Pediculus humanus (PhumU2)

Pediculus humanus Assembly and Gene Annotation

The Pediculus humanus data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and VectorBase, a component of VEuPathDB.

About Pediculus humanus

The human body louse, Pediculus humanus corporis is the primary vector of the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. Epidemic typhus, one of the most significant historical human diseases, is caused by Rickettsia prowazekii, a category B bioterrorism agent that can cause persistent human infection. Besides its notoriety as the agent of the recurrent chronic disease, trench fever, Bartonella quintana can cause endocarditis and is a common infection among the homeless. Borrelia recurrentis causes another recurrent fever in central and Eastern Africa that is characterized by significant morbidity and mortality. The genome sequences of R. prowazekii and B. quintana have been determined, as well as those of two species of Borrelia, so the body louse genome will enhance studies of host-vector-pathogen interactions.

Picture credit (public domain): James Gathany (CDC) 2006

Strain USDA

The human body louse DNA (Pediculus humanus humanus strain) was provided by Dr. John Clark of the University of Massachusetts. Dr. Clark's colony originated from the colony maintained in Dr. Kosta Mumcuoglu's laboratory (Hebrew University, Jerusalem, Israel). Dr. Mumcuoglu's louse colony was established from the strain maintained at the USDA laboratory (Gainesville, FL). The colony has been maintained at the University of Massachusetts on rabbits for 8 years. According to the initial report by Culpepper (1944), he first colonized the body lice in 1942 at the laboratory of the Bureau of Entomology and Plant Quarantine (Orlando, FL). In 1945, Culpepper successfully reared his body lice on rabbits. Although it is not clear if the louse strain maintained at the USDA Gainesville laboratory was from Culpepper's strain, the rearing methods are identical.

Assembly

The Pediculus humanus USDA strain genomes sequence was sequenced by the J. Craig Venter Institute (JCVI). Assembly of 8.5x shotgun coverage was performed at the JCVI. The assembly presented here (PhumU2, April 2014) consists of 1,882 supercontigs totalling 110 Mb [1], plus 18 mitochondrial
"minichromosomes
" [2].

Annotation

The annotation of the Pediculus humanus genome is a collaboration between VectorBase, JCVI and the University of Geneva. Automated annotation pipelines were run at each centre and the resulting set of predictions merged into a canonical set. A first round of manual appraisal and editing was undertaken by JCVI to improve the quality of the prediction set. The geneset presented here (PhumU2.5, July 2019) represents the original set integrated with mitochondrial genes and non-coding RNA genes from the Ensembl Genomes pipeline.

References

  1. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.
    Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E et al. 2010. PNAS. 107:12168-12173.
  2. The single mitochondrial chromosome typical of animals has evolved into 18 minichromosomes in the human body louse, Pediculus humanus.
    Shao R, Kirkness EF, Barker SC. 2009. Genome Research. 19:904-912.

Statistics

Summary

AssemblyPhumU2, INSDC Assembly GCA_000006295.1, Nov 2008
Database version106.2
Golden Path Length110,804,242
Genebuild byVEuPathDB
Genebuild methodFull genebuild
Data sourceVectorBase

Gene counts

Coding genes10,785
Non coding genes927
Small non coding genes927
Gene transcripts11,715

About this species