Evidences show that not only one gene but also a gene cluster can be lateral transferred. The ACE1 gene cluster contains 15 genes co-expressed during the process of the fungi penetrates into host tissues. This horizontal transferred cluster is found by comparing 26 fungal genomes and search continual orthologs genes. The ACE1 cluster is transferred from Magnapothe grisea to few fungal species. According to the phylogenetic analysis, the genes of the cluster of Magnapothe grisea are more closed to the genes in Aspergillus clavatus and the Aspergillus clavatus contains only six genes in the ACE1 cluster. The observation suggests the ACE1 cluster is transferred from Magnapothe grisea into an ancestor of Aspergillus clavatus. Comparison of ACE1 clusters in the few recipient fungi, the cluster is through duplication or gene
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loss after transferred process and become different pattens in the fungi.
Horizontal gene transfer events could be predicted depending on phylogenetic incongruencies or parametric methods. Phylogenetic approaches are mainly based on the accepted species taxonomy. First, align a set of genes of the candidate that have the same function but in different species. Second, use the alignment to construct a phylogenetic tree. Then, compare the phylogenetic tree with the species taxonomy or the accepted phylogeny of the gene. The incongruencies between the two phylogenies may indicate HGT events[13]. Parametric methods involve GC content, codon usage, di- and tetra-nucleotide frequencies of the sequences[14]. Because these genomic characteristics are specific to particular species, the atypical regions compared to the general pattern of the genome suggest the possibility of HGT [13].
Because of different composition of tRNA pool, there are different level and special codon usage bias in different species genome. Most amino acids are encoded by more than one codon. In different organisms, there exist different preferences for synonymous codons of the same amino acid. Therefore, the particular codon frequencies in coding sequences, called codon usage bias, can sometimes represent for particular organism[15]. In this study, we used GC content and codon usage bias to explore the origin of the genes or to inference the causation relation for the horizontal gene transfer events.
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