Microbiology Resource of the Month: The Red Mite GenomeThe scope of the ASM Journal Genome Announcements has been expanded in a big way to create Microbiology Resource Announcements. The new journal publishes all resources that may be valuable to researchers in the microbial sciences.
Each month, we are highlighting a new Microbiology Resource and how it will help researchers with their scientific endeavors.
Month: November 2018.
Announcement: Draft Genome Assembly of the Poultry Red Mite, Dermanyssus gallinae
Resource: The Dermanyssus gallinae genome sequence.
What is Dermanyssus gallinae?
Also called the red mite or poultry mite, D. gallinae is an ectoparasite of poultry that primarily feeds on the blood of poultry but can also feed on the blood of mammals, including humans.
Why is the D. gallinae genome the MRA of the Month? D. gallinae isn’t a microbe!
D. gallinae may not be a microorganism itself, but like other blood-feeding parasites, it can spread a large number of diseases between its avian hosts. These diseases cause substantial animal morbidity and mortality as well as economic loss for poultry farmers. The large array of microorganisms transmitted by the red mite include:
- Newcastle disease virus.
- Eastern, Western and Venezuelan equine encephalomyelitis viruses.
- Escherichia coli.
- Pasteurella multocida.
- Salmonella gallinarum and S. enteritidis.
- Avian influenza A virus.
MRA first author Stewart Burgess provided insights into how his group and others will use this new resource.
How did you use new sequencing technologies to read the D. gallinae genome?
Burgess: This was by far the largest mite genome that we have encountered so far, so the expertise of our international team was vital in bringing the sequencing together into the assembled genome. The genome for Dermanyssus gallinae (~960 Mb) is quite large compared to other closely related mites (which are typically 60-300 Mb). We also do not have access to a clonal or ”inbred” population of the mite, which meant that we were potentially working with a polymorphic population.
To get around these limitations, we exploited the new 3rd-generation sequencing technologies, particularly PacBio and Oxford Nanopore minION sequencing, to make use of the extra-long-read capabilities. These made a huge difference in the quality of the genome assembly that we were able to achieve. When combined with the PacBio Iso-seq sequencing of the D. gallinae transcriptome, we were also able to successfully perform gene predictions for D. gallinae.
What unique features of the D. gallinae genome did its sequence reveal?
Burgess: The size of the genome was obviously larger than we initially anticipated, so we're just starting to explore the unique features of the genome. We are starting with an analysis of horizontal gene transfer, but then will use the genome to inform aspects of the development of parasitism and the host-parasite interaction in this species.
How will you use the D. gallinae genome in your research?
Burgess: We’re obviously delighted to have produced this resource, which will be a huge asset to those involved in poultry red mite research, as we search for new ways to control such a devastating and important parasite.
The genome is still being improved, as we look to incorporate further transcriptomic datasets and also to use additional minION data to further reduce the number of scaffolds in the genome assembly. That said, we are currently using the genome to identify SNPs associated with particular proteins that may be useful in mite control and also that might confer acaricide resistance, for example. As we mentioned, we're also starting to determine genes that may have been horizontally transferred to D. gallinae from bacteria or viruses.
How will the D. gallinae genome help other scientists in their research?
Burgess: One of the cornerstones of developing new control methods for D. gallinae is understanding the biology of the parasite to identify targets within it at which to aim new weapons. The genome sequencing project now represents a significant tool allowing the design of new methods of control through a greater understanding of the biology of the parasite. It will also be a really valuable tool for molecular epidemiologists trying to understand the source and spread of the parasite in populations of birds.