This folder contains the genome assembly and annotation for Plasmodium chabaudi CB (version 2)

The original, draft assembly of P. chabaudi CB was published by Otto et al. (2014, PMID:25359557)

Version 2 was generated using PacBio RSII long-read sequencing and represents a complete genome sequence

Genome annotation involved manual curation and is of high quality

This data is currently unpublished, but a paper is in preparation:

	Genomic and transcriptomic comparisons of closely related malaria parasites differing in virulence and sequestration pattern

	Jing-wen Lin1,2*#, Adam James Reid3*#, Deirdre Cunningham1, Ulrike Boehme3, Irene Tumwine1, Sara Keller-Mclaughlin1, Mandy Sanders3, Matthew Berriman3, Jean Langhorne1#

	1 Malaria Immunology laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, United Kingdom. 2 Division of Pediatric Infectious Diseases, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaboration Innovation Centre, Chengdu 610041, China. 3 Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
	* These authors contributed equally to this work
	# Corresponding authors: Jing-wen Lin, lin.jingwen@scu.edu.cn; Adam Reid, ar11@sanger.ac.uk; Jean Langhorne, jean.langhorne@crick.ac.uk. 

	Malaria parasite species differ greatly in the harm they do to humans. While P. falciparum kills hundreds of thousands per year, P. vivax kills much less often and P. malariae is relatively benign. Strains of the rodent malaria parasite Plasmodium chabaudi show phenotypic variation in virulence during infections of laboratory mice. This make it an excellent species to study genes which may  be responsible for this trait. By understanding the mechanisms which underlie differences in virulence we can learn how parasites adapt to their hosts and how we might prevent disease. Here we present a complete reference genome sequence for a more virulent  P. chabaudi strain, PcCB, and perform a detailed comparison with the genome of the less virulent PcAS strain. We found the greatest variation in the subtelomeric regions, in particular amongst the sequences of the pir gene family, which has been associated with virulence and establishment of chronic infection. However, despite substantial variation at the sequence level, the repertoire of these genes has been largely maintained, highlighting the requirement for functional conservation as well as diversification in host-parasite interactions. We found that core genes involved in red blood cell invasion and sexual development have been under positive selection and these parallel phenotypic differences between parasite strains. These results provide the basis for a mechanistic understanding of the phenotypic differences between Plasmodium chabaudi strains, which might ultimately be translated into a better understanding of malaria parasites affecting humans.

Please contact Adam Reid (ar11@sanger.ac.uk) if you wish to use the data pre-publication


Files are:

*embl				EMBL files for each chromosome
PccCB_v2_all.fa			Genome assembly
PccCB_v2.gff			GFF3 annotation
PccCB_v2_transcripts.fa		Nucleotide coding sequences
PccCB_v2.desc			Product descriptions for genes
PccCB_pir.list			List of pirs and their subfamily classifications