A comprehensive evaluation of rodent malaria parasite genomes and gene expression

Table 1 Features of the reference genomes of P. berghei ANKA, P. c. chabaudi AS and P. y. yoelii YM

Genome features	*P. berghei* ANKA		*P. c. chabaudi* AS		*P. y. yoelii* YM	*P. falciparum 3D7* ^a
	Previous assembly [ [17]]	New assembly	Previous assembly [ [17]]	New assembly	New assembly	*P. falciparum 3D7* ^a
Nuclear genome
Genome size (Mb)	18.0	18.5	16.9	18.8	21.9	23.3
G + C content (%)	-	22.1	-	23.6	21.1	19.4
Chromosomes	14	14	14	14	14	14
Synteny breaks^b	-	-	1	1	0	ND
Contigs	7497	220	10,679	40	195	14
Sequence coverage	4x	237x	4x	109x	627x	-
Genes^c	5,864	4,979	5,698	5,139	5,675	5,419
Genes with functional annotation^d	-	2,781 (56%)	-	2,927 (57%)	3,485 (61%)	3,234 (60%)
Novel genes (see Additional file 1)	-	487	-	409	-	-
Mitochondrial genome
Genome size (bp)	-	5,957	-	5,949	6,512	5,967
G + C content (%)	-	30.9	-	30.9	30.7	31.6
Number of genes	-	3	-	3	3	3
Apicoplast genome
Genome size (bp)	-	30,302	-	29,468	29,736	29,430
G + C content (%)	-	13.5	-	13.7	14.1	13.1
Genes	-	30	-	30	30	30

^aGenome version: 1.5.2013; Apicoplast genome from accession numbers: X95275, X95276; ^bcompared to the PbA genome; ^cin new versions, this includes pseudogenes and partial genes, but does not include non-coding RNA genes; ^dfigures include all genes except those annotated as `hypothetical', `conserved Plasmodium protein, unknown function', `conserved protein, unknown function', `conserved rodent malaria protein, unknown function' or `Plasmodium exported protein, unknown function'.

ISSN: 1741-7007