Identification And Analysis Of Horizontal Gene Transfer In Insects

Horizontal gene transfer (HGT) is a process in which exogenic DNA is introduced and integrated into a recipient genome. HGT is ubiquitous and abundant among prokaryotic organisms, and it is a major source of genetic variation in prokaryotes. Making use of foreign genetic materials, microorganisms acquire novel functions to promote their fitness to particular niches. Thus, HGT events among bacteria have biological significance for the evolution of prokaryotic organisms. Compared with transfer frequency and amount in bacteria, HGT events among eukaryotes and between prokaryotes and eukaryotes are rare, especially for multicellular eukaryotes. This is partly attributed to the development of nuclear membrane and predominance of sexual reproduction in eukaryotic organisms. Studies of HGT related to multicellular eukaryotes are not as prevalent as that among prokaryotes and unicellular eukaryotes. One reason is that contribution of HGT to the evolution of metazoan recipients may be small because of its rareness in multicellular eukaryotes. Nevertheless, case studies on HGT revealed that some of the transferred genes effectively participated in the biochemical metabolism and phenotypic divergence of multicellular eukaryotic hosts, implying that HGT may also have biological importance in the functional evolution of metazoan recipients. However, convincing evidence supporting the significant contribution of the transferred genes to the evolution of metazoan recipients is rare.HGT involved in insects has been intensively investigated. Based on population size and metabolic diversity, prokaryotes are considered as the major donor organisms for eukaryotic recipients. Bioinformatics methods are commonly applied to detect candidate HGT events at genomics era. The accumulated genome data of nearly1000bacteria and several insects make it possible to computationally detect HGT between microorganisms and insects at a genome level. We employ a comparative strategy to detect HGT in the five insects with available genome sequences, Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera, which belong to four different insect orders. Furthermore, the annotation information of their genomes is relatively abundant.1. Identification of HGTs between insects and bacteria.With the pipeline of similarity search and phylogenetic analysis, we found22silkworm genes and79honeybee genes that are the candidate horizontal transferred genes (HTGs) between insects and bacteria. Unexpectedly, no candidate was detected in the fly, mosquito, and beetle in this study. Based on available sequence data, these79sequences may be genomic contaminations primarily coming from prokaryotes, and these genes were not included in the following analyses because of their uncertainty of genetic origin. All of the detected candidates are intron-free genes, which is a trace of the bacteria-origin transferred genes. Additionally, the average similarity between14types of candidates and their bacterial hits is significantly larger than the mean value of random sampling distribution. As expected, GC contents of the transferred genes in silkworm display a more centralized distribution compared with that of the predicted bacterial donors. Thus, the detected14types of22genes should be horizontally transferred genes (HTGs) between prokaryotes and silkworm.2. Predication of transfer donors in HGTs.We used three methods, neighbor-joining tree (NJ), Bayesian inference (BI), and maximum likelihood (ML), to construct more refined phylogenetic trees of the detected candidates for the purpose of inferring the possible donors of HGT events. Potential prokaryotic donors of insects include symbionts, parasites, pathogens and bacteria in diet and surrounding environments. In this paper, we also found that one gene might be transferred from Wolbachia bacterium (endosymbiont bacteria). At least7types of HTGs may be introduced from entomopathogenic bacteria (pathogenic bacteria) and another donor is an endophytic bacterium (bacteria in food). Thus, these observations imply that insect pathogenic bacteria were the major donors of lepidopteran HTGs. Importantly, our results imply that pathogens may be advantageous to the subsistence and prosperity of hosts through effective HGT events at a large evolutionary scale.3. Estimation of transfer times for these HGTsUsing the detected14types of silkworm HTGs as queries, we searched for their homologous sequences in other Lepidoptera insects based on EST sequences and genomic data. We found that homologs of the detected HTGs are widely distributed in the Ditrysia insects rather than only in the silkworm. Thus, the majority of them are not HTGs between bacteria and silkworm as previously thought, instead, they are bacterial genes fixed into the ancient lepidopteran insect genomes. Thus, most of these genes may be introduced into Lepidoptera before radiation of Ditrysia group.4. Evolutionary analysis and function predication of these HGTs.At least more than a quarter of the detected HTGs were duplicated after HGT events in Lepidoptera. This tendency is consistent with the findings in prokaryotes that the transferred genes are more frequently duplicated than endogenetic genes in hosts. We also found that some detected HTGs harbour respective homologs which are vertically transferred genes in the silkworm and other insect genomes. That is, these HTGs and their homologs belong to the same protein family. Thus, HGT events also affect the evolution of protein families in Lepidoptera insects, more or less. Almost all of the detected HTGs are functional enzymes. Most of lepidopteran HTGs might perform physiological functions in nutritional metabolism and detoxification. The HTGs from bacteria may have contributed novel functions for Lepidoptera hosts to adapt to various diets and niches.5. Pathogen-origin HTGs contribute to the evolution of Lepidoptera insectsThe estimate of the transfer time of these HTGs into Lepidoptera corresponds to the evolutionary age of angiosperm expansion. Since most Lepidoptera are phytophagous insects and the majority of HTGs may perform physiological functions in nutritional metabolism and detoxification, these HTGs facilitated Lepidoptera to adapt to the evolution of their plant hosts. These genes potentially contributed to functional innovation and adaptability of Lepidoptera hosts in their ancient lineages associated with the diversification of angiosperms. Thus, our results provide some insight into understanding the biological significance of HGT to the evolution of Lepidoptera insects.We try to reveal the general features of bacteria-insect transferred genes such as transfer amount, transfer time, possible donor, evolutionary process and predicted functions. These general features will help understand the contribution and biological significance of foreign variations to the evolution of metazoan hosts.