Leptotrombidium deliense (Harvest mite, UoL-UT) Assembly and Gene Annotation

About Leptotrombidium deliense

There are very few known human diseases that involve pathogens transmitted by mites; the most important is tsutsugamushi disease, or scrub typhus, caused by the bacterium (Orientia tsutsugamushi) that is transmitted by several members of the genus Leptotrombidium (/ˌlɛptoʊtrɒmˈbɪdiəm/) (Family Trombiculidae) in south eastern Asia, Australia and the pacific islands (Mullen and Durden, 2002).

The life cycle of the mite includes 7 stages: egg, deutovum (or prelarva), larva, nymphochrysalis, nymph, imagochrysalis and adult. Of these stages only the larva (known as 'chiggers') is an ectoparasitic stage which feeds on a wide variety of hosts (rodents, but also occasionally humans and other large mammals) , whereas the nymphs and adults are predators of other arthropods (Makepeace B.L. et al,
"Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism
", Giga Science, 2018). Larvae ingest tissue exudates via a feeding tube ('stylostome') that is formed at the attachemnet site, but which is extraneous to the larval mouthparts.

Strain UoL-UT

Leptotrombidium deliense isolate UoL-UT collected from Berdmore's ground squirrels (Menetes berdmorei) captured in Udonthani Province, Thailand, in September 2015. BioSample record SAMN06473100.

UoL-UT represents an isolate from the wild, and is not a propagated laboratory strain. It was used for the generation of the VectorBase reference assembly LdelU1

Sources: VectorBase and Wikipedia.

Picture credit: Dr Kittipong Chaisiri, Mahidol University

Assembly

The Leptotrombidium deliense genome was sequenced and assembled at the University of Liverpool.

The LdelU1 assembly was produced from a pool of 50 larvae. The DNA from the pool was partially degraded but of sufficient quality for sequencing (full details are availabale in
"Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism
", Makepeace BL et al, GigaScience, 2018. Assembly was conducted using Velvet to produce a preliminary assembly that was filtered for contaminants using blobtools, followed by a second assembly of the filtered reads using the SPAdes assembler.

The final assembly comprosises 66,710 scaffolds (N50 = 2,941bp), with a total sequence length of 117,319,042bp (slightly smaller than the estimate of 158.31--160.95 Mb based on kmer analysis).

Annotation

Gene models were predicted by University of Liverpool and submitted to NCBI. Ensembl Genomes imported gene models form NCBI, and later added non-coding RNA genes using the Ensembl Genomes pipeline. The gene set currenty shown (LdelU1.1, July 2019) is an improvement of the initial set, with the addition of community annotation.

References

1. Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism.
   Xiaofeng Dong, Kittipong Chaisiri, Dong Xia, Stuart D. Armstrong, Yongxiang Fang, Martin J. Donnelly, Tatsuhiko Kadowaki, John W. McGarry, Alistair C. Darby, Benjamin L. Makepeace. 2018. Gigascience. Volume 7, Issue 12

Picture credit: Dr Kittipong Chaisiri, Mahidol University.