---
# System prepended metadata

title: Genome Annotation Hackathon / Workshop

---

# Genome Annotation Hackathon / Workshop

# Project 1: Genome Annotation of Hippobosca

**Assign**: 

Hippoboscid dipterans (flies), are hematophagous or blood-sucking, obligate ectoparasites that infest birds, mammals and rarely humans. They are vectors responsible for the transmission of infectious pathogens such as Rickettsiae (e.g. Coxiella and Anaplasma), Acanthocheilonema dracunculoides, T.evansi and T.vivax during the blood-feeding process. The bites inflict pain when feeding to the host and lead to blood loss and anaemia with a heavy infestation and, finally, death of the organism if not checked.
The scientific community neglected and disregarded these flies for decades, despite their devastating health effects on livestock and subsequent yield reduction.
The preliminary research on the genetics of these little-known Hippoboscids demonstrates the necessity to develop full-scale genomic resources to address their vector competence, their genetic makeup and the epidemiology of the various pathogens they harbour. The genomes of Hippobosca variegata, Hippobosca longipennis and Hippobosca camelina have been assembled. In this hackathon, we will focus on annotating key gene families. 



## Project 2: Investigating Endosymbionts in Hippobosca species

**Assign**: 

Endosymbiosis, the close mutualistic relationship between two species, has been well-documented in various organisms, including insects. In particular, endosymbiotic bacteria play an important role in insect nutrition and health and have been shown to significantly impact the biology of their insect hosts [1–3]. The Hippobosca genus is a group of fly species that have been shown to harbor endosymbiotic bacteria [4], but the role of the endosymbionts has not been investigated.
Recently whole genome sequences from Hippobosca camelina, H. longipennis, and H.  variegata have been generated, with initial investigation revealing potential reduced genome size. We hypothesize that to support their obligate hematophagy; they will harbour obligate and other endosymbionts.  In this study, we aim to use whole genome sequences to investigate the endosymbionts present in three species of Hippobosca. The initial focus would be to detect the presence of endosymbionts by identifying genomic regions characteristic that map to known endosymbiont genomes. We will also attempt to use the contig re-assembly approach to assemble some endosymbionts. However, the key focus is to identify the endosymbiont present and investigate their impact on the biology of these insects in the Hippobosca species based on known function. The results of this study will have important implications for our understanding of endosymbiosis in Hippobosca and its role in association with their hosts. By characterizing the endosymbionts present in these species, we may identify new targets for vector control efforts to reduce the transmission of diseases by these insects and explore novel technology that may apply to other disease vectors. 

## Project : Genome Annotation of Stomoxys indica

**Assign**: 

Stomoxyine flies (Diptera: Muscidae) are economically important animal pests; males and females are blood-sucking. They irritate the area of the bite since their saliva contains no anaesthetics, making their bites more painful and a nuisance to animals and sometimes humans. Stomoxys species include Stomoxys calcitrans, the most abundant species, Stomoxys sitiens, Stomoxys indica, Stomoxys bengalensis, and Stomoxys niger (African stable fly). Stomoxys calcitrans is widely studied with a recently available whole genome assembly. However, the rest remain understudied. Whole genome sequencing has recently been done in icipe for Stomoxys indica. The objective of this study would be to assemble the genome of Stomoxys indica and perform a comparative analysis with Stomoxys calcitrans and other close Dipterans.

1.	To perform genome annotation of Stomoxys indica gene families
2.	To perform a comparative analysis of immunity genes in Stomoxys indica, Stomoxys calcitrans, and other close Dipterans.