## Project 1: Metabarcoding of Rumen Microbiome

**Assign**:
- Samwel
- **Victor**
This Project aims to **establish rumen microbiome diversity and variation between cattle, camels, goats and sheep**. Genomic rumen microbiome DNA was isolated and characterized using bacterial and archaeal 16S rRNA, protozoal 18S rRNA genes and fungal ITS1 gene amplicons sequencing from the harvested bovine rumen fluid samples using next-generation sequencing technology.

For this Project, you are provided with 160 fastq samples generated using multiple primers. In addition to establishing the diversity, especially for the 16S data, you are expected to perform functional analysis.
Resources: https://github.com/mbbu/Reviewing-16s-Analysis-Workflows

Role during this pereiod: Finalize the necessary visualizations and work on the manuscript.

## Project 2: *De novo* genome assembly of Stomoxys indica

**Assign**: Parcelli and

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

## Project 3: Investigating Endosymbionts in Hippobosca species using Whole Genome Sequencing

**Assign**: Anne, Caleb

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.

**Hypothesis:** We hypothesize that because Hippobosca has a reduced genome compared to related Diptera, they supplement their limited genome by harboring obligate and other endosymbionts.

**Objectives:**
1. To identify the endosymbiotic bacteria present in Hippobosca camelina, Hippobosca longipennis, and Hippobosca variegata using whole genome sequencing data.
2. Investigate the genome content of obligate endosymbionts for genes that supplement Hippoboscids through their nutrition, immunity and reproduction.
3. Determine the extent to which endosymbiotic bacteria may influence the transmission of diseases by Hippobosca species.

## References

1. Wernegreen JJ. Endosymbiont evolution: Predictions from theory and surprises from genomes. , DOI: 10.1111/nyas.12740.
6. Gupta JP, Shyma KP, Ranjan S et al. Genetic manipulation of endosymbionts to control vector and vector borne diseases. Vet World 2012;5:571–6.
7. Zhao M, Lin X, Guo X. The Role of Insect Symbiotic Bacteria in Metabolizing Phytochemicals and Agrochemicals. Insects 2022;13, DOI: 10.3390/insects13070583.
8. Boucheikhchoukh M, Mechouk N, Benakhla A et al. Molecular evidence of bacteria in Melophagus ovinus sheep keds and Hippobosca equina forest flies collected from sheep and horses in northeastern Algeria. Comp Immunol Microbiol Infect Dis 2019;65:103–9.
9. Herren JK, Mbaisi L, Mararo E et al. A microsporidian impairs Plasmodium falciparum transmission in Anopheles arabiensis mosquitoes. , DOI: 10.1038/s41467-020-16121-y.