Resources & Tools
About the Parasitoid Wasps Project
Parasitoid wasps are a numerous and diverse group of insects that obligately infect other arthropod species. These wasps lay their eggs within the body cavity of their hosts, and the resulting offspring exploit the hosts’ resources to complete their development. Many parasitoids also introduce venom proteins into the host during infection. These venom proteins act through a variety of mechanisms to manipulate host immunity, physiology and metabolism in order to increase the fitness of the developing parasitoid offspring. In the Mortimer lab at Illinois State University we use the Drosophila melanogaster-parasitoid wasp host-parasite system as a model to study the mechanisms used by parasitoids to manipulate host signaling, and our work has demonstrated that parasitoid venom proteins can modify conserved signaling mechanisms including signal transduction pathways and second messenger systems in their hosts (Mortimer, 2013; Alvarado et al., 2019).
In this project we will be annotating venom encoding genes from three species of parasitoid wasps that infect Drosophila melanogaster (Mortimer et al., 2013; Goecks et al., 2013). The gene models generated in this project will allow us to investigate the evolution of venom proteins and to better characterize the proteins for follow up functional studies. Understanding the genome evolution and mechanisms underlying venom protein function will provide a powerful tool to study the regulation of signaling events and will allow us to gain novel insight into conserved signaling mechanisms in Drosophila, an important model of human health. Overall, this project will provide further insight into the function and evolution of parasitoid venoms, and open new areas of research within this exciting field.
The Parasitoid Wasps Project Leader gave a scientific talk on this GEP Research Project at the Texas/Oklahoma Regional Node Meeting on January 5, 2021.
Parasitoid Wasps Project: Annotation Walkthrough
This exercise will walkthrough an example of annotating a wasp venom gene for the Parasitoid Wasps Project. It will discuss wasp versions of common GEP annotation tools—Genome Browser, Gene Record Finder, and Gene Model Checker—and provide background for the interpretation of data tracks that are unique to the Parasitoid Wasps Project.
Parasitoid Wasps Project: Annotation Workbook Directions
This document provides directions for how to complete and obtain the items needed to submit a Parasitoid Wasps Project annotation—a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein.
Parasitoid Wasps Project: Annotation Workbook
For the Parasitoid Wasps Project, project submission will consist of a completed Annotation Workbook, a screenshot of the user track on the Genome Browser, and sequence files for the entire transcript and encoded protein. This Annotation Workbook is an Excel file with space to fill out all the necessary information for the gene annotation.
completion recommended in order from left to right, top to bottom
Module 1. Introduction to the Genome Browser: What is a gene?
This module introduces students to the GEP UCSC Genome Browser. After completing this module students will be able to navigate to a genomic region and to control the display setting for different evidence tracks.
Module 2. Transcription, Part I: From DNA sequence to transcription unit
This module illustrates how a primary transcript (pre-mRNA) is synthesized using a DNA molecule as the template. After completing this module students will be able to explain the importance of the 5′ and 3′ regions of the gene for initiation and termination of transcription by RNA polymerase II, and identify the beginning and end of a transcript using the capabilities of the genome browser (RNA-Seq, Short Match).
Module 3. Transcription, Part II: What happens to the initial transcript made by RNA pol II?
This module demonstrates how the transcript generated by RNA polymerase II (the pre-mRNA) is processed to become mature mRNA using the sequence signals identified in Module 2. After completing this module students will be able to use the genome browser to explain the relationships among pre-mRNA, 5′ capping, 3′ polyadenylation, splicing, and mRNA.
Module 4. Removal of introns from pre-mRNA by splicing
This module uses mRNA data to identify splice sites. After completing this module students will be able to identify intron-exon boundaries using canonical splice donor and acceptor sequences and determine which are best supported by RNA-Seq and TopHat splice junction predictions.
Module 5. Translation: The need for an Open Reading Frame
In this module students will learn how mRNA is translated into a string of amino acids. After completing this module students will be able to determine the codons for specific amino acids as well as start and stop codons. They will be able to identify open reading frames for a given gene, define the phases of splice donor and acceptor sites and describe how they impact the maintenance of the open reading frame.
Module 6. Alternative splicing
This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs and illustrate how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.