Abstract
The innate immune system is an ancient component of host defense. Since innate immunity pathways are well conserved throughout many eukaryotes, immune genes in model animals can be used to putatively identify homologous genes in newly sequenced genomes of non-model organisms. With the initiation of the “i5k” project, which aims to sequence 5,000 insect genomes by 2016, many novel insect genomes will soon become publicly available, yet few annotation resources are currently available for insects. Thus, we developed an online tool called the Insect Innate Immunity Database (IIID) to provide an open access resource for insect immunity and comparative biology research (http://www.vanderbilt.edu/IIID). The database provides users with simple exploratory tools to search the immune repertoires of five insect models (including Nasonia), spanning three orders, for specific immunity genes or genes within a particular immunity pathway. As a proof of principle, we used an initial database with only four insect models to annotate potential immune genes in the parasitoid wasp genus Nasonia. Results specify 306 putative immune genes in the genomes of N. vitripennis and its two sister species N. giraulti and N. longicornis. Of these genes, 146 were not found in previous annotations of Nasonia immunity genes. Combining these newly identified immune genes with those in previous annotations, Nasonia possess 489 putative immunity genes, the largest immune repertoire found in insects to date. While these computational predictions need to be complemented with functional studies, the IIID database can help initiate and augment annotations of the immune system in the plethora of insect genomes that will soon become available.
Highlights
The innate immune system evolved early in the evolution of multicellular life, while the adaptive immune system evolved in the ancestor of the vertebrate lineage [1]
Using this dataset to perform homology searches against the N. vitripennis transcriptome, we identified 306 putative immune genes. 138 of these genes were previously reported as immune genes in the Nasonia genome (Nvit_1.2) paper, which identified a total of 270 putative immune genes using Hidden Markov Models (HMMs) for protein domains common in immunity gene families [16]
Using the Innate Immunity Database (IIID), we increased the putative Nasonia immune repertoire by 58% in comparison to the number of immune genes originally published in the Nasonia genomes [16], while only finding 46% of the immune genes originally published
Summary
The innate immune system evolved early in the evolution of multicellular life, while the adaptive immune system evolved in the ancestor of the vertebrate lineage [1]. Annotation of immunity genes in these novel insect genomes will provide valuable insight into the diverse mechanisms insects employ for defense, but may contribute to the development of new insecticides for the control of agricultural pests. To facilitate the annotation of immunity genes in insects, including our own model system of Nasonia parasitoid wasps, we have generated an open-access database called the Insect Innate Immunity Database (IIID, http://www.vanderbilt.edu/IIID) to serve as a starting point for researchers interested in using comparative biology to identify potential immune genes in insects. The database contains the immune repertoires of five insect models (including Nasonia) that span several orders, and each gene is categorized based on the pathway it participates in and the role it plays in that pathway. The intuitive web interface allows researchers to search for specific immunity genes by name, retrieve all immunity genes in the database for a particular species, pathway or class, and find putative homologs for a gene of interest using an internal BLAST tool
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